CRAN Package Check Results for Package RSurveillance

Last updated on 2018-12-17 08:48:26 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.2.0	3.02	15.45	18.47	ERROR
r-devel-linux-x86_64-debian-gcc	0.2.0	2.37	16.94	19.31	ERROR
r-devel-linux-x86_64-fedora-clang	0.2.0			43.16	ERROR
r-devel-linux-x86_64-fedora-gcc	0.2.0			40.34	ERROR
r-devel-windows-ix86+x86_64	0.2.0	7.00	60.00	67.00	ERROR
r-patched-linux-x86_64	0.2.0	2.86	15.24	18.10	ERROR
r-patched-solaris-x86	0.2.0			57.00	ERROR
r-release-linux-x86_64	0.2.0	2.72	32.20	34.92	ERROR
r-release-windows-ix86+x86_64	0.2.0	5.00	43.00	48.00	ERROR
r-release-osx-x86_64	0.2.0				NOTE
r-oldrel-windows-ix86+x86_64	0.2.0	5.00	62.00	67.00	ERROR
r-oldrel-osx-x86_64	0.2.0				NOTE

Check Details

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in ‘RSurveillance-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: adj.risk.sim
    > ### Title: Adjusted risk for simulation models
    > ### Aliases: adj.risk.sim
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > # examples for adj.risk.sim
    > its<- 10
    > risk.cat<- 3
    > rr<- matrix(0, nrow=its, ncol=risk.cat)
    > rr[,1]<- mc2d::rpert(its, 5,10,20)
    Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mvtnorm/libs/mvtnorm.so':
     /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mvtnorm/libs/mvtnorm.so: failed to map segment from shared object
    Calls: :: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘RSurveillance.R’ [1s/1s]
    Running the tests in ‘tests/RSurveillance.R’ failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lattice/libs/lattice.so':
     /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lattice/libs/lattice.so: failed to map segment from shared object
     Calls: tp ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in ‘RSurveillance-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: adj.risk.sim
    > ### Title: Adjusted risk for simulation models
    > ### Aliases: adj.risk.sim
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > # examples for adj.risk.sim
    > its<- 10
    > risk.cat<- 3
    > rr<- matrix(0, nrow=its, ncol=risk.cat)
    > rr[,1]<- mc2d::rpert(its, 5,10,20)
    Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/libs/mvtnorm.so':
     /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/libs/mvtnorm.so: failed to map segment from shared object
    Calls: :: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘RSurveillance.R’ [1s/1s]
    Running the tests in ‘tests/RSurveillance.R’ failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/lattice/libs/lattice.so':
     /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/lattice/libs/lattice.so: failed to map segment from shared object
     Calls: tp ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘mc2d’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘RSurveillance.R’
    Running the tests in ‘tests/RSurveillance.R’ failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     Error: all(abs(observed_result - expected_result) < tol) is not TRUE
     Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'RSurveillance.R' [4s]
    Running the tests in 'tests/RSurveillance.R' failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     Error: all(abs(observed_result - expected_result) < tol) is not TRUE
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in ‘RSurveillance-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: adj.risk.sim
    > ### Title: Adjusted risk for simulation models
    > ### Aliases: adj.risk.sim
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > # examples for adj.risk.sim
    > its<- 10
    > risk.cat<- 3
    > rr<- matrix(0, nrow=its, ncol=risk.cat)
    > rr[,1]<- mc2d::rpert(its, 5,10,20)
    Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/mvtnorm/libs/mvtnorm.so':
     /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/mvtnorm/libs/mvtnorm.so: failed to map segment from shared object
    Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘RSurveillance.R’ [1s/1s]
    Running the tests in ‘tests/RSurveillance.R’ failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     Error in dyn.load(file, DLLpath = DLLpath, ...) :
     unable to load shared object '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/lattice/libs/lattice.so':
     /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/lattice/libs/lattice.so: failed to map segment from shared object
     Calls: tp ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘RSurveillance.R’ [3s/3s]
    Running the tests in ‘tests/RSurveillance.R’ failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     Error: all(abs(observed_result - expected_result) < tol) is not TRUE
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'RSurveillance.R' [3s]
    Running the tests in 'tests/RSurveillance.R' failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     Error: all(abs(observed_result - expected_result) < tol) is not TRUE
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'RSurveillance.R' [5s]
    Running the tests in 'tests/RSurveillance.R' failed.
    Complete output:
     > library(RSurveillance)
     >
     > ## Define a tolerance
     > tol = 1e-5
     >
     > ## Test case - sep.binom
     > tested<- seq(10,100, by=10)
     > prev<- 0.05
     > sens<- 0.9
     > expected_result <- c(0.368993670137906, 0.60183101167397, 0.748752848011488, 0.841461456735425,
     + 0.899961175672938, 0.936874868617662, 0.960167642524368, 0.974865530299547,
     + 0.984139990521287, 0.989992233627259)
     > observed_result <- sep.binom(tested, prev, sens)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.exact
     > expected_result <- c(0.80000, 0.96000, 0.99200, 0.99840, 0.99968)
     > observed_result <- sep.exact(d=1:5, se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hypergeo
     > N<- c(10, 50, 100, 250, 500)
     > expected_result <- c(0.40000, 0.40000, 0.40000, 0.78400, 0.92224)
     > observed_result <- sep.hypergeo(se=0.8, N=N, n=c(5, 25, 50, 125, 250), d = ceiling(0.01*N))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - spp
     > expected_result <- c(0.9043821, 0.8179069, 0.6050061, 0.3660323)
     > observed_result <- spp(c(10, 20, 50, 100), 0.99)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep
     > N<- seq(30, 100, by = 5)
     > se<- 0.95
     > pstar<- 0.1
     > n<- rep(30, length(N))
     > expected_result <- c(0.9998750, 0.9988105, 0.9931679, 0.9933724, 0.9852992,
     + 0.9874888, 0.9790610, 0.9823942, 0.9742575, 0.9781660,
     + 0.9705057, 0.9746682, 0.9675142, 0.9717525, 0.9650811)
     > observed_result <- sep(N, n, pstar, se = se)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - sep.var.se
     > sens<- c(rep(0.9, 50), rep(0.95, 100))
     > expected_result <- 0.8065082
     > observed_result <- sep.var.se(N=500, sens, 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.sys
     > H<- 500
     > N<- rep(1000, 150)
     > N[5]<- NA
     > n<- rep(30, 150)
     > expected_result <- 0.9008415
     > observed_result <- sep.sys(NA, N, n, 0.02, 0.05, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.binom
     > expected_result <- c(328, 164, 65, 32, 15)
     > observed_result <- n.binom(sep=0.95, pstar=c(0.01, 0.02, 0.05, 0.1, 0.2), 0.91)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hypergeo
     > expected_result <- c(195, 282, 324, 369)
     > observed_result <- n.hypergeo(sep=0.95, N=c(200, 500, 1000, 10000), d=ceiling(0.01*c(200, 500, 1000, 10000)), se=0.8)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freedom
     > expected_result <- c(173, 251, 288, 324, 328, 333, 332)
     > observed_result <- n.freedom(N=c(200, 500, 1000, 5000, 10000, 100000, NA), sep=0.95, pstar=0.01, se=0.9)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.2stage
     > expected_result.1 <- 518
     > expected_result.2 <- c(13, 17, 17, 18, 18, 18, 17)
     > observed_result.1 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[1]]
     > observed_result.2 <- n.2stage(1000, c(50, 100, 200, 500, 1000, 5000, NA), 0.95, 0.5, 0.01, 0.05, 0.8)[[2]]
     > stopifnot(all(abs(observed_result.1 - expected_result.1) < tol))
     > stopifnot(all(abs(observed_result.2 - expected_result.2) < tol))
     >
     > ## Test case - pstar.calc
     > expected_result <- c(0.11680795, 0.09683112, 0.08256039,
     + 0.07185595, 0.06352901, 0.05747207, 0.05686632)
     > observed_result <- pstar.calc(500, n=50, sep=0.95, se=c(0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.equ
     > expected_result <- c(0.9848485, 0.9876543, 0.9898990, 0.9917355, 0.9932660,
     + 0.9945610, 0.9956710, 0.9966330, 0.9974747, 0.9982175,
     + 0.9988777, 0.9994684)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## prior.pfree.equ
     > expected_result <- c(0.9750000, 0.9777778, 0.9800000, 0.9818182, 0.9833333,
     + 0.9846154, 0.9857143, 0.9866667, 0.9875000, 0.9882353,
     + 0.9888889, 0.9894737)
     > observed_result <- pfree.equ(seq(0.4, 0.95, by = 0.05), 0.01)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - disc.prior
     > expected_result <- c(0.4950, 0.5940, 0.6930, 0.7920, 0.8910, 0.9405)
     > observed_result <- disc.prior(c(0.5, 0.6, 0.7, 0.8, 0.9, 0.95), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.1
     > expected_result <- c(0.6364104, 0.6667116, 0.7000424,
     + 0.6203008, 0.7101865, 0.6490526)
     > observed_result <- pfree.1(c(0.44, 0.51, 0.58, 0.4, 0.6, 0.47), 0.01, 0.5)[,4]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - pfree.calc
     > expected_result <- c(0.6203008, 0.7261937, 0.8099976, 0.8709093,
     + 0.9124970, 0.9396922, 0.9569776, 0.9677666,
     + 0.9744246, 0.9785045)
     > observed_result <- pfree.calc(rep(0.4,10), 0.01, 0.5)[,5]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pfree
     > expected_result <- c(0.7500000, 0.8888889, 0.9473684, 0.9898990)
     > observed_result <- sep.pfree(0.5, c(0.8, 0.9, 0.95, 0.99))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.prior
     > expected_result <- c(0.1, 0.2, 0.5, 1.0)
     > observed_result <- sep.prior(c(0.9, 0.95, 0.98, 0.99), 0.01)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pfree
     > expected_result <- c(249, 321, 405, 463)
     > observed_result <- n.pfree(pfree = c(0.9, 0.95, 0.98, 0.99), prior = 0.5, 0.01, 0.01, 0.8, 1000)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.series
     > expected_result <- 0.7524
     > observed_result <- se.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - se.parallel
     > expected_result <- 0.9999
     > observed_result <- se.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.series
     > expected_result <- 0.9999
     > observed_result <- sp.series(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sp.parallel
     > expected_result <- 0.7524
     > observed_result <- sp.parallel(c(0.99, 0.95, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.pooled
     > expected_result <- c(0.3946345, 0.6335326, 0.7781533, 0.8657016,
     + 0.9187004, 0.9507840, 0.9702064, 0.9819640,
     + 0.9890816, 0.9933904)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > ## spp.pooled
     > expected_result <- c(0.9509900, 0.9043821, 0.8600584, 0.8179069,
     + 0.7778214, 0.7397004, 0.7034477, 0.6689718,
     + 0.6361855, 0.6050061)
     > observed_result <- sep.pooled(1:10*5, 5, 0.02, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.pooled
     > expected_result <- c(15, 6, 3, 2)
     > observed_result <- n.pooled(0.95, c(2, 5, 10, 20), 0.1, c(0.99, 0.98, 0.97, 0.95), 1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.freecalc
     > expected_result <- 0.870566
     > observed_result <- sep.freecalc(150, 30, 2, 0.9, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.hp
     > expected_result <- 0.878252
     > observed_result <- sep.hp(150, 30, 2, 0.9, 0.98, 15)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.binom.imperfect
     > expected_result <- c(0.1012041, 0.3144826, 0.5181777, 0.6775625,
     + 0.7911787, 0.8678935, 0.9178840, 0.9496525,
     + 0.9694677, 0.9816500)
     > observed_result <- sep.binom.imperfect(1:10*5, 2, 0.95, 0.98, 0.1)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.hp
     > expected_result <- c(0.5487535, 0.6594135, 0.7747132, 0.8839634,
     + 0.9688938, 1.0000000)
     > observed_result <- sph.hp(500, 30, 2, 95:100/100)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sph.binom
     > expected_result <- c(0.99615761, 0.98382236, 0.96466169, 0.94010102,
     + 0.87945431, 0.73577139, 0.40327171, 0.08937548)
     > observed_result <- sph.binom(c(5, 10, 15, 20, 30, 50, 100, 200), 2, 0.98)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.hp
     > expected_result <- c(10, 0.467678, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.hp(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.hp
     > expected_result <- c(52, 0.9544449, 0.9044236, 65, 2, 0.05)
     > observed_result <- n.c.hp(65,0.95,c=5,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.freecalc
     > expected_result <- c(10, 0.4411522, 0.9043821, 65, 1, 0.05)
     > observed_result <- n.freecalc(65,0.95,c=1,se=0.95,sp=0.99,pstar=0.05, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.c.freecalc
     > expected_result <- c(27, 0.9555394, 0.9999933, 120, 1, 0.1)
     > observed_result <- n.c.freecalc(120,0.95,c=5,se=0.9,sp=0.99,pstar=0.1, minSpH=0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - adj.risk
     > expected_result <- c(3.125, 1.875, 0.625)
     > observed_result <- adj.risk(c(5, 3, 1), c(0.1, 0.1, 0.8))
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - epi.calc
     > expected_result <- c(0.0625, 0.0375, 0.0125)
     > observed_result <- epi.calc(0.02, c(5, 3, 1), c(0.1, 0.1, 0.8))[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.bin
     > expected_result <- 0.9430056
     > observed_result <- sep.rb.bin(0.1, c(5, 3, 1), c(0.1, 0.1, 0.8), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rp.hypergeo
     > expected_result <- 0.9623211
     > observed_result <- sep.rb.hypergeo(0.1, c(5, 3, 1), c(10, 10, 80), c(5, 5, 5), 0.9)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.bin.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9800017
     > observed_result <- sep.rb.bin.varse(0.01, c(5, 1), c(0.1, 0.9), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb.hypergeo.varse
     > rg<- c(1, 1, 2, 2)
     > se<- c(0.92, 0.85, 0.92, 0.85)
     > n<- c(80, 30, 20, 30)
     > df<- data.frame(rg, se, n)
     > expected_result <- 0.9938065
     > observed_result <- sep.rb.hypergeo.varse(0.01, c(5, 1), c(200, 1800), df)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.bin
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > ppr1<- c(0.2, 0.8)
     > rr2<- rbind(c(4,1), c(4,1))
     > ppr2<- rbind(c(0.1, 0.9), c(0.3, 0.7))
     > se<- 0.8
     > n<- rbind(c(50, 20), c(20, 10))
     > expected_result <- 0.9611147
     > observed_result <- sep.rb2.binom(pstar, rr1, ppr1, rr2, ppr2, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2.hypergeo
     > pstar<- 0.01
     > rr1<- c(3, 1)
     > rr2<- rbind(c(4,1), c(4,1))
     > N<- rbind(c(100, 500), c(300, 1000))
     > n<- rbind(c(50, 20), c(20, 10))
     > se<- 0.8
     > expected_result <- 0.9487643
     > observed_result <- sep.rb2.hypergeo(pstar, rr1, rr2, N, n, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sep.rb2stage
     > pstar.c<- 0.02
     > pstar.u<- 0.1
     > rr.c<- c(5, 1)
     > ppr.c<- c(0.1, 0.9)
     > rr.u<- c(3, 1)
     > se<- 0.9
     > n<- cbind(rep(10, 50), rep(5, 50))
     > rg<- c(rep(1, 30), rep(2, 20))
     > ppr.u<- cbind(rep(0.2, 50), rep(0.8, 50))
     > N<- cbind(rep(30, 50), rep(120, 50))
     > C<- 500
     > expected_result <- 0.8990356
     > observed_result <- sse.rb.2stage(C=NA, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N=NA, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     > expected_result <- 0.9581237
     > observed_result <- sse.rb.2stage(C, pstar.c, pstar.u, rr.c, ppr.c, rr.u, ppr.u, N, n, rg, se)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - sse.combined
     > C<- c(300, 1200)
     > pstar<- 0.01
     > rr<- c(3,1)
     > ppr<- c(0.2, 0.8)
     > comp1<- data.frame(id=1:100, rg=c(rep(1,50), rep(2,50)), cse=rep(0.5,100))
     > comp2<- data.frame(id=seq(2, 120, by=2), rg=c(rep(1,25), rep(2,35)), cse=rep(0.8,60))
     > comp3<- data.frame(id=seq(5, 120, by=5), rg=c(rep(1,10), rep(2,14)), cse=rep(0.9,24))
     > sep<- list(comp1, comp2, comp3)
     > expected_result <- matrix(c(0.6858347, 0.6954111, 0.8051234, 0.8121286), ncol=2, byrow=T)
     > observed_result <- sse.combined(C, pstar, rr, sep = sep)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb
     > expected_result <- c(7,5,2)
     > observed_result <- n.rb(0.1, c(5, 3, 1), c(0.1, 0.10, 0.80),
     + c(0.5, 0.3, 0.2), 0.9, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.rb.varse
     > m<- rbind(c(0.8, 0.2), c(0.5, 0.5), c(0.7, 0.3))
     > expected_result <- matrix(c(52, 12, 64, 32, 32, 64, 22, 9, 31, 106, 53, 159),
     + nrow = 4, byrow = T)
     > observed_result <- n.rb.varse(0.01, c(5, 3, 1), c(0.1, 0.1, 0.8),
     + c(0.4, 0.4, 0.2), c(0.92, 0.8), m, 0.95)[[1]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.ap
     > expected_result <- c(139, 246, 323, 369, 385)
     > observed_result <- n.ap(seq(0.1, 0.5, by = 0.1), 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.agresti
     > expected_result <- c(25, 200, 0.125, 0.08558957, 0.1785444, 0.95)
     > observed_result <- binom.agresti(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.jeffreys
     > expected_result <- c(25, 200, 0.125, 0.08462743, 0.176126, 0.95)
     > observed_result <- binom.jeffreys(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - binom.cp
     > expected_result <- c(25, 200, 0.125, 0.08255234, 0.1789738, 0.95)
     > observed_result <- binom.cp(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - ap
     > expected_result <- c(25, 200, 0.125, 0.08611974, 0.1780143, 0.95)
     > observed_result <- ap(25, 200)[1,1:6]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - n.tp
     > expected_result <- 174
     > observed_result <- n.tp(0.1, 0.9, 0.99, 0.05)
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     >
     > ## Test case - tp.normal
     > expected_result <- c(0.2228464, 0.1412036, 0.3044893)
     > observed_result <- tp.normal(25, 120, 0.9, 0.99)[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     >
     > ## Test case - tp
     > expected_result <- c(0.02941176, 0, 0.09291029)
     > observed_result <- tp(25, 200, 0.95, 0.9, "c-p")[[2]]
     > stopifnot(all(abs(observed_result - expected_result) < tol))
     Error: all(abs(observed_result - expected_result) < tol) is not TRUE
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64