Last updated on 2022-02-06 07:51:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5-2 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 1.5-2 | 11.33 | 110.52 | 121.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.5-2 | 198.35 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.5-2 | 191.95 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 1.5-2 | 86.00 | 203.00 | 289.00 | ERROR | |
| r-devel-windows-x86_64-new-TK | 1.5-2 | ERROR | ||||
| r-patched-linux-x86_64 | 1.5-2 | 14.41 | 156.23 | 170.64 | OK | |
| r-release-linux-x86_64 | 1.5-2 | 15.66 | 152.43 | 168.09 | OK | |
| r-release-macos-arm64 | 1.5-2 | OK | ||||
| r-release-macos-x86_64 | 1.5-2 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.5-2 | 28.00 | 196.00 | 224.00 | OK | |
| r-oldrel-macos-x86_64 | 1.5-2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.5-2 | 28.00 | 191.00 | 219.00 | OK |
Version: 1.5-2
Check: examples
Result: ERROR
Running examples in 'sensR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clm2twoAC
> ### Title: Extract 2-AC coefficient table from a cumulative link model
> ### Aliases: clm2twoAC
> ### Keywords: models
>
> ### ** Examples
>
>
> ## Example of a simple 2-AC model. First the conventional way:
> twoAC(c(2, 2, 6))
Results for the 2-AC protocol with data c(2, 2, 6):
Estimate Std. Error
tau 0.4160 0.2674
d.prime 0.7743 0.5417
Two-sided 95% confidence interval for d-prime based on the
likelihood root statistic:
Lower Upper
d.prime -0.271 1.859
Significance test:
Likelihood root statistic = 1.446718 p-value = 0.14798
Alternative hypothesis: d-prime is different from 0
> ## Don't show:
> ## Testing stability of twoAC function:
> fm1 <- twoAC(c(2, 2, 6))
> ## str(fm1)
> nm <- c("coefficients", "stat.value", "p.value", "confint", "vcov", "logLik")
> b <- as.vector(unlist(fm1[nm]))
> ## b2 := dput(b)
> b2 <- c(0.415972626828703, 0.774259536071287, 0.26743108470048, 0.541673720311043,
+ 1.44671786297779, 0.147975959384948, -0.27098319957656, 1.85925113345333,
+ 0.0715193850640751, 0.0216722514182911, 0.0216722514182911, 0.293410419275606,
+ -9.50270539233235)
> stopifnot(isTRUE(all.equal(b, b2)))
> ## End(Don't show)
> ## The using a cumulative link model (clm from package ordinal):
> if(require(ordinal)) {
+ response <- gl(3,1)
+ fit.clm <- clm(response ~ 1, weights = c(2, 2, 6), link = "probit")
+ clm2twoAC(fit.clm)
+ ## Alternatively we could get estimates and standard errors "by hand":
+ tab <- coef(summary(fit.clm))
+ theta <- tab[,1]
+ (tau <- (theta[2] - theta[1])/sqrt(2))
+ (d.prime <- (-theta[2] - theta[1])/sqrt(2))
+ VCOV <- vcov(fit.clm)
+ (se.tau <- sqrt((VCOV[1,1] + VCOV[2,2] - 2*VCOV[2,1])/2))
+ (se.d.prime <- sqrt((VCOV[1,1] + VCOV[2,2] + 2*VCOV[2,1])/2))
+
+ ## Extended example with a regression model for d.prime
+ ## (see the referenced paper for details):
+ n.women <- c(2, 2, 6)*10
+ n.men <- c(1, 2, 7)*10
+ wt <- c(n.women, n.men)
+ response <- gl(3,1, length = 6)
+ gender <- gl(2, 3, labels = c("women", "men"))
+ fm2 <- clm(response ~ gender, weights = wt, link = "probit")
+ clm2twoAC(fm2)
+ }
Loading required package: ordinal
Estimate Std. Error z value Pr(>|z|)
tau 0.4670001 0.06700014 6.970135 3.1664e-12
d-prime 0.7898785 0.17021271 4.640538 3.4750e-06
gendermen 0.4533125 0.24627746 1.840658 0.065672
> ## Don't show:
> ## Test equality of hand calculations, twoAC and clm2twoAC:
> if(require(ordinal)){
+ b <- clm2twoAC(fit.clm)
+ b2 <- c(tau, d.prime, se.tau, se.d.prime)
+ stopifnot(
+ isTRUE(all.equal(unlist(b[, 1:2]), b2, c(coef(fm1)), check.attributes=FALSE))
+ )
+ ## Test stability of clm2twoAC results:
+ tab <- unlist(clm2twoAC(fm2)[, 1:3])
+ ## tab2 := dput(tab)
+ tab2 <- c(0.467000059796145, 0.78987850607203, 0.453312459391865,
+ 0.0670001441456634, 0.170212706442409, 0.246277460374108, 6.9701351504685,
+ 4.64053784574117, 1.84065751978788)
+ stopifnot(
+ isTRUE(all.equal(tab, tab2, check.attributes=FALSE))
+ )
+ }
Error in all.equal.numeric(unlist(b[, 1:2]), b2, c(coef(fm1)), check.attributes = FALSE) :
length(tolerance) == 1L is not TRUE
Calls: stopifnot ... isTRUE -> all.equal -> all.equal.numeric -> stopifnot
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.5-2
Check: examples
Result: ERROR
Running examples in ‘sensR-Ex.R’ failed
The error most likely occurred in:
> ### Name: clm2twoAC
> ### Title: Extract 2-AC coefficient table from a cumulative link model
> ### Aliases: clm2twoAC
> ### Keywords: models
>
> ### ** Examples
>
>
> ## Example of a simple 2-AC model. First the conventional way:
> twoAC(c(2, 2, 6))
Results for the 2-AC protocol with data c(2, 2, 6):
Estimate Std. Error
tau 0.4160 0.2674
d.prime 0.7743 0.5417
Two-sided 95% confidence interval for d-prime based on the
likelihood root statistic:
Lower Upper
d.prime -0.271 1.859
Significance test:
Likelihood root statistic = 1.446718 p-value = 0.14798
Alternative hypothesis: d-prime is different from 0
> ## Don't show:
> ## Testing stability of twoAC function:
> fm1 <- twoAC(c(2, 2, 6))
> ## str(fm1)
> nm <- c("coefficients", "stat.value", "p.value", "confint", "vcov", "logLik")
> b <- as.vector(unlist(fm1[nm]))
> ## b2 := dput(b)
> b2 <- c(0.415972626828703, 0.774259536071287, 0.26743108470048, 0.541673720311043,
+ 1.44671786297779, 0.147975959384948, -0.27098319957656, 1.85925113345333,
+ 0.0715193850640751, 0.0216722514182911, 0.0216722514182911, 0.293410419275606,
+ -9.50270539233235)
> stopifnot(isTRUE(all.equal(b, b2)))
> ## End(Don't show)
> ## The using a cumulative link model (clm from package ordinal):
> if(require(ordinal)) {
+ response <- gl(3,1)
+ fit.clm <- clm(response ~ 1, weights = c(2, 2, 6), link = "probit")
+ clm2twoAC(fit.clm)
+ ## Alternatively we could get estimates and standard errors "by hand":
+ tab <- coef(summary(fit.clm))
+ theta <- tab[,1]
+ (tau <- (theta[2] - theta[1])/sqrt(2))
+ (d.prime <- (-theta[2] - theta[1])/sqrt(2))
+ VCOV <- vcov(fit.clm)
+ (se.tau <- sqrt((VCOV[1,1] + VCOV[2,2] - 2*VCOV[2,1])/2))
+ (se.d.prime <- sqrt((VCOV[1,1] + VCOV[2,2] + 2*VCOV[2,1])/2))
+
+ ## Extended example with a regression model for d.prime
+ ## (see the referenced paper for details):
+ n.women <- c(2, 2, 6)*10
+ n.men <- c(1, 2, 7)*10
+ wt <- c(n.women, n.men)
+ response <- gl(3,1, length = 6)
+ gender <- gl(2, 3, labels = c("women", "men"))
+ fm2 <- clm(response ~ gender, weights = wt, link = "probit")
+ clm2twoAC(fm2)
+ }
Loading required package: ordinal
Estimate Std. Error z value Pr(>|z|)
tau 0.4670001 0.06700014 6.970135 3.1664e-12
d-prime 0.7898785 0.17021271 4.640538 3.4750e-06
gendermen 0.4533125 0.24627746 1.840658 0.065672
> ## Don't show:
> ## Test equality of hand calculations, twoAC and clm2twoAC:
> if(require(ordinal)){
+ b <- clm2twoAC(fit.clm)
+ b2 <- c(tau, d.prime, se.tau, se.d.prime)
+ stopifnot(
+ isTRUE(all.equal(unlist(b[, 1:2]), b2, c(coef(fm1)), check.attributes=FALSE))
+ )
+ ## Test stability of clm2twoAC results:
+ tab <- unlist(clm2twoAC(fm2)[, 1:3])
+ ## tab2 := dput(tab)
+ tab2 <- c(0.467000059796145, 0.78987850607203, 0.453312459391865,
+ 0.0670001441456634, 0.170212706442409, 0.246277460374108, 6.9701351504685,
+ 4.64053784574117, 1.84065751978788)
+ stopifnot(
+ isTRUE(all.equal(tab, tab2, check.attributes=FALSE))
+ )
+ }
Error in all.equal.numeric(unlist(b[, 1:2]), b2, c(coef(fm1)), check.attributes = FALSE) :
length(tolerance) == 1L is not TRUE
Calls: stopifnot ... isTRUE -> all.equal -> all.equal.numeric -> stopifnot
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK