Last updated on 2022-04-27 11:54:02 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 8.06 | 109.31 | 117.37 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 5.87 | 78.75 | 84.62 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 134.84 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 130.76 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.0 | 17.00 | 127.00 | 144.00 | OK | |
| r-patched-linux-x86_64 | 1.2.0 | 5.43 | 101.94 | 107.37 | OK | |
| r-release-linux-x86_64 | 1.2.0 | 6.94 | 103.53 | 110.47 | OK | |
| r-release-macos-arm64 | 1.2.0 | 36.00 | OK | |||
| r-release-macos-x86_64 | 1.2.0 | 64.00 | OK | |||
| r-release-windows-x86_64 | 1.2.0 | 19.00 | 125.00 | 144.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | 46.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.0 | 67.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 1.2.0 | 15.00 | 112.00 | 127.00 | OK |
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘MultiGHQuad-Ex.R’ failed
The error most likely occurred in:
> ### Name: eval.quad
> ### Title: Evaluation of multivariate normal distributed expectations
> ### Aliases: eval.quad
>
> ### ** Examples
>
> ### Basic example; E(X), X ~ N(0,1)
> grid <- init.quad(Q = 1, prior = list(mu = 0, Sigma = diag(1)))
> eval.quad(X = grid)
[1] -2.178954e-16
attr(,"variance")
[,1]
[1,] 1
>
> ### Example; Rasch model person parameter
> # E(theta), theta ~ N(0,1) * P(X = 1 | theta, beta), P is simplified rasch model
> # set up rasch model with fixed beta, returns LL
> rasch <- function(theta, beta, responses){
+ p <- exp(theta - beta)/(1 + exp(theta - beta))
+ q <- 1 - p
+ return(log(p) * sum(responses == 1) + log(q) * sum(responses == 0))
+ }
>
> # when theta == beta, P(X = 1) = .5, generate some bernoulli trials with p = .5
> responses <- rbinom(5, 1, .5)
>
> # get EAP estimate for theta, prior N(0,1)
> eval.quad(rasch, grid, beta = 0, responses = responses)
[1] -0.2471169
attr(,"variance")
[,1]
[1,] 0.4852284
>
> # with more data, the estimate becomes more accurate, and variance decreases
> eval.quad(rasch, grid, beta = 0, responses = rbinom(20, 1, .5))
[1] 0.3393648
attr(,"variance")
[,1]
[1,] 0.2671098
> eval.quad(rasch, grid, beta = 0, responses = rbinom(50, 1, .5))
[1] -0.5869554
attr(,"variance")
[,1]
[1,] 0.0358114
> eval.quad(rasch, grid, beta = 0, responses = rbinom(100, 1, .5))
[1] -1.80146e-16
attr(,"variance")
[,1]
[1,] 0.380327
>
> ### problem; the result starts to 'snap' to the closest quadrature point when
> # the posterior distribution is too dissimilar to the prior.
> evals <- eval.quad(rasch, grid, beta = 0, responses = rbinom(100, 1, .5), debug = TRUE)
> evals.values <- attr(evals, "values")
>
> # posterior density after 40 items
> p <- plot(function(x) exp(dnorm(x, log = TRUE) +
+ rasch(x, beta = 1, responses = rbinom(100, 1, .5))),
+ from = -3, to = 3)
>
> # quadrature points used
> points(grid$X, exp(grid$W)*max(p$y), pch = 20)
>
> # the evaluation relies almost completely on one quadrature point,
> # which causes results to 'snap' to that point.
> # we could add more quadrature points...
> grid2 <- init.quad(Q = 1, ip = 20)
> points(grid2$X, exp(grid2$W)*max(p$y), pch = 20, col = "grey")
>
> # but if the posterior is not centered on the prior, this quickly fails:
> p <- plot(function(x) exp(dnorm(x, log = TRUE) +
+ rasch(x, beta = 2, responses = rbinom(100, 1, .5))),
+ from = -3, to = 3)
> points(grid2$X, exp(grid2$W)*max(p$y), pch = 20, col = "grey")
>
> # additionally, adding extra quadrature points in a multidimensional
> # problem quickly grows out of control.
>
> ### a better solution; adaptive quadrature grid.
> # say we have an idea of where our parameter is located, through another estimator,
> # or a previous estimate.
> # we can then use this to adapt where our quadrature grid should be.
> # get an estimate;
> responses <- rbinom(10, 1, .5)
> est <- eval.quad(rasch, grid, beta = 2, responses = responses)
> print( est )
[1] 1.751766
attr(,"variance")
[,1]
[1,] 0.2102369
>
> # adapt the grid;
> grid3 <- init.quad(Q = 1, adapt = est)
Error in !is.list(adapt) || length(adapt$mu) != Q || dim(adapt$Sigma) != :
'length = 2' in coercion to 'logical(1)'
Calls: init.quad
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MultiGHQuad)
Loading required package: mvtnorm
Loading required package: Matrix
>
> test_check("MultiGHQuad")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_generate_quadpoints.R:22:3): Adapt accepts previous estimate ────
Error in `!is.list(adapt) || length(adapt$mu) != Q || dim(adapt$Sigma) !=
c(Q, Q)`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
▆
1. ├─testthat::expect_is(init.quad(2, adapt = estimate), "list") at test_generate_quadpoints.R:22:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MultiGHQuad::init.quad(2, adapt = estimate)
── Error (test_generate_quadpoints.R:32:3): Adapt accepts list ─────────────────
Error in `!is.list(adapt) || length(adapt$mu) != Q || dim(adapt$Sigma) !=
c(Q, Q)`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
▆
1. ├─testthat::expect_is(init.quad(2, adapt = adapt), "list") at test_generate_quadpoints.R:32:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MultiGHQuad::init.quad(2, adapt = adapt)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [40s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MultiGHQuad)
Loading required package: mvtnorm
Loading required package: Matrix
>
> test_check("MultiGHQuad")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_generate_quadpoints.R:22:3): Adapt accepts previous estimate ────
Error in `!is.list(adapt) || length(adapt$mu) != Q || dim(adapt$Sigma) !=
c(Q, Q)`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
▆
1. ├─testthat::expect_is(init.quad(2, adapt = estimate), "list") at test_generate_quadpoints.R:22:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MultiGHQuad::init.quad(2, adapt = estimate)
── Error (test_generate_quadpoints.R:32:3): Adapt accepts list ─────────────────
Error in `!is.list(adapt) || length(adapt$mu) != Q || dim(adapt$Sigma) !=
c(Q, Q)`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
▆
1. ├─testthat::expect_is(init.quad(2, adapt = adapt), "list") at test_generate_quadpoints.R:32:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MultiGHQuad::init.quad(2, adapt = adapt)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc