Last updated on 2026-10-24 09:51:04 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.7 | 10.72 | 119.63 | 130.35 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.7 | 7.43 | 76.28 | 83.71 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.7 | 10.00 | 105.31 | 115.31 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.7 | 86.44 | OK | |||
| r-devel-windows-x86_64 | 1.0.7 | 11.00 | 127.00 | 138.00 | OK | |
| r-patched-linux-x86_64 | 1.0.7 | 10.00 | 108.91 | 118.91 | OK | |
| r-release-linux-x86_64 | 1.0.7 | 9.21 | 108.56 | 117.77 | OK | |
| r-release-macos-arm64 | 1.0.7 | 3.00 | 32.00 | 35.00 | OK | |
| r-release-macos-x86_64 | 1.0.7 | 7.00 | 138.00 | 145.00 | OK | |
| r-release-windows-x86_64 | 1.0.7 | 11.00 | 119.00 | 130.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.7 | 2.00 | 37.00 | 39.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.7 | 7.00 | 110.00 | 117.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.7 | 16.00 | 148.00 | 164.00 | OK |
Version: 1.0.7
Check: examples
Result: ERROR
Running examples in ‘stdReg2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: standardize
> ### Title: Get standardized estimates using the g-formula with a custom
> ### model
> ### Aliases: standardize
>
> ### ** Examples
>
>
> set.seed(6)
> n <- 100
> Z <- rnorm(n)
> X <- rnorm(n, mean = Z)
> Y <- rbinom(n, 1, prob = (1 + exp(X + Z))^(-1))
> dd <- data.frame(Z, X, Y)
> prob_predict.glm <- function(...) predict.glm(..., type = "response")
>
> x <- standardize(
+ fitter = "glm",
+ arguments = list(
+ formula = Y ~ X * Z,
+ family = "binomial"
+ ),
+ predict_fun = prob_predict.glm,
+ data = dd,
+ values = list(X = seq(-1, 1, 0.1)),
+ B = 100,
+ reference = 0,
+ contrasts = "difference"
+ )
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|==================================================| 100%> x
Number of bootstraps: 100
Confidence intervals are based on percentile bootstrap confidence intervals
Exposure: X
Tables:
X Estimate lower.0.95 upper.0.95
1 -1.0 0.689 0.537 0.882
2 -0.9 0.671 0.526 0.865
3 -0.8 0.653 0.521 0.845
4 -0.7 0.635 0.515 0.822
5 -0.6 0.617 0.508 0.797
6 -0.5 0.600 0.493 0.770
7 -0.4 0.583 0.476 0.745
8 -0.3 0.566 0.466 0.720
9 -0.2 0.550 0.450 0.699
10 -0.1 0.534 0.429 0.679
11 0.0 0.519 0.409 0.658
12 0.1 0.504 0.389 0.638
13 0.2 0.490 0.369 0.621
14 0.3 0.476 0.348 0.608
15 0.4 0.462 0.322 0.595
16 0.5 0.449 0.298 0.587
17 0.6 0.437 0.275 0.583
18 0.7 0.425 0.254 0.577
19 0.8 0.413 0.235 0.571
20 0.9 0.401 0.222 0.561
21 1.0 0.391 0.207 0.551
Reference level: = 0
Contrast: difference
X Estimate lower.0.95 upper.0.95
1 -1.0 0.1697 0.04037 0.30879
2 -0.9 0.1516 0.03562 0.28505
3 -0.8 0.1335 0.03104 0.25348
4 -0.7 0.1156 0.02663 0.22134
5 -0.6 0.0980 0.02238 0.19201
6 -0.5 0.0807 0.01829 0.16211
7 -0.4 0.0637 0.01435 0.13054
8 -0.3 0.0472 0.01056 0.09810
9 -0.2 0.0310 0.00691 0.06525
10 -0.1 0.0153 0.00339 0.03243
11 0.0 0.0000 0.00000 0.00000
12 0.1 -0.0148 -0.03177 -0.00326
13 0.2 -0.0292 -0.06286 -0.00641
14 0.3 -0.0432 -0.09365 -0.00944
15 0.4 -0.0566 -0.12370 -0.01237
16 0.5 -0.0697 -0.15192 -0.01519
17 0.6 -0.0823 -0.17663 -0.01791
18 0.7 -0.0945 -0.19954 -0.02054
19 0.8 -0.1062 -0.22074 -0.02308
20 0.9 -0.1176 -0.24033 -0.02553
21 1.0 -0.1285 -0.25891 -0.02790
>
> require(survival)
Loading required package: survival
> prob_predict.coxph <- function(object, newdata, times) {
+ fit.detail <- suppressWarnings(basehaz(object))
+ cum.haz <- fit.detail$hazard[sapply(times, function(x) max(which(fit.detail$time <= x)))]
+ predX <- predict(object = object, newdata = newdata, type = "risk")
+ res <- matrix(NA, ncol = length(times), nrow = length(predX))
+ for (ti in seq_len(length(times))) {
+ res[, ti] <- exp(-predX * cum.haz[ti])
+ }
+ res
+ }
> set.seed(68)
> n <- 500
> Z <- rnorm(n)
> X <- rnorm(n, mean = Z)
> T <- rexp(n, rate = exp(X + Z + X * Z)) # survival time
> C <- rexp(n, rate = exp(X + Z + X * Z)) # censoring time
> U <- pmin(T, C) # time at risk
> D <- as.numeric(T < C) # event indicator
> dd <- data.frame(Z, X, U, D)
> x <- standardize(
+ fitter = "coxph",
+ arguments = list(
+ formula = Surv(U, D) ~ X + Z + X * Z,
+ method = "breslow",
+ x = TRUE,
+ y = TRUE
+ ),
+ predict_fun = prob_predict.coxph,
+ data = dd,
+ times = 1:5,
+ values = list(X = c(-1, 0, 1)),
+ B = 100,
+ reference = 0,
+ contrasts = "difference"
+ )
Error in a$specials[[i]] : subscript out of bounds
Calls: standardize ... predict_fun -> predict -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(stdReg2)
>
> test_check("stdReg2")
Loading required package: survival
Saving _problems/test-standardize-37.R
Saving _problems/test-standardize-86.R
Saving _problems/test-standardize_coxph-15.R
Saving _problems/test-standardize_coxph-40.R
Loading required package: drgee
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 19 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-standardize.R:37:5'): standardize with survival data (no bootstrap) gives the same as standardize_coxph ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─stdReg2::standardize(...) at test-standardize.R:53:3
2. └─stdReg2 (local) estimate_fun(valuesout, times, data, fit_outcome)
3. ├─base::colMeans(...)
4. │ └─base::is.data.frame(x)
5. └─stdReg2 (local) predict_fun(object = fit_outcome, newdata = data_x, times = times)
6. ├─stats::predict(object = object, newdata = newdata, type = "risk") at test-standardize.R:37:5
7. └─survival:::predict.coxph(...)
8. └─stats::delete.response(Terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-standardize.R:86:5'): standardize generates output with survival data (single time point) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─stdReg2::standardize(...) at test-standardize.R:102:3
2. └─stdReg2 (local) estimate_fun(valuesout, times, data, fit_outcome)
3. ├─base::colMeans(...)
4. │ └─base::is.data.frame(x)
5. └─stdReg2 (local) predict_fun(object = fit_outcome, newdata = data_x, times = times)
6. ├─stats::predict(object = object, newdata = newdata, type = "risk") at test-standardize.R:86:5
7. └─survival:::predict.coxph(...)
8. └─stats::delete.response(Terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-standardize_coxph.R:12:3'): check estimates and standard errors against older package (coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─stdReg2::standardize_coxph(...) at test-standardize_coxph.R:12:3
2. └─stdReg2::sandwich(...)
3. ├─stats::predict(object = fit, type = "risk")
4. └─survival:::predict.coxph(object = fit, type = "risk")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-standardize_coxph.R:39:3'): standard error for coxph with factors bug is fixed ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::tidy(...) at test-standardize_coxph.R:39:3
2. └─stdReg2::standardize_coxph(...)
3. └─stdReg2::sandwich(...)
4. ├─stats::predict(object = fit, type = "risk")
5. └─survival:::predict.coxph(object = fit, type = "risk")
6. └─stats::delete.response(Terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 19 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc