Last updated on 2024-06-06 05:57:53 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.7 | 6.84 | 641.29 | 648.13 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.8.7 | 4.25 | 488.36 | 492.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.8.7 | ERROR | ||||
| r-devel-linux-x86_64-fedora-gcc | 0.8.7 | ERROR | ||||
| r-devel-windows-x86_64 | 0.8.7 | 6.00 | 115.00 | 121.00 | OK | |
| r-patched-linux-x86_64 | 0.8.7 | 6.93 | 655.19 | 662.12 | OK | |
| r-release-linux-x86_64 | 0.8.7 | 5.29 | 600.05 | 605.34 | NOTE | |
| r-release-macos-arm64 | 0.8.7 | 154.00 | OK | |||
| r-release-macos-x86_64 | 0.8.7 | 265.00 | OK | |||
| r-release-windows-x86_64 | 0.8.7 | 6.00 | 5910.00 | 5916.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.8.7 | 143.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.8.7 | 296.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.8.7 | 6.00 | 153.00 | 159.00 | OK |
Version: 0.8.7
Check: examples
Result: ERROR
Running examples in ‘modelbased-Ex.R’ failed
The error most likely occurred in:
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
>
> ### ** Examples
>
> ## Don't show:
> if (require("emmeans") && require("ggplot2") && require("see")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # Get an idea of the data
+ ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) +
+ geom_point(aes(color = Species)) +
+ geom_smooth(color = "black", se = FALSE) +
+ geom_smooth(aes(color = Species), linetype = "dotted", se = FALSE) +
+ geom_smooth(aes(color = Species), method = "lm", se = FALSE)
+
+ # Model it
+ model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
+ # Compute the marginal effect of Petal.Length at each level of Species
+ slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
+ slopes
+
+ # Plot it
+ plot(slopes)
+
+ standardize(slopes)
+ ## Don't show:
+ }) # examplesIf
Loading required package: emmeans
Welcome to emmeans.
Caution: You lose important information if you filter this package's results.
See '? untidy'
Loading required package: ggplot2
Loading required package: see
> ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) + geom_point(aes(color = Species)) +
+ geom_smooth(color = "black", se = FALSE) + geom_smooth(aes(color = Species),
+ linetype = "dotted", se = FALSE) + geom_smooth(aes(color = Species), method = "lm",
+ se = FALSE)
`geom_smooth()` using method = 'loess' and formula = 'y ~ x'
`geom_smooth()` using method = 'loess' and formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
> model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
> slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
Warning: Argument `at` is deprecated and will be removed in a future release.
Please use `by` instead.
> slopes
Estimated Marginal Effects
Species | Coefficient | SE | 95% CI | t(144) | p
-----------------------------------------------------------------
setosa | 0.39 | 0.26 | [-0.13, 0.90] | 1.49 | 0.138
versicolor | 0.37 | 0.10 | [ 0.18, 0.56] | 3.89 | < .001
virginica | 0.23 | 0.08 | [ 0.07, 0.40] | 2.86 | 0.005
Marginal effects estimated for Petal.Length> plot(slopes)
> standardize(slopes)
Estimated Marginal Effects (standardized)
Species | Coefficient | SE | 95% CI | t(144) | p
-----------------------------------------------------------------
setosa | 0.89 | 0.60 | [-0.29, 2.07] | 1.49 | 0.138
versicolor | 0.86 | 0.22 | [ 0.42, 1.29] | 3.89 | < .001
virginica | 0.54 | 0.19 | [ 0.17, 0.91] | 2.86 | 0.005
Marginal effects estimated for Petal.Length> ## End(Don't show)
> ## Don't show:
> if (require("mgcv") && require("emmeans") && require("see")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+ slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
+ summary(slopes)
+ plot(slopes)
+
+ model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+ slopes <- estimate_slopes(model,
+ trend = "Petal.Length",
+ at = c("Petal.Length", "Species"), length = 20
+ )
+ summary(slopes)
+ plot(slopes)
+ ## Don't show:
+ }) # examplesIf
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
> model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
> slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Length"`.
Warning: Argument `at` is deprecated and will be removed in a future release.
Please use `by` instead.
> summary(slopes)
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [316s/506s]
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?
> #
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> library(testthat)
> library(modelbased)
>
> test_check("modelbased")
Starting 2 test processes
[ FAIL 9 | WARN 103 | SKIP 2 | PASS 160 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is not TRUE (1):
'test-estimate_predicted.R:56:3'
• empty test (1): 'test-estimate_contrasts.R:188:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-estimate_contrasts.R:28:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 6 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:35:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 30 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:58:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 18 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:74:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 12 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:136:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 6 8
`expected`: 3 8
── Failure ('test-estimate_contrasts.R:150:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 30 8
`expected`: 3 8
── Failure ('test-estimate_means.R:97:3'): estimate_means() - core ─────────────
dim(estim) (`actual`) not equal to c(3, 6) (`expected`).
`actual`: 30 6
`expected`: 3 6
── Failure ('test-estimate_means.R:134:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(6, 7) (`expected`).
`actual`: 12 7
`expected`: 6 7
── Failure ('test-estimate_means.R:148:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(4, 7) (`expected`).
`actual`: 8 7
`expected`: 4 7
[ FAIL 9 | WARN 103 | SKIP 2 | PASS 160 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [11m/16m]
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?
> #
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> library(testthat)
> library(modelbased)
>
> test_check("modelbased")
Starting 2 test processes
[ FAIL 9 | WARN 103 | SKIP 2 | PASS 160 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is not TRUE (1):
'test-estimate_predicted.R:56:3'
• empty test (1): 'test-estimate_contrasts.R:188:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-estimate_contrasts.R:28:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 6 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:35:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 30 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:58:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 18 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:74:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 12 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:136:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 6 8
`expected`: 3 8
── Failure ('test-estimate_contrasts.R:150:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 30 8
`expected`: 3 8
── Failure ('test-estimate_means.R:97:3'): estimate_means() - core ─────────────
dim(estim) (`actual`) not equal to c(3, 6) (`expected`).
`actual`: 30 6
`expected`: 3 6
── Failure ('test-estimate_means.R:134:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(6, 7) (`expected`).
`actual`: 12 7
`expected`: 6 7
── Failure ('test-estimate_means.R:148:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(4, 7) (`expected`).
`actual`: 8 7
`expected`: 4 7
[ FAIL 9 | WARN 103 | SKIP 2 | PASS 160 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.8.7
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘rstanarm’
Flavor: r-release-linux-x86_64
Version: 0.8.7
Check: examples
Result: ERROR
Running examples in 'modelbased-Ex.R' failed
The error most likely occurred in:
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
>
> ### ** Examples
>
> ## Don't show:
> if (require("emmeans") && require("ggplot2") && require("see")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # Get an idea of the data
+ ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) +
+ geom_point(aes(color = Species)) +
+ geom_smooth(color = "black", se = FALSE) +
+ geom_smooth(aes(color = Species), linetype = "dotted", se = FALSE) +
+ geom_smooth(aes(color = Species), method = "lm", se = FALSE)
+
+ # Model it
+ model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
+ # Compute the marginal effect of Petal.Length at each level of Species
+ slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
+ slopes
+
+ # Plot it
+ plot(slopes)
+
+ standardize(slopes)
+ ## Don't show:
+ }) # examplesIf
Loading required package: emmeans
Welcome to emmeans.
Caution: You lose important information if you filter this package's results.
See '? untidy'
Loading required package: ggplot2
Loading required package: see
> ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) + geom_point(aes(color = Species)) +
+ geom_smooth(color = "black", se = FALSE) + geom_smooth(aes(color = Species),
+ linetype = "dotted", se = FALSE) + geom_smooth(aes(color = Species), method = "lm",
+ se = FALSE)
`geom_smooth()` using method = 'loess' and formula = 'y ~ x'
`geom_smooth()` using method = 'loess' and formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
> model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
> slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
Warning: Argument `at` is deprecated and will be removed in a future release.
Please use `by` instead.
> slopes
Estimated Marginal Effects
Species | Coefficient | SE | 95% CI | t(144) | p
-----------------------------------------------------------------
setosa | 0.39 | 0.26 | [-0.13, 0.90] | 1.49 | 0.138
versicolor | 0.37 | 0.10 | [ 0.18, 0.56] | 3.89 | < .001
virginica | 0.23 | 0.08 | [ 0.07, 0.40] | 2.86 | 0.005
Marginal effects estimated for Petal.Length> plot(slopes)
> standardize(slopes)
Estimated Marginal Effects (standardized)
Species | Coefficient | SE | 95% CI | t(144) | p
-----------------------------------------------------------------
setosa | 0.89 | 0.60 | [-0.29, 2.07] | 1.49 | 0.138
versicolor | 0.86 | 0.22 | [ 0.42, 1.29] | 3.89 | < .001
virginica | 0.54 | 0.19 | [ 0.17, 0.91] | 2.86 | 0.005
Marginal effects estimated for Petal.Length> ## End(Don't show)
> ## Don't show:
> if (require("mgcv") && require("emmeans") && require("see")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+ slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
+ summary(slopes)
+ plot(slopes)
+
+ model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+ slopes <- estimate_slopes(model,
+ trend = "Petal.Length",
+ at = c("Petal.Length", "Species"), length = 20
+ )
+ summary(slopes)
+ plot(slopes)
+ ## Don't show:
+ }) # examplesIf
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
> model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
> slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Length"`.
Warning: Argument `at` is deprecated and will be removed in a future release.
Please use `by` instead.
> summary(slopes)
Warning in Make.row.names(nmi, ri, ni, nrow) :
NAs introduced by coercion to integer range
Warning in nrow + ni : NAs produced by integer overflow
Error: cannot allocate vector of size 11.7 Gb
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.8.7
Check: tests
Result: ERROR
Running 'testthat.R' [37s]
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?
> #
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> library(testthat)
> library(modelbased)
>
> test_check("modelbased")
Starting 2 test processes
[ FAIL 9 | WARN 101 | SKIP 2 | PASS 159 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Windows (1): 'test-brms.R:1:1'
• empty test (1): 'test-estimate_contrasts.R:188:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-estimate_means.R:97:3'): estimate_means() - core ─────────────
dim(estim) (`actual`) not equal to c(3, 6) (`expected`).
`actual`: 30 6
`expected`: 3 6
── Failure ('test-estimate_means.R:134:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(6, 7) (`expected`).
`actual`: 12 7
`expected`: 6 7
── Failure ('test-estimate_means.R:148:3'): estimate_means() - core ────────────
dim(estim) (`actual`) not equal to c(4, 7) (`expected`).
`actual`: 8 7
`expected`: 4 7
── Failure ('test-estimate_contrasts.R:28:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 6 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:35:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(3, 10) (`expected`).
`actual`: 30 10
`expected`: 3 10
── Failure ('test-estimate_contrasts.R:58:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 18 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:74:3'): estimate_contrasts - Frequentist ──
dim(estim) (`actual`) not equal to c(6, 10) (`expected`).
`actual`: 12 10
`expected`: 6 10
── Failure ('test-estimate_contrasts.R:136:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 6 8
`expected`: 3 8
── Failure ('test-estimate_contrasts.R:150:3'): estimate_contrasts - Bayesian ──
dim(estim) (`actual`) not equal to c(3, 8) (`expected`).
`actual`: 30 8
`expected`: 3 8
[ FAIL 9 | WARN 101 | SKIP 2 | PASS 159 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64