Last updated on 2025-12-21 17:51:19 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| bayestestR | 13 | ||
| insight | 4 | 1 | 8 |
| modelbased | 3 | 10 | |
| parameters | 4 | 2 | 7 |
| performance | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 4, NOTE: 1, OK: 8
Version: 1.4.4
Check: examples
Result: ERROR
Running examples in ‘insight-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datagrid.emmGrid
> ### Title: Extract a reference grid from objects created by '{emmeans}' and
> ### '{marginaleffects}'
> ### Aliases: get_datagrid.emmGrid
>
> ### ** Examples
>
> data("mtcars")
> mtcars$cyl <- factor(mtcars$cyl)
>
> mod <- glm(am ~ cyl + hp + wt,
+ family = binomial("logit"),
+ data = mtcars
+ )
>
> ## Don't show:
> if (insight::check_if_installed("emmeans", quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ em1 <- emmeans::emmeans(mod, ~ cyl + hp, at = list(hp = c(100, 150)))
+ get_datagrid(em1)
+
+ contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
+ get_datagrid(contr1)
+
+ eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100, 150)))
+ get_datagrid(eml1) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> em1 <- emmeans::emmeans(mod, ~cyl + hp, at = list(hp = c(100, 150)))
> get_datagrid(em1)
cyl hp
1 4 100
2 6 100
3 8 100
4 4 150
5 6 150
6 8 150
> contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
> get_datagrid(contr1)
contrast hp
1 cyl6 - cyl4 100
2 cyl8 - cyl6 100
3 cyl6 - cyl4 150
4 cyl8 - cyl6 150
> eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100,
+ 150)))
> get_datagrid(eml1)
hp cyl contrast
1 100 4 <NA>
2 100 6 <NA>
3 100 8 <NA>
4 150 4 <NA>
5 150 6 <NA>
6 150 8 <NA>
7 100 <NA> cyl4 - cyl6
8 100 <NA> cyl4 - cyl8
9 100 <NA> cyl6 - cyl8
10 150 <NA> cyl4 - cyl6
11 150 <NA> cyl4 - cyl8
12 150 <NA> cyl6 - cyl8
> ## End(Don't show)
> ## Don't show:
> if (insight::check_if_installed("marginaleffects", quietly = TRUE, minimum_version = "0.29.0")) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ mfx1 <- marginaleffects::slopes(mod, variables = "hp")
+ get_datagrid(mfx1) # not a "true" grid
+
+ mfx2 <- marginaleffects::slopes(mod, variables = c("hp", "wt"), by = "am")
+ get_datagrid(mfx2)
+
+ contr2 <- marginaleffects::avg_comparisons(mod)
+ get_datagrid(contr2) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> mfx1 <- marginaleffects::slopes(mod, variables = "hp")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 19/19 in VECTOR_ELT
Calls: withAutoprint ... <Anonymous> -> do.call -> get_comparisons -> [ -> [.data.table
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
find_algorithm 4.11 0.21 5.642
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.4.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [333s/170s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(insight)
> test_check("insight")
Starting 2 test processes.
> test-find_transformation.R: boundary (singular) fit: see help('isSingular')
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 365.2328
> test-gamlss.R: GAMLSS-RS iteration
> test-gamlss.R: 2: Global Deviance = 365.1292
> test-gamlss.R: GAMLSS-RS iteration 3: Global Deviance = 365.1269
> test-gamlss.R: GAMLSS-RS iteration 4: Global Deviance = 365.1268
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 703.1164
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 703.1164
> test-get_model.R: Loading required namespace: GPArotation
> test-get_random.R: boundary (singular) fit: see help('isSingular')
Saving _problems/test-get_datagrid-486.R
Saving _problems/test-get_datagrid-1143.R
> test-glmmPQL.R: iteration 1
> test-is_converged.R: boundary (singular) fit: see help('isSingular')
> test-mmrm.R: mmrm() registered as emmeans extension
> test-mmrm.R: mmrm() registered as car::Anova extension
> test-model_info.R: boundary (singular) fit: see help('isSingular')
> test-nestedLogit.R: list(work = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,
> test-nestedLogit.R: 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L
> test-nestedLogit.R: ), full = c(1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
══ Skipped tests (96) ══════════════════════════════════════════════════════════
• On CRAN (89): 'test-GLMMadaptive.R:2:1', 'test-averaging.R:1:1',
'test-bias_correction.R:1:1', 'test-betareg.R:197:5', 'test-brms.R:1:1',
'test-brms_aterms.R:1:1', 'test-brms_gr_random_effects.R:1:1',
'test-brms_missing.R:1:1', 'test-blmer.R:262:3', 'test-brms_mm.R:1:1',
'test-brms_von_mises.R:1:1', 'test-clean_names.R:109:3',
'test-clean_parameters.R:1:1', 'test-coxme.R:1:1', 'test-clmm.R:170:3',
'test-cpglmm.R:152:3', 'test-display.R:1:1', 'test-display.R:15:1',
'test-export_table.R:3:1', 'test-export_table.R:7:1',
'test-export_table.R:134:3', 'test-export_table.R:164:3',
'test-export_table.R:193:1', 'test-export_table.R:278:1',
'test-export_table.R:296:3', 'test-export_table.R:328:3',
'test-export_table.R:385:1', 'test-export_table.R:406:3',
'test-export_table.R:470:3', 'test-find_smooth.R:39:3', 'test-fixest.R:2:1',
'test-format_table.R:2:1', 'test-format_table_ci.R:72:1',
'test-find_random.R:43:3', 'test-gam.R:2:1', 'test-get_data.R:507:1',
'test-get_loglikelihood.R:143:3', 'test-get_loglikelihood.R:223:3',
'test-get_predicted.R:2:1', 'test-get_priors.R:1:1',
'test-get_varcov.R:43:3', 'test-get_varcov.R:57:3',
'test-get_datagrid.R:1068:3', 'test-get_datagrid.R:1105:5',
'test-is_converged.R:47:1', 'test-iv_robust.R:120:3', 'test-lavaan.R:1:1',
'test-lcmm.R:1:1', 'test-lme.R:28:3', 'test-lme.R:212:3',
'test-glmmTMB.R:67:3', 'test-glmmTMB.R:767:3', 'test-glmmTMB.R:803:3',
'test-glmmTMB.R:1142:3', 'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1',
'test-mipo.R:1:1', 'test-mlogit.R:1:1', 'test-model_info.R:106:3',
'test-modelbased.R:1:1', 'test-mvrstanarm.R:1:1', 'test-null_model.R:85:3',
'test-panelr-asym.R:165:3', 'test-panelr.R:301:3', 'test-phylolm.R:1:1',
'test-print_parameters.R:1:1', 'test-r2_nakagawa_bernoulli.R:1:1',
'test-r2_nakagawa_beta.R:1:1', 'test-r2_nakagawa_binomial.R:1:1',
'test-r2_nakagawa_gamma.R:1:1', 'test-r2_nakagawa_linear.R:1:1',
'test-r2_nakagawa_negbin.R:1:1', 'test-r2_nakagawa_negbin_zi.R:1:1',
'test-r2_nakagawa_ordered_beta.R:1:1', 'test-r2_nakagawa_poisson.R:1:1',
'test-r2_nakagawa_poisson_zi.R:1:1',
'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1',
'test-rlmer.R:276:3', 'test-rms.R:1:1', 'test-rqss.R:1:1',
'test-rstanarm.R:1:1', 'test-sdmTMB.R:1:1', 'test-selection.R:2:1',
'test-spatial.R:2:1', 'test-svylme.R:1:1', 'test-tidymodels.R:1:1',
'test-vgam.R:2:1', 'test-weightit.R:1:1'
• On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1',
'test-get_data.R:161:3'
• Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1'
• works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3'
• {bigglm} is not installed (1): 'test-model_info.R:24:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_datagrid.R:481:3'): get_datagrid - marginaleffects ─────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...) at test-get_datagrid.R:481:3
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-get_datagrid.R:1143:3'): get_datagrid - marginaleffects, avg_slopes, non-Bayesian ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 19/19 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.4.4
Check: examples
Result: ERROR
Running examples in ‘insight-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datagrid.emmGrid
> ### Title: Extract a reference grid from objects created by '{emmeans}' and
> ### '{marginaleffects}'
> ### Aliases: get_datagrid.emmGrid
>
> ### ** Examples
>
> data("mtcars")
> mtcars$cyl <- factor(mtcars$cyl)
>
> mod <- glm(am ~ cyl + hp + wt,
+ family = binomial("logit"),
+ data = mtcars
+ )
>
> ## Don't show:
> if (insight::check_if_installed("emmeans", quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ em1 <- emmeans::emmeans(mod, ~ cyl + hp, at = list(hp = c(100, 150)))
+ get_datagrid(em1)
+
+ contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
+ get_datagrid(contr1)
+
+ eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100, 150)))
+ get_datagrid(eml1) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> em1 <- emmeans::emmeans(mod, ~cyl + hp, at = list(hp = c(100, 150)))
> get_datagrid(em1)
cyl hp
1 4 100
2 6 100
3 8 100
4 4 150
5 6 150
6 8 150
> contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
> get_datagrid(contr1)
contrast hp
1 cyl6 - cyl4 100
2 cyl8 - cyl6 100
3 cyl6 - cyl4 150
4 cyl8 - cyl6 150
> eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100,
+ 150)))
> get_datagrid(eml1)
hp cyl contrast
1 100 4 <NA>
2 100 6 <NA>
3 100 8 <NA>
4 150 4 <NA>
5 150 6 <NA>
6 150 8 <NA>
7 100 <NA> cyl4 - cyl6
8 100 <NA> cyl4 - cyl8
9 100 <NA> cyl6 - cyl8
10 150 <NA> cyl4 - cyl6
11 150 <NA> cyl4 - cyl8
12 150 <NA> cyl6 - cyl8
> ## End(Don't show)
> ## Don't show:
> if (insight::check_if_installed("marginaleffects", quietly = TRUE, minimum_version = "0.29.0")) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ mfx1 <- marginaleffects::slopes(mod, variables = "hp")
+ get_datagrid(mfx1) # not a "true" grid
+
+ mfx2 <- marginaleffects::slopes(mod, variables = c("hp", "wt"), by = "am")
+ get_datagrid(mfx2)
+
+ contr2 <- marginaleffects::avg_comparisons(mod)
+ get_datagrid(contr2) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> mfx1 <- marginaleffects::slopes(mod, variables = "hp")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 19/19 in VECTOR_ELT
Calls: withAutoprint ... <Anonymous> -> do.call -> get_comparisons -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [207s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(insight)
> test_check("insight")
Starting 2 test processes.
> test-find_transformation.R: boundary (singular) fit: see help('isSingular')
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 365.2328
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 365.1292
> test-gamlss.R: GAMLSS-RS iteration 3: Global Deviance = 365.1269
> test-gamlss.R: GAMLSS-RS iteration 4: Global Deviance = 365.1268
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 703.1164
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 703.1164
> test-get_model.R: Loading required namespace: GPArotation
> test-get_random.R: boundary (singular) fit: see help('isSingular')
Saving _problems/test-get_datagrid-486.R
Saving _problems/test-get_datagrid-1143.R
> test-glmmPQL.R: iteration 1
> test-is_converged.R: boundary (singular) fit: see help('isSingular')
> test-mmrm.R: mmrm() registered as emmeans extension
> test-mmrm.R: mmrm() registered as car::Anova extension
> test-model_info.R: boundary (singular) fit: see help('isSingular')
> test-nestedLogit.R: list(work = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,
> test-nestedLogit.R: 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L
> test-nestedLogit.R: ), full = c(1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
══ Skipped tests (96) ══════════════════════════════════════════════════════════
• On CRAN (89): 'test-GLMMadaptive.R:2:1', 'test-averaging.R:1:1',
'test-bias_correction.R:1:1', 'test-betareg.R:197:5', 'test-brms.R:1:1',
'test-brms_aterms.R:1:1', 'test-brms_gr_random_effects.R:1:1',
'test-brms_missing.R:1:1', 'test-blmer.R:262:3', 'test-brms_mm.R:1:1',
'test-brms_von_mises.R:1:1', 'test-clean_names.R:109:3',
'test-clean_parameters.R:1:1', 'test-coxme.R:1:1', 'test-clmm.R:170:3',
'test-cpglmm.R:152:3', 'test-display.R:1:1', 'test-display.R:15:1',
'test-export_table.R:3:1', 'test-export_table.R:7:1',
'test-export_table.R:134:3', 'test-export_table.R:164:3',
'test-export_table.R:193:1', 'test-export_table.R:278:1',
'test-export_table.R:296:3', 'test-export_table.R:328:3',
'test-export_table.R:385:1', 'test-export_table.R:406:3',
'test-export_table.R:470:3', 'test-find_smooth.R:39:3', 'test-fixest.R:2:1',
'test-format_table.R:2:1', 'test-format_table_ci.R:72:1',
'test-find_random.R:43:3', 'test-gam.R:2:1', 'test-get_data.R:507:1',
'test-get_loglikelihood.R:143:3', 'test-get_loglikelihood.R:223:3',
'test-get_predicted.R:2:1', 'test-get_priors.R:1:1',
'test-get_varcov.R:43:3', 'test-get_varcov.R:57:3',
'test-get_datagrid.R:1068:3', 'test-get_datagrid.R:1105:5',
'test-is_converged.R:47:1', 'test-iv_robust.R:120:3', 'test-lavaan.R:1:1',
'test-lcmm.R:1:1', 'test-lme.R:28:3', 'test-lme.R:212:3',
'test-glmmTMB.R:67:3', 'test-glmmTMB.R:767:3', 'test-glmmTMB.R:803:3',
'test-glmmTMB.R:1142:3', 'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1',
'test-mipo.R:1:1', 'test-mlogit.R:1:1', 'test-model_info.R:106:3',
'test-modelbased.R:1:1', 'test-mvrstanarm.R:1:1', 'test-null_model.R:85:3',
'test-panelr-asym.R:165:3', 'test-panelr.R:301:3', 'test-phylolm.R:1:1',
'test-print_parameters.R:1:1', 'test-r2_nakagawa_bernoulli.R:1:1',
'test-r2_nakagawa_beta.R:1:1', 'test-r2_nakagawa_binomial.R:1:1',
'test-r2_nakagawa_gamma.R:1:1', 'test-r2_nakagawa_linear.R:1:1',
'test-r2_nakagawa_negbin.R:1:1', 'test-r2_nakagawa_negbin_zi.R:1:1',
'test-r2_nakagawa_ordered_beta.R:1:1', 'test-r2_nakagawa_poisson.R:1:1',
'test-r2_nakagawa_poisson_zi.R:1:1',
'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1',
'test-rlmer.R:276:3', 'test-rms.R:1:1', 'test-rqss.R:1:1',
'test-rstanarm.R:1:1', 'test-sdmTMB.R:1:1', 'test-selection.R:2:1',
'test-spatial.R:2:1', 'test-svylme.R:1:1', 'test-tidymodels.R:1:1',
'test-vgam.R:2:1', 'test-weightit.R:1:1'
• On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1',
'test-get_data.R:161:3'
• Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1'
• works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3'
• {bigglm} is not installed (1): 'test-model_info.R:24:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_datagrid.R:481:3'): get_datagrid - marginaleffects ─────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...) at test-get_datagrid.R:481:3
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-get_datagrid.R:1143:3'): get_datagrid - marginaleffects, avg_slopes, non-Bayesian ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 19/19 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.4
Check: examples
Result: ERROR
Running examples in ‘insight-Ex.R’ failed
The error most likely occurred in:
> ### Name: get_datagrid.emmGrid
> ### Title: Extract a reference grid from objects created by '{emmeans}' and
> ### '{marginaleffects}'
> ### Aliases: get_datagrid.emmGrid
>
> ### ** Examples
>
> data("mtcars")
> mtcars$cyl <- factor(mtcars$cyl)
>
> mod <- glm(am ~ cyl + hp + wt,
+ family = binomial("logit"),
+ data = mtcars
+ )
>
> ## Don't show:
> if (insight::check_if_installed("emmeans", quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ em1 <- emmeans::emmeans(mod, ~ cyl + hp, at = list(hp = c(100, 150)))
+ get_datagrid(em1)
+
+ contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
+ get_datagrid(contr1)
+
+ eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100, 150)))
+ get_datagrid(eml1) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> em1 <- emmeans::emmeans(mod, ~cyl + hp, at = list(hp = c(100, 150)))
> get_datagrid(em1)
cyl hp
1 4 100
2 6 100
3 8 100
4 4 150
5 6 150
6 8 150
> contr1 <- emmeans::contrast(em1, method = "consec", by = "hp")
> get_datagrid(contr1)
contrast hp
1 cyl6 - cyl4 100
2 cyl8 - cyl6 100
3 cyl6 - cyl4 150
4 cyl8 - cyl6 150
> eml1 <- emmeans::emmeans(mod, pairwise ~ cyl | hp, at = list(hp = c(100,
+ 150)))
> get_datagrid(eml1)
hp cyl contrast
1 100 4 <NA>
2 100 6 <NA>
3 100 8 <NA>
4 150 4 <NA>
5 150 6 <NA>
6 150 8 <NA>
7 100 <NA> cyl4 - cyl6
8 100 <NA> cyl4 - cyl8
9 100 <NA> cyl6 - cyl8
10 150 <NA> cyl4 - cyl6
11 150 <NA> cyl4 - cyl8
12 150 <NA> cyl6 - cyl8
> ## End(Don't show)
> ## Don't show:
> if (insight::check_if_installed("marginaleffects", quietly = TRUE, minimum_version = "0.29.0")) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ mfx1 <- marginaleffects::slopes(mod, variables = "hp")
+ get_datagrid(mfx1) # not a "true" grid
+
+ mfx2 <- marginaleffects::slopes(mod, variables = c("hp", "wt"), by = "am")
+ get_datagrid(mfx2)
+
+ contr2 <- marginaleffects::avg_comparisons(mod)
+ get_datagrid(contr2) # not a "true" grid
+ ## Don't show:
+ }) # examplesIf
> mfx1 <- marginaleffects::slopes(mod, variables = "hp")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 19/19 in VECTOR_ELT
Calls: withAutoprint ... <Anonymous> -> do.call -> get_comparisons -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.4.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [534s/535s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(insight)
> test_check("insight")
Starting 2 test processes.
> test-find_transformation.R: boundary (singular) fit: see help('isSingular')
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 365.2328
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 365.1292
> test-gamlss.R: GAMLSS-RS iteration
> test-gamlss.R: 3: Global Deviance = 365.1269
> test-gamlss.R: GAMLSS-RS iteration 4: Global Deviance = 365.1268
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 703.1164
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 703.1164
> test-get_model.R: Loading required namespace: GPArotation
> test-get_random.R: boundary (singular) fit: see help('isSingular')
Saving _problems/test-get_datagrid-486.R
Saving _problems/test-get_datagrid-1143.R
> test-glmmPQL.R: iteration 1
> test-is_converged.R: boundary (singular) fit: see help('isSingular')
> test-mmrm.R: mmrm() registered as emmeans extension
> test-mmrm.R: mmrm() registered as car::Anova extension
> test-model_info.R: boundary (singular) fit: see help('isSingular')
> test-nestedLogit.R: list(work = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,
> test-nestedLogit.R: 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L
> test-nestedLogit.R: ), full = c(1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
> test-survey_coxph.R: Stratified Independent Sampling design (with replacement)
> test-survey_coxph.R: dpbc <- survey::svydesign(
> test-survey_coxph.R: id = ~1,
> test-survey_coxph.R: prob = ~randprob,
> test-survey_coxph.R: strata = ~edema,
> test-survey_coxph.R: data = subset(pbc, randomized)
> test-survey_coxph.R: )
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
══ Skipped tests (96) ══════════════════════════════════════════════════════════
• On CRAN (89): 'test-GLMMadaptive.R:2:1', 'test-averaging.R:1:1',
'test-bias_correction.R:1:1', 'test-betareg.R:197:5', 'test-brms.R:1:1',
'test-brms_aterms.R:1:1', 'test-brms_gr_random_effects.R:1:1',
'test-blmer.R:262:3', 'test-brms_missing.R:1:1', 'test-brms_mm.R:1:1',
'test-brms_von_mises.R:1:1', 'test-clean_names.R:109:3',
'test-clean_parameters.R:1:1', 'test-coxme.R:1:1', 'test-cpglmm.R:152:3',
'test-clmm.R:170:3', 'test-display.R:1:1', 'test-display.R:15:1',
'test-export_table.R:3:1', 'test-export_table.R:7:1',
'test-export_table.R:134:3', 'test-export_table.R:164:3',
'test-export_table.R:193:1', 'test-export_table.R:278:1',
'test-export_table.R:296:3', 'test-export_table.R:328:3',
'test-export_table.R:385:1', 'test-export_table.R:406:3',
'test-export_table.R:470:3', 'test-find_random.R:43:3', 'test-fixest.R:2:1',
'test-format_table.R:2:1', 'test-format_table_ci.R:72:1', 'test-gam.R:2:1',
'test-find_smooth.R:39:3', 'test-get_data.R:507:1',
'test-get_loglikelihood.R:143:3', 'test-get_loglikelihood.R:223:3',
'test-get_predicted.R:2:1', 'test-get_priors.R:1:1',
'test-get_varcov.R:43:3', 'test-get_varcov.R:57:3',
'test-get_datagrid.R:1068:3', 'test-get_datagrid.R:1105:5',
'test-is_converged.R:47:1', 'test-iv_robust.R:120:3', 'test-lavaan.R:1:1',
'test-lcmm.R:1:1', 'test-lme.R:28:3', 'test-lme.R:212:3',
'test-glmmTMB.R:67:3', 'test-glmmTMB.R:767:3', 'test-glmmTMB.R:803:3',
'test-glmmTMB.R:1142:3', 'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1',
'test-mipo.R:1:1', 'test-mlogit.R:1:1', 'test-model_info.R:106:3',
'test-modelbased.R:1:1', 'test-mvrstanarm.R:1:1', 'test-null_model.R:85:3',
'test-panelr-asym.R:165:3', 'test-panelr.R:301:3', 'test-phylolm.R:1:1',
'test-print_parameters.R:1:1', 'test-r2_nakagawa_bernoulli.R:1:1',
'test-r2_nakagawa_beta.R:1:1', 'test-r2_nakagawa_binomial.R:1:1',
'test-r2_nakagawa_gamma.R:1:1', 'test-r2_nakagawa_linear.R:1:1',
'test-r2_nakagawa_negbin.R:1:1', 'test-r2_nakagawa_negbin_zi.R:1:1',
'test-r2_nakagawa_ordered_beta.R:1:1', 'test-r2_nakagawa_poisson.R:1:1',
'test-r2_nakagawa_poisson_zi.R:1:1',
'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1',
'test-rlmer.R:276:3', 'test-rms.R:1:1', 'test-rqss.R:1:1',
'test-rstanarm.R:1:1', 'test-sdmTMB.R:1:1', 'test-selection.R:2:1',
'test-spatial.R:2:1', 'test-svylme.R:1:1', 'test-tidymodels.R:1:1',
'test-vgam.R:2:1', 'test-weightit.R:1:1'
• On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1',
'test-get_data.R:161:3'
• Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1'
• works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3'
• {bigglm} is not installed (1): 'test-model_info.R:24:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_datagrid.R:481:3'): get_datagrid - marginaleffects ─────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...) at test-get_datagrid.R:481:3
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-get_datagrid.R:1143:3'): get_datagrid - marginaleffects, avg_slopes, non-Bayesian ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 19/19 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 2 | SKIP 96 | PASS 3510 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.4.4
Check: tests
Result: ERROR
Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(insight)
> test_check("insight")
Starting 2 test processes.
> test-find_transformation.R: boundary (singular) fit: see help('isSingular')
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 365.2328
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 365.1292
> test-gamlss.R: GAMLSS-RS iteration 3: Global Deviance = 365.1269
> test-gamlss.R: GAMLSS-RS iteration 4: Global Deviance = 365.1268
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 5779.746
> test-gamlss.R: GAMLSS-RS iteration 1: Global Deviance = 703.1164
> test-gamlss.R: GAMLSS-RS iteration 2: Global Deviance = 703.1164
> test-get_model.R: Loading required namespace: GPArotation
> test-get_random.R: boundary (singular) fit: see help('isSingular')
> test-glmmPQL.R: iteration 1
> test-is_converged.R: boundary (singular) fit: see help('isSingular')
> test-mmrm.R: mmrm() registered as emmeans extension
> test-mmrm.R: mmrm() registered as car::Anova extension
> test-model_info.R: boundary (singular) fit: see help('isSingular')
> test-nestedLogit.R: list(work = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L,
> test-nestedLogit.R: 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,
> test-nestedLogit.R: 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L
> test-nestedLogit.R: ), full = c(1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L,
> test-nestedLogit.R: 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L,
> test-nestedLogit.R: 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-polr.R:
> test-polr.R: Re-fitting to get Hessian
> test-polr.R:
> test-print_parameters.R:
Error:
! testthat subprocess exited in file 'test-print_parameters.R'.
Caused by error:
! R session crashed with exit code -1073741819
Backtrace:
▆
1. └─testthat::test_check("insight")
2. └─testthat::test_dir(...)
3. └─testthat:::test_files(...)
4. └─testthat:::test_files_parallel(...)
5. ├─withr::with_dir(...)
6. │ └─base::force(code)
7. ├─testthat::with_reporter(...)
8. │ └─base::tryCatch(...)
9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
13. └─queue$poll(Inf)
14. └─base::lapply(...)
15. └─testthat (local) FUN(X[[i]], ...)
16. └─private$handle_error(msg, i)
17. └─cli::cli_abort(...)
18. └─rlang::abort(...)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.4.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'fungible'
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 3, OK: 10
Version: 0.13.1
Check: examples
Result: ERROR
Running examples in ‘modelbased-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
>
> ### ** Examples
>
> ## Don't show:
> if (all(insight::check_if_installed(c("marginaleffects", "emmeans", "effectsize", "mgcv", "ggplot2", "see"), quietly = TRUE))) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ library(ggplot2)
+ # 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", by = "Species")
+ slopes
+
+ # What is the *average* slope of Petal.Length? This can be calculated by
+ # taking the average of the slopes across all Species, using `comparison`.
+ # We pass a function to `comparison` that calculates the mean of the slopes.
+ estimate_slopes(
+ model,
+ trend = "Petal.Length",
+ by = "Species",
+ comparison = ~I(mean(x))
+ )
+
+ ## Not run:
+ ##D # Plot it
+ ##D plot(slopes)
+ ##D standardize(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+ ##D slopes <- estimate_slopes(model, by = "Petal.Length", length = 50)
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+ ##D slopes <- estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 20
+ ##D )
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D # marginal effects, grouped by Species, at different values of Petal.Length
+ ##D estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 10
+ ##D )
+ ##D
+ ##D # marginal effects at different values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length", length = 10)
+ ##D
+ ##D # marginal effects at very specific values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length=c(1, 3, 5)")
+ ##D
+ ##D # average marginal effects of Petal.Length,
+ ##D # just for the trend within a certain range
+ ##D estimate_slopes(model, trend = "Petal.Length=seq(2, 4, 0.01)")
+ ## End(Not run)
+ ## Don't show:
+ }) # examplesIf
> library(ggplot2)
> 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", by = "Species")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 10/10 in VECTOR_ELT
Calls: withAutoprint ... eval -> eval -> estimate_slopes -> get_marginaltrends
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
estimate_contrasts 9.928 0.563 11.512
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [63s/31s]
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.
Saving _problems/test-attributes_estimatefun-108.R
Saving _problems/test-estimate_slopes-10.R
Saving _problems/test-estimate_slopes-63.R
Saving _problems/test-estimate_slopes-124.R
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
Saving _problems/test-transform_response-65.R
Saving _problems/test-visualisation_recipe-151.R
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
══ Skipped tests (54) ══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is not TRUE (1):
'test-estimate_predicted.R:58:3'
• On CRAN (45): 'test-backtransform_invlink.R:1:1', 'test-betareg.R:1:1',
'test-bias_correction.R:1:1', 'test-brms-marginaleffects.R:1:1',
'test-brms.R:1:1', 'test-equivalence.R:1:1',
'test-estimate_contrasts-average.R:1:1', 'test-estimate_contrasts.R:1:1',
'test-estimate_contrasts_bookexamples.R:1:1',
'test-estimate_contrasts_counterfactual.R:1:1',
'test-estimate_contrasts_effectsize.R:1:1',
'test-estimate_contrasts_inequality.R:1:1',
'test-estimate_contrasts_methods.R:1:1', 'test-estimate_filter.R:1:1',
'test-estimate_grouplevel.R:54:3', 'test-estimate_grouplevel.R:72:3',
'test-estimate_grouplevel.R:93:3', 'test-estimate_grouplevel.R:123:3',
'test-estimate_grouplevel.R:150:5', 'test-estimate_grouplevel.R:182:3',
'test-estimate_grouplevel.R:261:3', 'test-estimate_grouplevel.R:308:3',
'test-estimate_means-average.R:1:1', 'test-estimate_means.R:1:1',
'test-estimate_means_ci.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',
'test-estimate_means_dotargs.R:1:1',
'test-estimate_means_marginalization.R:1:1',
'test-estimate_means_mixed.R:1:1', 'test-estimate_slopes.R:129:1',
'test-g_computation.R:1:1', 'test-get_marginaltrends.R:1:1',
'test-glmmTMB.R:1:1', 'test-joint_test.R:1:1', 'test-keep_iterations.R:1:1',
'test-maihda.R:1:1', 'test-mice.R:1:1', 'test-ordinal.R:1:1',
'test-plot-grouplevel.R:1:1', 'test-predict-dpar.R:1:1',
'test-standardize.R:1:1', 'test-summary_estimate_slopes.R:3:1',
'test-transform_response.R:3:1', 'test-vcov.R:1:1', 'test-zeroinfl.R:1:1'
• On Linux (8): 'test-plot-facet.R:1:1', 'test-plot-flexible_numeric.R:1:1',
'test-plot-ordinal.R:1:1', 'test-plot-slopes.R:1:1', 'test-plot.R:1:1',
'test-print.R:1:1', 'test-residualize_over_grid.R:1:1',
'test-scoping_issues.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-attributes_estimatefun.R:108:3'): attributes_means, slopes ─────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-attributes_estimatefun.R:108:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, "Sepal.Width", backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:10:3'): estimate_slopes ──────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(estimate_slopes(model, backend = "marginaleffects")) at test-estimate_slopes.R:10:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:63:3'): estimate_slopes, johnson-neyman p-adjust ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, "Petal.Width", by = "Petal.Length") at test-estimate_slopes.R:63:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:124:3'): estimate_slopes, custom comparison ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─modelbased::estimate_contrasts(...) at test-estimate_slopes.R:124:3
2. └─modelbased:::estimate_contrasts.default(...)
3. └─modelbased::get_marginalcontrasts(...)
4. └─modelbased::estimate_slopes(...)
5. └─modelbased::get_marginaltrends(...)
6. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
7. │ └─base::withCallingHandlers(...)
8. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
9. ├─marginaleffects (local) `<fn>`(...)
10. │ └─base::eval.parent(call_attr)
11. │ └─base::eval(expr, p)
12. │ └─base::eval(expr, p)
13. ├─marginaleffects::slopes(...)
14. │ └─base::eval.parent(call_attr_c)
15. │ └─base::eval(expr, p)
16. │ └─base::eval(expr, p)
17. └─marginaleffects::comparisons(...)
18. ├─base::do.call("get_comparisons", args)
19. └─marginaleffects:::get_comparisons(...)
20. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
21. └─data.table:::`[.data.table`(...)
── Error ('test-transform_response.R:65:3'): estimate_slopes, transform ────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(mod, trend = "Sepal.Width", by = "Species") at test-transform_response.R:65:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-visualisation_recipe.R:151:3'): visualization_recipe ───────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 15/15 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, trend = "Sepal.Width") at test-visualisation_recipe.R:151:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13.1
Check: examples
Result: ERROR
Running examples in ‘modelbased-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
>
> ### ** Examples
>
> ## Don't show:
> if (all(insight::check_if_installed(c("marginaleffects", "emmeans", "effectsize", "mgcv", "ggplot2", "see"), quietly = TRUE))) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ library(ggplot2)
+ # 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", by = "Species")
+ slopes
+
+ # What is the *average* slope of Petal.Length? This can be calculated by
+ # taking the average of the slopes across all Species, using `comparison`.
+ # We pass a function to `comparison` that calculates the mean of the slopes.
+ estimate_slopes(
+ model,
+ trend = "Petal.Length",
+ by = "Species",
+ comparison = ~I(mean(x))
+ )
+
+ ## Not run:
+ ##D # Plot it
+ ##D plot(slopes)
+ ##D standardize(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+ ##D slopes <- estimate_slopes(model, by = "Petal.Length", length = 50)
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+ ##D slopes <- estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 20
+ ##D )
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D # marginal effects, grouped by Species, at different values of Petal.Length
+ ##D estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 10
+ ##D )
+ ##D
+ ##D # marginal effects at different values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length", length = 10)
+ ##D
+ ##D # marginal effects at very specific values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length=c(1, 3, 5)")
+ ##D
+ ##D # average marginal effects of Petal.Length,
+ ##D # just for the trend within a certain range
+ ##D estimate_slopes(model, trend = "Petal.Length=seq(2, 4, 0.01)")
+ ## End(Not run)
+ ## Don't show:
+ }) # examplesIf
> library(ggplot2)
> 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", by = "Species")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 10/10 in VECTOR_ELT
Calls: withAutoprint ... eval -> eval -> estimate_slopes -> get_marginaltrends
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
estimate_contrasts 7.196 0.499 11.883
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.13.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [41s/24s]
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.
Saving _problems/test-attributes_estimatefun-108.R
Saving _problems/test-estimate_slopes-10.R
Saving _problems/test-estimate_slopes-63.R
Saving _problems/test-estimate_slopes-124.R
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
Saving _problems/test-transform_response-65.R
Saving _problems/test-visualisation_recipe-151.R
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
══ Skipped tests (54) ══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is not TRUE (1):
'test-estimate_predicted.R:58:3'
• On CRAN (45): 'test-backtransform_invlink.R:1:1', 'test-betareg.R:1:1',
'test-bias_correction.R:1:1', 'test-brms-marginaleffects.R:1:1',
'test-brms.R:1:1', 'test-equivalence.R:1:1',
'test-estimate_contrasts-average.R:1:1',
'test-estimate_contrasts_bookexamples.R:1:1',
'test-estimate_contrasts_counterfactual.R:1:1',
'test-estimate_contrasts.R:1:1', 'test-estimate_contrasts_effectsize.R:1:1',
'test-estimate_contrasts_inequality.R:1:1',
'test-estimate_contrasts_methods.R:1:1', 'test-estimate_filter.R:1:1',
'test-estimate_means-average.R:1:1', 'test-estimate_means.R:1:1',
'test-estimate_means_ci.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',
'test-estimate_means_dotargs.R:1:1', 'test-estimate_grouplevel.R:54:3',
'test-estimate_grouplevel.R:72:3', 'test-estimate_grouplevel.R:93:3',
'test-estimate_grouplevel.R:123:3', 'test-estimate_grouplevel.R:150:5',
'test-estimate_grouplevel.R:182:3', 'test-estimate_grouplevel.R:261:3',
'test-estimate_grouplevel.R:308:3',
'test-estimate_means_marginalization.R:1:1',
'test-estimate_means_mixed.R:1:1', 'test-estimate_slopes.R:129:1',
'test-g_computation.R:1:1', 'test-get_marginaltrends.R:1:1',
'test-glmmTMB.R:1:1', 'test-joint_test.R:1:1', 'test-keep_iterations.R:1:1',
'test-maihda.R:1:1', 'test-mice.R:1:1', 'test-ordinal.R:1:1',
'test-plot-grouplevel.R:1:1', 'test-predict-dpar.R:1:1',
'test-standardize.R:1:1', 'test-summary_estimate_slopes.R:3:1',
'test-transform_response.R:3:1', 'test-vcov.R:1:1', 'test-zeroinfl.R:1:1'
• On Linux (8): 'test-plot-facet.R:1:1', 'test-plot-flexible_numeric.R:1:1',
'test-plot-ordinal.R:1:1', 'test-plot-slopes.R:1:1', 'test-plot.R:1:1',
'test-print.R:1:1', 'test-residualize_over_grid.R:1:1',
'test-scoping_issues.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-attributes_estimatefun.R:108:3'): attributes_means, slopes ─────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-attributes_estimatefun.R:108:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, "Sepal.Width", backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:10:3'): estimate_slopes ──────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(estimate_slopes(model, backend = "marginaleffects")) at test-estimate_slopes.R:10:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:63:3'): estimate_slopes, johnson-neyman p-adjust ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, "Petal.Width", by = "Petal.Length") at test-estimate_slopes.R:63:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:124:3'): estimate_slopes, custom comparison ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─modelbased::estimate_contrasts(...) at test-estimate_slopes.R:124:3
2. └─modelbased:::estimate_contrasts.default(...)
3. └─modelbased::get_marginalcontrasts(...)
4. └─modelbased::estimate_slopes(...)
5. └─modelbased::get_marginaltrends(...)
6. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
7. │ └─base::withCallingHandlers(...)
8. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
9. ├─marginaleffects (local) `<fn>`(...)
10. │ └─base::eval.parent(call_attr)
11. │ └─base::eval(expr, p)
12. │ └─base::eval(expr, p)
13. ├─marginaleffects::slopes(...)
14. │ └─base::eval.parent(call_attr_c)
15. │ └─base::eval(expr, p)
16. │ └─base::eval(expr, p)
17. └─marginaleffects::comparisons(...)
18. ├─base::do.call("get_comparisons", args)
19. └─marginaleffects:::get_comparisons(...)
20. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
21. └─data.table:::`[.data.table`(...)
── Error ('test-transform_response.R:65:3'): estimate_slopes, transform ────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(mod, trend = "Sepal.Width", by = "Species") at test-transform_response.R:65:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-visualisation_recipe.R:151:3'): visualization_recipe ───────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 15/15 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, trend = "Sepal.Width") at test-visualisation_recipe.R:151:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.13.1
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 (all(insight::check_if_installed(c("marginaleffects", "emmeans", "effectsize", "mgcv", "ggplot2", "see"), quietly = TRUE))) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ library(ggplot2)
+ # 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", by = "Species")
+ slopes
+
+ # What is the *average* slope of Petal.Length? This can be calculated by
+ # taking the average of the slopes across all Species, using `comparison`.
+ # We pass a function to `comparison` that calculates the mean of the slopes.
+ estimate_slopes(
+ model,
+ trend = "Petal.Length",
+ by = "Species",
+ comparison = ~I(mean(x))
+ )
+
+ ## Not run:
+ ##D # Plot it
+ ##D plot(slopes)
+ ##D standardize(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+ ##D slopes <- estimate_slopes(model, by = "Petal.Length", length = 50)
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+ ##D slopes <- estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 20
+ ##D )
+ ##D summary(slopes)
+ ##D plot(slopes)
+ ##D
+ ##D # marginal effects, grouped by Species, at different values of Petal.Length
+ ##D estimate_slopes(model,
+ ##D trend = "Petal.Length",
+ ##D by = c("Petal.Length", "Species"), length = 10
+ ##D )
+ ##D
+ ##D # marginal effects at different values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length", length = 10)
+ ##D
+ ##D # marginal effects at very specific values of Petal.Length
+ ##D estimate_slopes(model, trend = "Petal.Length", by = "Petal.Length=c(1, 3, 5)")
+ ##D
+ ##D # average marginal effects of Petal.Length,
+ ##D # just for the trend within a certain range
+ ##D estimate_slopes(model, trend = "Petal.Length=seq(2, 4, 0.01)")
+ ## End(Not run)
+ ## Don't show:
+ }) # examplesIf
> library(ggplot2)
> 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", by = "Species")
Error in `[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp) :
attempt access index 10/10 in VECTOR_ELT
Calls: withAutoprint ... eval -> eval -> estimate_slopes -> get_marginaltrends
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.13.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [105s/181s]
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.
Saving _problems/test-attributes_estimatefun-108.R
Saving _problems/test-estimate_slopes-10.R
Saving _problems/test-estimate_slopes-63.R
Saving _problems/test-estimate_slopes-124.R
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
> test-multivariate_response.R: Confidence intervals are not yet supported for models of class `mlm`.
Saving _problems/test-transform_response-65.R
Saving _problems/test-visualisation_recipe-151.R
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
══ Skipped tests (54) ══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is not TRUE (1):
'test-estimate_predicted.R:58:3'
• On CRAN (45): 'test-backtransform_invlink.R:1:1', 'test-betareg.R:1:1',
'test-bias_correction.R:1:1', 'test-brms-marginaleffects.R:1:1',
'test-brms.R:1:1', 'test-equivalence.R:1:1',
'test-estimate_contrasts-average.R:1:1', 'test-estimate_contrasts.R:1:1',
'test-estimate_contrasts_bookexamples.R:1:1',
'test-estimate_contrasts_counterfactual.R:1:1',
'test-estimate_contrasts_effectsize.R:1:1',
'test-estimate_contrasts_inequality.R:1:1',
'test-estimate_contrasts_methods.R:1:1', 'test-estimate_filter.R:1:1',
'test-estimate_means-average.R:1:1', 'test-estimate_means.R:1:1',
'test-estimate_means_ci.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',
'test-estimate_grouplevel.R:54:3', 'test-estimate_grouplevel.R:72:3',
'test-estimate_grouplevel.R:93:3', 'test-estimate_grouplevel.R:123:3',
'test-estimate_grouplevel.R:150:5', 'test-estimate_grouplevel.R:182:3',
'test-estimate_grouplevel.R:261:3', 'test-estimate_grouplevel.R:308:3',
'test-estimate_means_dotargs.R:1:1', 'test-estimate_means_mixed.R:1:1',
'test-estimate_means_marginalization.R:1:1', 'test-estimate_slopes.R:129:1',
'test-g_computation.R:1:1', 'test-get_marginaltrends.R:1:1',
'test-glmmTMB.R:1:1', 'test-joint_test.R:1:1', 'test-keep_iterations.R:1:1',
'test-maihda.R:1:1', 'test-mice.R:1:1', 'test-ordinal.R:1:1',
'test-plot-grouplevel.R:1:1', 'test-predict-dpar.R:1:1',
'test-standardize.R:1:1', 'test-summary_estimate_slopes.R:3:1',
'test-transform_response.R:3:1', 'test-vcov.R:1:1', 'test-zeroinfl.R:1:1'
• On Linux (8): 'test-plot-facet.R:1:1', 'test-plot-flexible_numeric.R:1:1',
'test-plot-ordinal.R:1:1', 'test-plot-slopes.R:1:1', 'test-plot.R:1:1',
'test-print.R:1:1', 'test-residualize_over_grid.R:1:1',
'test-scoping_issues.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-attributes_estimatefun.R:108:3'): attributes_means, slopes ─────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-attributes_estimatefun.R:108:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, "Sepal.Width", backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:10:3'): estimate_slopes ──────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(estimate_slopes(model, backend = "marginaleffects")) at test-estimate_slopes.R:10:3
2. │ └─base::withCallingHandlers(...)
3. └─modelbased::estimate_slopes(model, backend = "marginaleffects")
4. └─modelbased::get_marginaltrends(...)
5. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
6. │ └─base::withCallingHandlers(...)
7. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
8. ├─marginaleffects (local) `<fn>`(...)
9. │ └─base::eval.parent(call_attr)
10. │ └─base::eval(expr, p)
11. │ └─base::eval(expr, p)
12. ├─marginaleffects::slopes(...)
13. │ └─base::eval.parent(call_attr_c)
14. │ └─base::eval(expr, p)
15. │ └─base::eval(expr, p)
16. └─marginaleffects::comparisons(...)
17. ├─base::do.call("get_comparisons", args)
18. └─marginaleffects:::get_comparisons(...)
19. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
20. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:63:3'): estimate_slopes, johnson-neyman p-adjust ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, "Petal.Width", by = "Petal.Length") at test-estimate_slopes.R:63:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-estimate_slopes.R:124:3'): estimate_slopes, custom comparison ──
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─modelbased::estimate_contrasts(...) at test-estimate_slopes.R:124:3
2. └─modelbased:::estimate_contrasts.default(...)
3. └─modelbased::get_marginalcontrasts(...)
4. └─modelbased::estimate_slopes(...)
5. └─modelbased::get_marginaltrends(...)
6. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
7. │ └─base::withCallingHandlers(...)
8. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
9. ├─marginaleffects (local) `<fn>`(...)
10. │ └─base::eval.parent(call_attr)
11. │ └─base::eval(expr, p)
12. │ └─base::eval(expr, p)
13. ├─marginaleffects::slopes(...)
14. │ └─base::eval.parent(call_attr_c)
15. │ └─base::eval(expr, p)
16. │ └─base::eval(expr, p)
17. └─marginaleffects::comparisons(...)
18. ├─base::do.call("get_comparisons", args)
19. └─marginaleffects:::get_comparisons(...)
20. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
21. └─data.table:::`[.data.table`(...)
── Error ('test-transform_response.R:65:3'): estimate_slopes, transform ────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(mod, trend = "Sepal.Width", by = "Species") at test-transform_response.R:65:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
── Error ('test-visualisation_recipe.R:151:3'): visualization_recipe ───────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 15/15 in VECTOR_ELT
Backtrace:
▆
1. └─modelbased::estimate_slopes(model, trend = "Sepal.Width") at test-visualisation_recipe.R:151:3
2. └─modelbased::get_marginaltrends(...)
3. ├─base::suppressWarnings(do.call(marginaleffects::avg_slopes, fun_args))
4. │ └─base::withCallingHandlers(...)
5. ├─base::do.call(marginaleffects::avg_slopes, fun_args)
6. ├─marginaleffects (local) `<fn>`(...)
7. │ └─base::eval.parent(call_attr)
8. │ └─base::eval(expr, p)
9. │ └─base::eval(expr, p)
10. ├─marginaleffects::slopes(...)
11. │ └─base::eval.parent(call_attr_c)
12. │ └─base::eval(expr, p)
13. │ └─base::eval(expr, p)
14. └─marginaleffects::comparisons(...)
15. ├─base::do.call("get_comparisons", args)
16. └─marginaleffects:::get_comparisons(...)
17. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
18. └─data.table:::`[.data.table`(...)
[ FAIL 6 | WARN 0 | SKIP 54 | PASS 194 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 0.28.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [158s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(parameters)
> library(testthat)
>
> test_check("parameters")
Starting 2 test processes.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: treatment, gender
Saving _problems/test-marginaleffects-11.R
Saving _problems/test-marginaleffects-94.R
Saving _problems/test-marginaleffects-130.R
Saving _problems/test-marginaleffects-153.R
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 11 (84.62%) methods out of 13 (Bartlett, Anderson, Lawley, Optimal coordinates, Acceleration factor, Parallel analysis, Kaiser criterion, Scree (SE), Scree (R2), VSS complexity 1, Velicer's MAP)."
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 3 (60.00%) methods out of 5 (Velicer's MAP, BIC, BIC (adjusted))."
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
══ Skipped tests (129) ═════════════════════════════════════════════════════════
• On CRAN (120): 'test-GLMMadaptive.R:1:1', 'test-Hmisc.R:1:1',
'test-averaging.R:1:1', 'test-backticks.R:1:1',
'test-bootstrap_emmeans.R:1:1', 'test-bootstrap_parameters.R:1:1',
'test-brms.R:1:1', 'test-compare_parameters.R:90:5',
'test-compare_parameters.R:95:5', 'test-complete_separation.R:4:1',
'test-complete_separation.R:18:1', 'test-complete_separation.R:28:1',
'test-coxph.R:69:1', 'test-efa.R:1:1', 'test-emmGrid-df_colname.R:1:1',
'test-equivalence_test.R:3:1', 'test-equivalence_test.R:13:1',
'test-equivalence_test.R:22:3', 'test-equivalence_test.R:112:3',
'test-factor_analysis.R:2:3', 'test-factor_analysis.R:124:3',
'test-format_model_parameters2.R:2:3', 'test-gam.R:30:1',
'test-get_scores.R:1:1', 'test-glmer.R:1:1', 'test-glmmTMB-2.R:1:1',
'test-glmmTMB-profile_CI.R:2:3', 'test-glmmTMB.R:1:1',
'test-group_level_total.R:2:1', 'test-helper.R:1:1', 'test-ivreg.R:45:1',
'test-lcmm.R:1:1', 'test-lmerTest.R:1:1', 'test-include_reference.R:4:1',
'test-include_reference.R:62:1', 'test-include_reference.R:110:1',
'test-mipo.R:5:1', 'test-mipo.R:23:1', 'test-mmrm.R:1:1',
'test-model_parameters.anova.R:1:1', 'test-model_parameters.aov.R:1:1',
'test-model_parameters.aov_es_ci.R:183:3',
'test-model_parameters.aov_es_ci.R:294:3',
'test-model_parameters.aov_es_ci.R:344:3',
'test-model_parameters.aov_es_ci.R:397:3', 'test-marginaleffects.R:170:1',
'test-marginaleffects.R:199:3', 'test-model_parameters.bracl.R:1:1',
'test-model_parameters.cgam.R:1:1', 'test-model_parameters.coxme.R:1:1',
'test-model_parameters.epi2x2.R:1:1', 'test-model_parameters.efa_cfa.R:30:3',
'test-model_parameters.fixest_multi.R:1:1',
'test-model_parameters.fixest.R:2:3', 'test-model_parameters.fixest.R:77:3',
'test-model_parameters.fixest.R:145:1', 'test-model_parameters.glmgee.R:1:1',
'test-model_parameters.logistf.R:1:1', 'test-model_parameters.logitr.R:1:1',
'test-model_parameters.mclogit.R:1:1', 'test-model_parameters.mediate.R:1:1',
'test-model_parameters.glm.R:35:1', 'test-model_parameters.glm.R:67:1',
'test-model_parameters.mixed.R:2:1', 'test-model_parameters.nnet.R:5:1',
'test-model_parameters.vgam.R:3:1', 'test-model_parameters_df.R:1:1',
'test-model_parameters_ordinal.R:1:1',
'test-model_parameters_random_pars.R:1:1', 'test-model_parameters_std.R:1:1',
'test-model_parameters_std_mixed.R:1:1', 'test-n_factors.R:10:3',
'test-n_factors.R:26:3', 'test-n_factors.R:76:3', 'test-p_adjust.R:1:1',
'test-p_direction.R:1:1', 'test-p_significance.R:1:1', 'test-p_value.R:14:1',
'test-panelr.R:1:1', 'test-pipe.R:1:1', 'test-pca.R:64:1', 'test-polr.R:1:1',
'test-plm.R:97:1', 'test-posterior.R:1:1', 'test-pool_parameters.R:1:1',
'test-pool_parameters.R:32:1', 'test-print_AER_labels.R:5:1',
'test-printing-stan.R:1:1', 'test-printing.R:1:1',
'test-pretty_names.R:40:1', 'test-pretty_names.R:73:5',
'test-quantreg.R:1:1', 'test-printing2.R:14:5', 'test-printing2.R:21:5',
'test-printing2.R:26:5', 'test-printing2.R:31:5', 'test-printing2.R:36:5',
'test-printing2.R:48:5', 'test-printing2.R:91:7', 'test-printing2.R:126:5',
'test-random_effects_ci-glmmTMB.R:3:1', 'test-random_effects_ci.R:1:1',
'test-robust.R:1:1', 'test-rstanarm.R:2:1', 'test-sampleSelection.R:2:1',
'test-serp.R:5:1', 'test-svylme.R:1:1', 'test-svyolr.R:1:1',
'test-visualisation_recipe.R:1:1', 'test-weightit.R:6:1',
'test-weightit.R:26:1', 'test-wrs2.R:55:1',
'test-standardize_parameters.R:28:1', 'test-standardize_parameters.R:36:3',
'test-standardize_parameters.R:61:3', 'test-standardize_parameters.R:173:3',
'test-standardize_parameters.R:297:3', 'test-standardize_parameters.R:332:3',
'test-standardize_parameters.R:425:3', 'test-standardize_parameters.R:515:3'
• On Linux (4): 'test-model_parameters.BFBayesFactor.R:1:1',
'test-nestedLogit.R:78:3', 'test-simulate_model.R:1:1',
'test-simulate_parameters.R:1:1'
• TODO: check this test locally, fails on CI, probably due to scoping issues?
(1): 'test-marginaleffects.R:280:3'
• TODO: fix this test (1): 'test-model_parameters.lqmm.R:40:3'
• TODO: this one actually is not correct. (1):
'test-model_parameters_robust.R:127:3'
• empty test (2): 'test-wrs2.R:69:1', 'test-wrs2.R:81:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-marginaleffects.R:7:3'): marginaleffects() ─────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:90:3'): comparisons() ────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:127:3'): slopes() ────────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:148:3'): multiple contrasts: Issue #779 ──────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-marginaleffects.R:148:3
2. │ └─base::withCallingHandlers(...)
3. └─marginaleffects::comparisons(...)
4. ├─base::do.call("get_comparisons", args)
5. └─marginaleffects:::get_comparisons(...)
6. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
7. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.28.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [98s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(parameters)
> library(testthat)
>
> test_check("parameters")
Starting 2 test processes.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confiden
> test-include_reference.R: ce intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: treatment, gender
Saving _problems/test-marginaleffects-11.R
Saving _problems/test-marginaleffects-94.R
Saving _problems/test-marginaleffects-130.R
Saving _problems/test-marginaleffects-153.R
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 11 (84.62%) methods out of 13 (Bartlett, Anderson, Lawley, Optimal coordinates, Acceleration factor, Parallel analysis, Kaiser criterion, Scree (SE), Scree (R2), VSS complexity 1, Velicer's MAP)."
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 3 (60.00%) methods out of 5 (Velicer's MAP, BIC, BIC (adjusted))."
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
══ Skipped tests (129) ═════════════════════════════════════════════════════════
• On CRAN (120): 'test-Hmisc.R:1:1', 'test-GLMMadaptive.R:1:1',
'test-averaging.R:1:1', 'test-backticks.R:1:1',
'test-bootstrap_emmeans.R:1:1', 'test-bootstrap_parameters.R:1:1',
'test-brms.R:1:1', 'test-compare_parameters.R:90:5',
'test-compare_parameters.R:95:5', 'test-complete_separation.R:4:1',
'test-complete_separation.R:18:1', 'test-complete_separation.R:28:1',
'test-coxph.R:69:1', 'test-efa.R:1:1', 'test-emmGrid-df_colname.R:1:1',
'test-equivalence_test.R:3:1', 'test-equivalence_test.R:13:1',
'test-equivalence_test.R:22:3', 'test-equivalence_test.R:112:3',
'test-factor_analysis.R:2:3', 'test-factor_analysis.R:124:3',
'test-format_model_parameters2.R:2:3', 'test-gam.R:30:1',
'test-get_scores.R:1:1', 'test-glmer.R:1:1', 'test-glmmTMB-2.R:1:1',
'test-glmmTMB-profile_CI.R:2:3', 'test-glmmTMB.R:1:1',
'test-group_level_total.R:2:1', 'test-helper.R:1:1', 'test-ivreg.R:45:1',
'test-lcmm.R:1:1', 'test-lmerTest.R:1:1', 'test-include_reference.R:4:1',
'test-include_reference.R:62:1', 'test-include_reference.R:110:1',
'test-mipo.R:5:1', 'test-mipo.R:23:1', 'test-mmrm.R:1:1',
'test-model_parameters.anova.R:1:1', 'test-model_parameters.aov.R:1:1',
'test-marginaleffects.R:170:1', 'test-marginaleffects.R:199:3',
'test-model_parameters.aov_es_ci.R:183:3',
'test-model_parameters.aov_es_ci.R:294:3',
'test-model_parameters.aov_es_ci.R:344:3',
'test-model_parameters.aov_es_ci.R:397:3',
'test-model_parameters.bracl.R:1:1', 'test-model_parameters.cgam.R:1:1',
'test-model_parameters.coxme.R:1:1', 'test-model_parameters.epi2x2.R:1:1',
'test-model_parameters.efa_cfa.R:30:3',
'test-model_parameters.fixest_multi.R:1:1',
'test-model_parameters.fixest.R:2:3', 'test-model_parameters.fixest.R:77:3',
'test-model_parameters.fixest.R:145:1', 'test-model_parameters.glmgee.R:1:1',
'test-model_parameters.logistf.R:1:1', 'test-model_parameters.logitr.R:1:1',
'test-model_parameters.mclogit.R:1:1', 'test-model_parameters.mediate.R:1:1',
'test-model_parameters.glm.R:35:1', 'test-model_parameters.glm.R:67:1',
'test-model_parameters.mixed.R:2:1', 'test-model_parameters.nnet.R:5:1',
'test-model_parameters_df.R:1:1', 'test-model_parameters.vgam.R:3:1',
'test-model_parameters_ordinal.R:1:1',
'test-model_parameters_random_pars.R:1:1', 'test-model_parameters_std.R:1:1',
'test-model_parameters_std_mixed.R:1:1', 'test-n_factors.R:10:3',
'test-n_factors.R:26:3', 'test-n_factors.R:76:3', 'test-p_adjust.R:1:1',
'test-p_direction.R:1:1', 'test-p_significance.R:1:1', 'test-p_value.R:14:1',
'test-panelr.R:1:1', 'test-pipe.R:1:1', 'test-pca.R:64:1', 'test-polr.R:1:1',
'test-plm.R:97:1', 'test-posterior.R:1:1', 'test-pool_parameters.R:1:1',
'test-pool_parameters.R:32:1', 'test-print_AER_labels.R:5:1',
'test-printing-stan.R:1:1', 'test-printing.R:1:1',
'test-pretty_names.R:40:1', 'test-pretty_names.R:73:5',
'test-quantreg.R:1:1', 'test-random_effects_ci-glmmTMB.R:3:1',
'test-random_effects_ci.R:1:1', 'test-robust.R:1:1', 'test-rstanarm.R:2:1',
'test-sampleSelection.R:2:1', 'test-serp.R:5:1', 'test-printing2.R:14:5',
'test-printing2.R:21:5', 'test-printing2.R:26:5', 'test-printing2.R:31:5',
'test-printing2.R:36:5', 'test-printing2.R:48:5', 'test-printing2.R:91:7',
'test-printing2.R:126:5', 'test-svylme.R:1:1', 'test-svyolr.R:1:1',
'test-visualisation_recipe.R:1:1', 'test-weightit.R:6:1',
'test-weightit.R:26:1', 'test-wrs2.R:55:1',
'test-standardize_parameters.R:28:1', 'test-standardize_parameters.R:36:3',
'test-standardize_parameters.R:61:3', 'test-standardize_parameters.R:173:3',
'test-standardize_parameters.R:297:3', 'test-standardize_parameters.R:332:3',
'test-standardize_parameters.R:425:3', 'test-standardize_parameters.R:515:3'
• On Linux (4): 'test-model_parameters.BFBayesFactor.R:1:1',
'test-nestedLogit.R:78:3', 'test-simulate_model.R:1:1',
'test-simulate_parameters.R:1:1'
• TODO: check this test locally, fails on CI, probably due to scoping issues?
(1): 'test-marginaleffects.R:280:3'
• TODO: fix this test (1): 'test-model_parameters.lqmm.R:40:3'
• TODO: this one actually is not correct. (1):
'test-model_parameters_robust.R:127:3'
• empty test (2): 'test-wrs2.R:69:1', 'test-wrs2.R:81:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-marginaleffects.R:7:3'): marginaleffects() ─────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:90:3'): comparisons() ────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:127:3'): slopes() ────────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:148:3'): multiple contrasts: Issue #779 ──────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-marginaleffects.R:148:3
2. │ └─base::withCallingHandlers(...)
3. └─marginaleffects::comparisons(...)
4. ├─base::do.call("get_comparisons", args)
5. └─marginaleffects:::get_comparisons(...)
6. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
7. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.28.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [246s/206s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(parameters)
> library(testthat)
>
> test_check("parameters")
Starting 2 test processes.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: treatment, gender
Saving _problems/test-marginaleffects-11.R
Saving _problems/test-marginaleffects-94.R
Saving _problems/test-marginaleffects-130.R
Saving _problems/test-marginaleffects-153.R
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 11 (84.62%) methods out of 13 (Bartlett, Anderson, Lawley, Optimal coordinates, Acceleration factor, Parallel analysis, Kaiser criterion, Scree (SE), Scree (R2), VSS complexity 1, Velicer's MAP)."
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 3 (60.00%) methods out of 5 (Velicer's MAP, BIC, BIC (adjusted))."
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
══ Skipped tests (129) ═════════════════════════════════════════════════════════
• On CRAN (120): 'test-GLMMadaptive.R:1:1', 'test-Hmisc.R:1:1',
'test-averaging.R:1:1', 'test-backticks.R:1:1',
'test-bootstrap_emmeans.R:1:1', 'test-bootstrap_parameters.R:1:1',
'test-brms.R:1:1', 'test-compare_parameters.R:90:5',
'test-compare_parameters.R:95:5', 'test-complete_separation.R:4:1',
'test-complete_separation.R:18:1', 'test-complete_separation.R:28:1',
'test-coxph.R:69:1', 'test-efa.R:1:1', 'test-emmGrid-df_colname.R:1:1',
'test-equivalence_test.R:3:1', 'test-equivalence_test.R:13:1',
'test-equivalence_test.R:22:3', 'test-equivalence_test.R:112:3',
'test-factor_analysis.R:2:3', 'test-factor_analysis.R:124:3',
'test-format_model_parameters2.R:2:3', 'test-gam.R:30:1',
'test-get_scores.R:1:1', 'test-glmer.R:1:1', 'test-glmmTMB-2.R:1:1',
'test-glmmTMB-profile_CI.R:2:3', 'test-glmmTMB.R:1:1', 'test-helper.R:1:1',
'test-group_level_total.R:2:1', 'test-ivreg.R:45:1', 'test-lcmm.R:1:1',
'test-lmerTest.R:1:1', 'test-include_reference.R:4:1',
'test-include_reference.R:62:1', 'test-include_reference.R:110:1',
'test-mipo.R:5:1', 'test-mipo.R:23:1', 'test-mmrm.R:1:1',
'test-model_parameters.anova.R:1:1', 'test-model_parameters.aov.R:1:1',
'test-model_parameters.aov_es_ci.R:183:3',
'test-model_parameters.aov_es_ci.R:294:3',
'test-model_parameters.aov_es_ci.R:344:3',
'test-model_parameters.aov_es_ci.R:397:3', 'test-marginaleffects.R:170:1',
'test-marginaleffects.R:199:3', 'test-model_parameters.bracl.R:1:1',
'test-model_parameters.cgam.R:1:1', 'test-model_parameters.coxme.R:1:1',
'test-model_parameters.epi2x2.R:1:1', 'test-model_parameters.efa_cfa.R:30:3',
'test-model_parameters.fixest_multi.R:1:1',
'test-model_parameters.fixest.R:2:3', 'test-model_parameters.fixest.R:77:3',
'test-model_parameters.fixest.R:145:1', 'test-model_parameters.glmgee.R:1:1',
'test-model_parameters.logistf.R:1:1', 'test-model_parameters.logitr.R:1:1',
'test-model_parameters.mclogit.R:1:1', 'test-model_parameters.mediate.R:1:1',
'test-model_parameters.glm.R:35:1', 'test-model_parameters.glm.R:67:1',
'test-model_parameters.mixed.R:2:1', 'test-model_parameters.nnet.R:5:1',
'test-model_parameters.vgam.R:3:1', 'test-model_parameters_df.R:1:1',
'test-model_parameters_ordinal.R:1:1',
'test-model_parameters_random_pars.R:1:1', 'test-model_parameters_std.R:1:1',
'test-model_parameters_std_mixed.R:1:1', 'test-n_factors.R:10:3',
'test-n_factors.R:26:3', 'test-n_factors.R:76:3', 'test-p_adjust.R:1:1',
'test-p_direction.R:1:1', 'test-p_significance.R:1:1', 'test-p_value.R:14:1',
'test-panelr.R:1:1', 'test-pipe.R:1:1', 'test-pca.R:64:1', 'test-polr.R:1:1',
'test-plm.R:97:1', 'test-posterior.R:1:1', 'test-pool_parameters.R:1:1',
'test-pool_parameters.R:32:1', 'test-print_AER_labels.R:5:1',
'test-printing-stan.R:1:1', 'test-printing.R:1:1', 'test-printing2.R:14:5',
'test-printing2.R:21:5', 'test-printing2.R:26:5', 'test-printing2.R:31:5',
'test-printing2.R:36:5', 'test-printing2.R:48:5', 'test-printing2.R:91:7',
'test-printing2.R:126:5', 'test-quantreg.R:1:1',
'test-random_effects_ci-glmmTMB.R:3:1', 'test-random_effects_ci.R:1:1',
'test-robust.R:1:1', 'test-rstanarm.R:2:1', 'test-sampleSelection.R:2:1',
'test-serp.R:5:1', 'test-pretty_names.R:40:1', 'test-pretty_names.R:73:5',
'test-svylme.R:1:1', 'test-svyolr.R:1:1', 'test-visualisation_recipe.R:1:1',
'test-weightit.R:6:1', 'test-weightit.R:26:1', 'test-wrs2.R:55:1',
'test-standardize_parameters.R:28:1', 'test-standardize_parameters.R:36:3',
'test-standardize_parameters.R:61:3', 'test-standardize_parameters.R:173:3',
'test-standardize_parameters.R:297:3', 'test-standardize_parameters.R:332:3',
'test-standardize_parameters.R:425:3', 'test-standardize_parameters.R:515:3'
• On Linux (4): 'test-model_parameters.BFBayesFactor.R:1:1',
'test-nestedLogit.R:78:3', 'test-simulate_model.R:1:1',
'test-simulate_parameters.R:1:1'
• TODO: check this test locally, fails on CI, probably due to scoping issues?
(1): 'test-marginaleffects.R:280:3'
• TODO: fix this test (1): 'test-model_parameters.lqmm.R:40:3'
• TODO: this one actually is not correct. (1):
'test-model_parameters_robust.R:127:3'
• empty test (2): 'test-wrs2.R:69:1', 'test-wrs2.R:81:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-marginaleffects.R:7:3'): marginaleffects() ─────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:90:3'): comparisons() ────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:127:3'): slopes() ────────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:148:3'): multiple contrasts: Issue #779 ──────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-marginaleffects.R:148:3
2. │ └─base::withCallingHandlers(...)
3. └─marginaleffects::comparisons(...)
4. ├─base::do.call("get_comparisons", args)
5. └─marginaleffects:::get_comparisons(...)
6. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
7. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.28.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [137s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(parameters)
> library(testthat)
>
> test_check("parameters")
Starting 2 test processes.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-include_reference.R: Your model may suffer from singularity (see `?lme4::isSingular` and
> test-include_reference.R: `?performance::check_singularity`).
> test-include_reference.R: Some of the confidence intervals of the random effects parameters are
> test-include_reference.R: probably not meaningful!
> test-include_reference.R: You may try to impose a prior on the random effects parameters, e.g.
> test-include_reference.R: using the glmmTMB package.
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: condition, talk
> test-model_parameters.afex_aov.R: Contrasts set to contr.sum for the following variables: treatment, gender
Saving _problems/test-marginaleffects-11.R
Saving _problems/test-marginaleffects-94.R
Saving _problems/test-marginaleffects-130.R
Saving _problems/test-marginaleffects-153.R
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 11 (84.62%) methods out of 13 (Bartlett, Anderson, Lawley, Optimal coordinates, Acceleration factor, Parallel analysis, Kaiser criterion, Scree (SE), Scree (R2), VSS complexity 1, Velicer's MAP)."
> test-n_factors.R: [1] "# Method Agreement Procedure:"
> test-n_factors.R: [2] ""
> test-n_factors.R: [3] "The choice of 1 dimensions is supported by 3 (60.00%) methods out of 5 (Velicer's MAP, BIC, BIC (adjusted))."
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
══ Skipped tests (129) ═════════════════════════════════════════════════════════
• On CRAN (120): 'test-GLMMadaptive.R:1:1', 'test-Hmisc.R:1:1',
'test-averaging.R:1:1', 'test-backticks.R:1:1',
'test-bootstrap_emmeans.R:1:1', 'test-bootstrap_parameters.R:1:1',
'test-brms.R:1:1', 'test-compare_parameters.R:90:5',
'test-compare_parameters.R:95:5', 'test-complete_separation.R:4:1',
'test-complete_separation.R:18:1', 'test-complete_separation.R:28:1',
'test-coxph.R:69:1', 'test-efa.R:1:1', 'test-emmGrid-df_colname.R:1:1',
'test-equivalence_test.R:3:1', 'test-equivalence_test.R:13:1',
'test-equivalence_test.R:22:3', 'test-equivalence_test.R:112:3',
'test-factor_analysis.R:2:3', 'test-factor_analysis.R:124:3',
'test-format_model_parameters2.R:2:3', 'test-gam.R:30:1',
'test-get_scores.R:1:1', 'test-glmer.R:1:1', 'test-glmmTMB-2.R:1:1',
'test-glmmTMB-profile_CI.R:2:3', 'test-glmmTMB.R:1:1',
'test-group_level_total.R:2:1', 'test-helper.R:1:1', 'test-ivreg.R:45:1',
'test-lcmm.R:1:1', 'test-lmerTest.R:1:1', 'test-include_reference.R:4:1',
'test-include_reference.R:62:1', 'test-include_reference.R:110:1',
'test-mipo.R:5:1', 'test-mipo.R:23:1', 'test-mmrm.R:1:1',
'test-model_parameters.anova.R:1:1', 'test-model_parameters.aov.R:1:1',
'test-marginaleffects.R:170:1', 'test-marginaleffects.R:199:3',
'test-model_parameters.bracl.R:1:1', 'test-model_parameters.cgam.R:1:1',
'test-model_parameters.aov_es_ci.R:183:3',
'test-model_parameters.aov_es_ci.R:294:3',
'test-model_parameters.aov_es_ci.R:344:3',
'test-model_parameters.aov_es_ci.R:397:3',
'test-model_parameters.coxme.R:1:1', 'test-model_parameters.epi2x2.R:1:1',
'test-model_parameters.efa_cfa.R:30:3',
'test-model_parameters.fixest_multi.R:1:1',
'test-model_parameters.fixest.R:2:3', 'test-model_parameters.fixest.R:77:3',
'test-model_parameters.fixest.R:145:1', 'test-model_parameters.glmgee.R:1:1',
'test-model_parameters.logistf.R:1:1', 'test-model_parameters.logitr.R:1:1',
'test-model_parameters.mclogit.R:1:1', 'test-model_parameters.mediate.R:1:1',
'test-model_parameters.glm.R:35:1', 'test-model_parameters.glm.R:67:1',
'test-model_parameters.mixed.R:2:1', 'test-model_parameters.nnet.R:5:1',
'test-model_parameters_df.R:1:1', 'test-model_parameters.vgam.R:3:1',
'test-model_parameters_ordinal.R:1:1',
'test-model_parameters_random_pars.R:1:1', 'test-model_parameters_std.R:1:1',
'test-model_parameters_std_mixed.R:1:1', 'test-n_factors.R:10:3',
'test-n_factors.R:26:3', 'test-n_factors.R:76:3', 'test-p_adjust.R:1:1',
'test-p_direction.R:1:1', 'test-p_significance.R:1:1', 'test-p_value.R:14:1',
'test-panelr.R:1:1', 'test-pipe.R:1:1', 'test-pca.R:64:1', 'test-polr.R:1:1',
'test-plm.R:97:1', 'test-posterior.R:1:1', 'test-pool_parameters.R:1:1',
'test-pool_parameters.R:32:1', 'test-print_AER_labels.R:5:1',
'test-printing-stan.R:1:1', 'test-printing.R:1:1', 'test-printing2.R:14:5',
'test-printing2.R:21:5', 'test-printing2.R:26:5', 'test-printing2.R:31:5',
'test-printing2.R:36:5', 'test-printing2.R:48:5', 'test-printing2.R:91:7',
'test-printing2.R:126:5', 'test-quantreg.R:1:1',
'test-random_effects_ci-glmmTMB.R:3:1', 'test-random_effects_ci.R:1:1',
'test-robust.R:1:1', 'test-rstanarm.R:2:1', 'test-sampleSelection.R:2:1',
'test-serp.R:5:1', 'test-pretty_names.R:40:1', 'test-pretty_names.R:73:5',
'test-svylme.R:1:1', 'test-svyolr.R:1:1', 'test-visualisation_recipe.R:1:1',
'test-weightit.R:6:1', 'test-weightit.R:26:1', 'test-wrs2.R:55:1',
'test-standardize_parameters.R:28:1', 'test-standardize_parameters.R:36:3',
'test-standardize_parameters.R:61:3', 'test-standardize_parameters.R:173:3',
'test-standardize_parameters.R:297:3', 'test-standardize_parameters.R:332:3',
'test-standardize_parameters.R:425:3', 'test-standardize_parameters.R:515:3'
• On Linux (4): 'test-model_parameters.BFBayesFactor.R:1:1',
'test-nestedLogit.R:78:3', 'test-simulate_model.R:1:1',
'test-simulate_parameters.R:1:1'
• TODO: check this test locally, fails on CI, probably due to scoping issues?
(1): 'test-marginaleffects.R:280:3'
• TODO: fix this test (1): 'test-model_parameters.lqmm.R:40:3'
• TODO: this one actually is not correct. (1):
'test-model_parameters_robust.R:127:3'
• empty test (2): 'test-wrs2.R:69:1', 'test-wrs2.R:81:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-marginaleffects.R:7:3'): marginaleffects() ─────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:90:3'): comparisons() ────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:127:3'): slopes() ────────────────────────────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─marginaleffects::comparisons(...)
2. ├─base::do.call("get_comparisons", args)
3. └─marginaleffects:::get_comparisons(...)
4. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
5. └─data.table:::`[.data.table`(...)
── Error ('test-marginaleffects.R:148:3'): multiple contrasts: Issue #779 ──────
Error in ``[.data.table`(out, , `:=`(tmp_idx, seq_len(.N)), by = tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-marginaleffects.R:148:3
2. │ └─base::withCallingHandlers(...)
3. └─marginaleffects::comparisons(...)
4. ├─base::do.call("get_comparisons", args)
5. └─marginaleffects:::get_comparisons(...)
6. ├─out[, `:=`(tmp_idx, seq_len(.N)), by = tmp]
7. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 129 | PASS 695 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.28.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘M3C’
Flavor: r-oldrel-macos-arm64
Version: 0.28.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'EGAnet'
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.15.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(performance)
>
> test_check("performance")
Starting 2 test processes.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_itemscale.R: Some of the values are negative. Maybe affected items need to be
> test-check_itemscale.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-check_collinearity.R: NOTE: 2 fixed-effect singletons were removed (2 observations).
Saving _problems/test-check_collinearity-157.R
Saving _problems/test-check_collinearity-185.R
> test-check_overdispersion.R: Overdispersion detected.
> test-check_overdispersion.R: Underdispersion detected.
> test-check_outliers.R: No outliers were detected (p = 0.238).
> test-glmmPQL.R: iteration 1
> test-item_discrimination.R: Some of the values are negative. Maybe affected items need to be
> test-item_discrimination.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-item_discrimination.R: Some of the values are negative. Maybe affected items need to be
> test-item_discrimination.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-item_discrimination.R: Some of the values are negative. Maybe affected items need to be
> test-item_discrimination.R: reverse-coded, e.g. using `datawizard::reverse()`.
> test-performance_aic.R: Model was not fitted with REML, however, `estimator = "REML"`. Set
> test-performance_aic.R: `estimator = "ML"` to obtain identical results as from `AIC()`.
[ FAIL 2 | WARN 2 | SKIP 41 | PASS 443 ]
══ Skipped tests (41) ══════════════════════════════════════════════════════════
• On CRAN (36): 'test-bootstrapped_icc_ci.R:2:3',
'test-bootstrapped_icc_ci.R:44:3', 'test-binned_residuals.R:163:3',
'test-binned_residuals.R:190:3', 'test-check_convergence.R:1:1',
'test-check_dag.R:1:1', 'test-check_distribution.R:1:1',
'test-check_itemscale.R:1:1', 'test-check_itemscale.R:100:1',
'test-check_model.R:1:1', 'test-check_collinearity.R:193:1',
'test-check_collinearity.R:226:1', 'test-check_residuals.R:2:3',
'test-check_singularity.R:2:3', 'test-check_singularity.R:30:3',
'test-check_zeroinflation.R:73:3', 'test-check_zeroinflation.R:112:3',
'test-check_outliers.R:115:3', 'test-check_outliers.R:339:3',
'test-helpers.R:1:1', 'test-compare_performance.R:1:1',
'test-item_omega.R:1:1', 'test-item_omega.R:31:3', 'test-mclogit.R:56:1',
'test-model_performance.bayesian.R:1:1',
'test-model_performance.lavaan.R:1:1', 'test-model_performance.merMod.R:2:3',
'test-model_performance.merMod.R:37:3', 'test-model_performance.psych.R:1:1',
'test-model_performance.rma.R:36:1', 'test-performance_reliability.R:23:3',
'test-pkg-ivreg.R:1:1', 'test-r2_nagelkerke.R:35:3', 'test-r2_bayes.R:39:3',
'test-rmse.R:39:3', 'test-test_likelihoodratio.R:55:1'
• On Mac (4): 'test-check_predictions.R:1:1', 'test-icc.R:1:1',
'test-nestedLogit.R:1:1', 'test-r2_nakagawa.R:1:1'
• getRversion() > "4.4.0" is TRUE (1): 'test-check_outliers.R:300:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-check_collinearity.R:157:3'): check_collinearity | afex ──────
Expected `expect_message(ccoW <- check_collinearity(aW))` to throw a warning.
── Failure ('test-check_collinearity.R:185:3'): check_collinearity | afex ──────
Expected `expect_message(ccoW <- check_collinearity(aW))` to throw a warning.
[ FAIL 2 | WARN 2 | SKIP 41 | PASS 443 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-arm64