CRAN Package Check Results for Package steppedwedge

Last updated on 2026-10-26 23:52:25 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.0	2.40	64.77	67.17	OK
r-devel-linux-x86_64-debian-gcc	1.0.0	1.83	37.76	39.59	ERROR
r-devel-linux-x86_64-fedora-clang	1.0.0			36.06	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.0			38.02	ERROR
r-devel-windows-x86_64	1.0.0	5.00	71.00	76.00	ERROR
r-patched-linux-x86_64	1.0.0	2.55	57.00	59.55	OK
r-release-linux-x86_64	1.0.0	2.16	42.26	44.42	ERROR
r-release-macos-arm64	1.0.0	1.00	22.00	23.00	OK
r-release-macos-x86_64	1.0.0	2.00	79.00	81.00	OK
r-release-windows-x86_64	1.0.0	4.00	81.00	85.00	OK
r-oldrel-macos-arm64	1.0.0				OK
r-oldrel-macos-x86_64	1.0.0	2.00	74.00	76.00	OK
r-oldrel-windows-x86_64	1.0.0	5.00	98.00	103.00	OK

Check Details

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘steppedwedge-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: analyze > ### Title: Analyze a stepped wedge dataset > ### Aliases: analyze > > ### ** Examples > > # Load data > test_data <- load_data(time ="period", cluster_id = "cluster", individual_id = NULL, + treatment = "trt", outcome = "outcome_cont", data = sw_data_example) Stepped wedge dataset loaded. Discrete time design with 15 clusters, 5 sequences, and 6 time points. > > # Analysis example 1: TATE estimand for exposure times 1 through 4 > results_tate <- analyze(dat = test_data, method = "mixed", estimand_type = "TATE", + estimand_time = c(1, 4), exp_time = "ETI") Error in model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, : invalid type (closure) for variable '(offset)' Calls: analyze ... mkFormula -> eval -> eval -> <Anonymous> -> model.frame.default Execution halted Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [3s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(steppedwedge) > > test_check("steppedwedge") Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Saving _problems/test-analyze_data-33.R Saving _problems/test-analyze_data-40.R Saving _problems/test-analyze_data-47.R Saving _problems/test-analyze_data-78.R Saving _problems/test-analyze_data-88.R Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-analyze_data.R:32:3'): Correct model type and estimand_type for IT mixed model ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:32:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:39:3'): Correct model type and estimand_type for ETI mixed model, TATE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:39:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:46:3'): Correct model type and estimand_type for ETI mixed model, PTE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:46:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:77:3'): Model coefficients are returned correctly ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:77:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:87:3'): Function handles different family and link functions ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:87:3 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘steppedwedge.Rmd’ using rmarkdown Quitting from steppedwedge.Rmd:62-73 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `model.frame.default()`: ! invalid type (closure) for variable '(offset)' --- Backtrace: ▆ 1. └─steppedwedge::analyze(...) 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'steppedwedge.Rmd' failed with diagnostics: invalid type (closure) for variable '(offset)' --- failed re-building ‘steppedwedge.Rmd’ SUMMARY: processing the following file failed: ‘steppedwedge.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘steppedwedge-Ex.R’ failed The error most likely occurred in: > ### Name: analyze > ### Title: Analyze a stepped wedge dataset > ### Aliases: analyze > > ### ** Examples > > # Load data > test_data <- load_data(time ="period", cluster_id = "cluster", individual_id = NULL, + treatment = "trt", outcome = "outcome_cont", data = sw_data_example) Stepped wedge dataset loaded. Discrete time design with 15 clusters, 5 sequences, and 6 time points. > > # Analysis example 1: TATE estimand for exposure times 1 through 4 > results_tate <- analyze(dat = test_data, method = "mixed", estimand_type = "TATE", + estimand_time = c(1, 4), exp_time = "ETI") Error in model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, : invalid type (closure) for variable '(offset)' Calls: analyze ... mkFormula -> eval -> eval -> <Anonymous> -> model.frame.default Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(steppedwedge) > > test_check("steppedwedge") Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Saving _problems/test-analyze_data-33.R Saving _problems/test-analyze_data-40.R Saving _problems/test-analyze_data-47.R Saving _problems/test-analyze_data-78.R Saving _problems/test-analyze_data-88.R Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-analyze_data.R:32:3'): Correct model type and estimand_type for IT mixed model ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:32:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:39:3'): Correct model type and estimand_type for ETI mixed model, TATE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:39:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:46:3'): Correct model type and estimand_type for ETI mixed model, PTE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:46:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:77:3'): Model coefficients are returned correctly ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:77:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:87:3'): Function handles different family and link functions ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:87:3 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] Error: ! Test failures. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘steppedwedge.Rmd’ using rmarkdown Quitting from steppedwedge.Rmd:62-73 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `model.frame.default()`: ! invalid type (closure) for variable '(offset)' --- Backtrace: ▆ 1. └─steppedwedge::analyze(...) 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'steppedwedge.Rmd' failed with diagnostics: invalid type (closure) for variable '(offset)' --- failed re-building ‘steppedwedge.Rmd’ SUMMARY: processing the following file failed: ‘steppedwedge.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running 'testthat.R' [5s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(steppedwedge) > > test_check("steppedwedge") Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Saving _problems/test-analyze_data-33.R Saving _problems/test-analyze_data-40.R Saving _problems/test-analyze_data-47.R Saving _problems/test-analyze_data-78.R Saving _problems/test-analyze_data-88.R Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-analyze_data.R:32:3'): Correct model type and estimand_type for IT mixed model ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:32:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:39:3'): Correct model type and estimand_type for ETI mixed model, TATE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:39:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:46:3'): Correct model type and estimand_type for ETI mixed model, PTE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:46:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:77:3'): Model coefficients are returned correctly ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:77:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:87:3'): Function handles different family and link functions ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:87:3 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/9s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(steppedwedge) > > test_check("steppedwedge") Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Saving _problems/test-analyze_data-33.R Saving _problems/test-analyze_data-40.R Saving _problems/test-analyze_data-47.R Saving _problems/test-analyze_data-78.R Saving _problems/test-analyze_data-88.R Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. Stepped wedge dataset loaded. Discrete time design with 2 clusters, 2 sequences, and 3 time points. [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-analyze_data.R:32:3'): Correct model type and estimand_type for IT mixed model ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:32:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:39:3'): Correct model type and estimand_type for ETI mixed model, TATE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:39:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:46:3'): Correct model type and estimand_type for ETI mixed model, PTE ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + factor(exposure_time) + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:46:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:77:3'): Model coefficients are returned correctly ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:77:3 2. ├─lme4::lmer(formula, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::lFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) ── Error ('test-analyze_data.R:87:3'): Function handles different family and link functions ── Error in `model.frame.default(data = dat, offset = offset, drop.unused.levels = TRUE, formula = outcome ~ factor(time) - 1 + treatment + (1 + cluster_id) + (1 + ij))`: invalid type (closure) for variable '(offset)' Backtrace: ▆ 1. └─steppedwedge::analyze(...) at test-analyze_data.R:87:3 2. ├─lme4::glmer(formula, family = family, data = dat, offset = offset) 3. │ └─base::eval(mc, parent.frame(1L)) 4. │ └─base::eval(mc, parent.frame(1L)) 5. ├─lme4::glFormula(...) 6. │ └─lme4:::mkFormula(...) 7. │ └─base::eval(mf, parent_env) 8. │ └─base::eval(mf, parent_env) 9. ├─stats::model.frame(...) 10. └─stats::model.frame.default(...) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 24 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64