CRAN Package Check Results for Package aba

Last updated on 2022-03-27 07:54:25 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.9 9.77 369.68 379.45 ERROR
r-devel-linux-x86_64-debian-gcc 0.0.9 8.02 266.53 274.55 ERROR
r-devel-linux-x86_64-fedora-clang 0.0.9 429.75 ERROR
r-devel-linux-x86_64-fedora-gcc 0.0.9 434.78 ERROR
r-devel-windows-x86_64-new-UL 0.0.9 31.00 443.00 474.00 OK
r-devel-windows-x86_64-new-TK 0.0.9 ERROR
r-patched-linux-x86_64 0.0.9 7.54 342.99 350.53 ERROR
r-release-linux-x86_64 0.0.9 6.09 345.84 351.93 ERROR
r-release-macos-arm64 0.0.9 OK
r-release-macos-x86_64 0.0.9 OK
r-release-windows-ix86+x86_64 0.0.9 31.00 442.00 473.00 OK
r-oldrel-macos-x86_64 0.0.9 OK
r-oldrel-windows-ix86+x86_64 0.0.9 19.00 454.00 473.00 OK

Check Details

Version: 0.0.9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'psychometric'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.0.9
Check: examples
Result: ERROR
    Running examples in 'aba-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: stat_ancova
    > ### Title: Create an ancova stat object.
    > ### Aliases: stat_ancova
    >
    > ### ** Examples
    >
    > # filter to 24 month visit; calculate change in cognition to use as outcome;
    > # assume abeta status as "treatment" variable.
    > # The goal is to see if "treatment" has an effect on 2y cognitive decline
    > data <- adnimerge %>%
    + dplyr::filter(
    + VISCODE == 'm24',
    + DX_bl %in% c('MCI', 'AD'),
    + !is.na(CSF_ABETA_STATUS_bl)
    + ) %>%
    + dplyr::mutate(
    + CDRSB = CDRSB - CDRSB_bl,
    + ADAS13 = ADAS13 - ADAS13_bl,
    + TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
    + labels=c('Placebo','Treatment'))
    + )
    >
    > # fit model. note that baseline outcome will be added based on the suffix.
    > # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
    > ancova_model <- data %>% aba_model() %>%
    + set_outcomes(CDRSB, ADAS13) %>%
    + set_covariates(AGE, GENDER, EDUCATION) %>%
    + set_stats(
    + stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
    + ) %>%
    + fit()
    >
    > # summarise model. treatment effect will be shown in the treatment coefficient
    > ancova_summary <- ancova_model %>% summary()
    Error in `mutate()`:
    ! Problem while computing `metrics = purrr::map2(...)`.
    Caused by error in `loadNamespace()`:
    ! there is no package called 'psychometric'
    Backtrace:
     x
     1. +-ancova_model %>% summary()
     2. +-base::summary(.)
     3. +-aba:::summary.abaModel(.)
     4. | \-object %>% aba_summary(...)
     5. +-aba::aba_summary(., ...)
     6. | \-object %>% calculate_metrics(control)
     7. +-aba:::calculate_metrics(., control)
     8. | \-r %>% ...
     9. +-dplyr::mutate(...)
     10. +-dplyr:::mutate.data.frame(...)
     11. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     12. | +-base::withCallingHandlers(...)
     13. | \-mask$eval_all_mutate(quo)
     14. +-purrr::map2(...)
     15. | \-aba .f(.x[[i]], .y[[i]], ...)
     16. | +-... %>% mutate(term = tolower(term))
     17. | +-aba:::aba_glance(model, basic_model)
     18. | \-aba:::aba_glance.lm(model, basic_model)
     19. +-dplyr::mutate(., term = tolower(term))
     20. +-dplyr::arrange(., match(term, metric_vars))
     21. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     22. +-dplyr::filter(., term %in% metric_vars)
     23. +-base::loadNamespace(x)
     24. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     25. | | \-base withOneRestart(expr, restarts[[1L]])
     26. | | \-base doWithOneRestart(return(expr), restart)
     27. | \-base::stop(cond)
     28. \-dplyr `<fn>`(`<pckgNtFE>`)
     29. \-rlang::abort(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.9
Check: tests
Result: ERROR
     Running 'testthat.R' [164s/193s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     == Skipped tests ===============================================================
     * On CRAN (2)
    
     == Failed tests ================================================================
     -- Failure (test-stat_ancova.R:28:3): example works ----------------------------
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     x
     1. +-testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. | \-testthat:::expect_condition_matching(...)
     3. | \-testthat:::quasi_capture(...)
     4. | +-testthat .capture(...)
     5. | | \-base::withCallingHandlers(...)
     6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. +-ancova_model %>% summary()
     8. +-base::summary(.)
     9. +-aba:::summary.abaModel(.)
     10. | \-object %>% aba_summary(...)
     11. +-aba::aba_summary(., ...)
     12. | \-object %>% calculate_metrics(control)
     13. +-aba:::calculate_metrics(., control)
     14. | \-r %>% ...
     15. +-dplyr::mutate(...)
     16. +-dplyr:::mutate.data.frame(...)
     17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. | +-base::withCallingHandlers(...)
     19. | \-mask$eval_all_mutate(quo)
     20. +-purrr::map2(...)
     21. | \-aba .f(.x[[i]], .y[[i]], ...)
     22. | +-... %>% mutate(term = tolower(term))
     23. | +-aba:::aba_glance(model, basic_model)
     24. | \-aba:::aba_glance.lm(model, basic_model)
     25. +-dplyr::mutate(., term = tolower(term))
     26. +-dplyr::arrange(., match(term, metric_vars))
     27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. +-dplyr::filter(., term %in% metric_vars)
     29. +-base::loadNamespace(x)
     30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. | | \-base withOneRestart(expr, restarts[[1L]])
     32. | | \-base doWithOneRestart(return(expr), restart)
     33. | \-base::stop(cond)
     34. \-dplyr `<fn>`(`<pckgNtFE>`)
     35. \-rlang::abort(...)
     -- Failure (test-stat_lm.R:6:3): complete.cases=F for lm works -----------------
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     x
     1. +-testthat::expect_error(...) at test-stat_lm.R:6:2
     2. | \-testthat:::expect_condition_matching(...)
     3. | \-testthat:::quasi_capture(...)
     4. | +-testthat .capture(...)
     5. | | \-base::withCallingHandlers(...)
     6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. +-... %>% aba_summary()
     8. +-aba::aba_summary(.)
     9. | \-object %>% calculate_metrics(control)
     10. +-aba:::calculate_metrics(., control)
     11. | \-r %>% ...
     12. +-dplyr::mutate(...)
     13. +-dplyr:::mutate.data.frame(...)
     14. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. | +-base::withCallingHandlers(...)
     16. | \-mask$eval_all_mutate(quo)
     17. +-purrr::map2(...)
     18. | \-aba .f(.x[[i]], .y[[i]], ...)
     19. | +-... %>% mutate(term = tolower(term))
     20. | +-aba:::aba_glance(model, basic_model)
     21. | \-aba:::aba_glance.lm(model, basic_model)
     22. +-dplyr::mutate(., term = tolower(term))
     23. +-dplyr::arrange(., match(term, metric_vars))
     24. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. +-dplyr::filter(., term %in% metric_vars)
     26. +-base::loadNamespace(x)
     27. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. | | \-base withOneRestart(expr, restarts[[1L]])
     29. | | \-base doWithOneRestart(return(expr), restart)
     30. | \-base::stop(cond)
     31. \-dplyr `<fn>`(`<pckgNtFE>`)
     32. \-rlang::abort(...)
     -- Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm -------
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     x
     1. +-testthat::expect_error(...) at test-stat_lm.R:41:2
     2. | \-testthat:::expect_condition_matching(...)
     3. | \-testthat:::quasi_capture(...)
     4. | +-testthat .capture(...)
     5. | | \-base::withCallingHandlers(...)
     6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. +-model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. +-base::summary(.)
     9. +-aba:::summary.abaModel(.)
     10. | \-object %>% aba_summary(...)
     11. +-aba::aba_summary(., ...)
     12. | \-object %>% calculate_metrics(control)
     13. +-aba:::calculate_metrics(., control)
     14. | \-r %>% ...
     15. +-dplyr::mutate(...)
     16. +-dplyr:::mutate.data.frame(...)
     17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. | +-base::withCallingHandlers(...)
     19. | \-mask$eval_all_mutate(quo)
     20. +-purrr::map2(...)
     21. | \-aba .f(.x[[i]], .y[[i]], ...)
     22. | +-... %>% mutate(term = tolower(term))
     23. | +-aba:::aba_glance(model, basic_model)
     24. | \-aba:::aba_glance.lm(model, basic_model)
     25. +-dplyr::mutate(., term = tolower(term))
     26. +-dplyr::arrange(., match(term, metric_vars))
     27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. +-dplyr::filter(., term %in% metric_vars)
     29. +-base::loadNamespace(x)
     30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. | | \-base withOneRestart(expr, restarts[[1L]])
     32. | | \-base doWithOneRestart(return(expr), restart)
     33. | \-base::stop(cond)
     34. \-dplyr `<fn>`(`<pckgNtFE>`)
     35. \-rlang::abort(...)
     -- Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm -------
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     x
     1. +-testthat::expect_error(...) at test-stat_lm.R:51:2
     2. | \-testthat:::expect_condition_matching(...)
     3. | \-testthat:::quasi_capture(...)
     4. | +-testthat .capture(...)
     5. | | \-base::withCallingHandlers(...)
     6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. +-model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. +-base::summary(.)
     9. +-aba:::summary.abaModel(.)
     10. | \-object %>% aba_summary(...)
     11. +-aba::aba_summary(., ...)
     12. | \-object %>% calculate_metrics(control)
     13. +-aba:::calculate_metrics(., control)
     14. | \-r %>% ...
     15. +-dplyr::mutate(...)
     16. +-dplyr:::mutate.data.frame(...)
     17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. | +-base::withCallingHandlers(...)
     19. | \-mask$eval_all_mutate(quo)
     20. +-purrr::map2(...)
     21. | \-aba .f(.x[[i]], .y[[i]], ...)
     22. | +-... %>% mutate(term = tolower(term))
     23. | +-aba:::aba_glance(model, basic_model)
     24. | \-aba:::aba_glance.lm(model, basic_model)
     25. +-dplyr::mutate(., term = tolower(term))
     26. +-dplyr::arrange(., match(term, metric_vars))
     27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. +-dplyr::filter(., term %in% metric_vars)
     29. +-base::loadNamespace(x)
     30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. | | \-base withOneRestart(expr, restarts[[1L]])
     32. | | \-base doWithOneRestart(return(expr), restart)
     33. | \-base::stop(cond)
     34. \-dplyr `<fn>`(`<pckgNtFE>`)
     35. \-rlang::abort(...)
     -- Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ---------
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     x
     1. +-testthat::expect_false(...) at test-stat_lm.R:61:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. +-base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. \-base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.9
Check: examples
Result: ERROR
    Running examples in ‘aba-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: stat_ancova
    > ### Title: Create an ancova stat object.
    > ### Aliases: stat_ancova
    >
    > ### ** Examples
    >
    > # filter to 24 month visit; calculate change in cognition to use as outcome;
    > # assume abeta status as "treatment" variable.
    > # The goal is to see if "treatment" has an effect on 2y cognitive decline
    > data <- adnimerge %>%
    + dplyr::filter(
    + VISCODE == 'm24',
    + DX_bl %in% c('MCI', 'AD'),
    + !is.na(CSF_ABETA_STATUS_bl)
    + ) %>%
    + dplyr::mutate(
    + CDRSB = CDRSB - CDRSB_bl,
    + ADAS13 = ADAS13 - ADAS13_bl,
    + TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
    + labels=c('Placebo','Treatment'))
    + )
    >
    > # fit model. note that baseline outcome will be added based on the suffix.
    > # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
    > ancova_model <- data %>% aba_model() %>%
    + set_outcomes(CDRSB, ADAS13) %>%
    + set_covariates(AGE, GENDER, EDUCATION) %>%
    + set_stats(
    + stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
    + ) %>%
    + fit()
    >
    > # summarise model. treatment effect will be shown in the treatment coefficient
    > ancova_summary <- ancova_model %>% summary()
    Error in `mutate()`:
    ! Problem while computing `metrics = purrr::map2(...)`.
    Caused by error in `loadNamespace()`:
    ! there is no package called ‘psychometric’
    Backtrace:
     ▆
     1. ├─ancova_model %>% summary()
     2. ├─base::summary(.)
     3. ├─aba:::summary.abaModel(.)
     4. │ └─object %>% aba_summary(...)
     5. ├─aba::aba_summary(., ...)
     6. │ └─object %>% calculate_metrics(control)
     7. ├─aba:::calculate_metrics(., control)
     8. │ └─r %>% ...
     9. ├─dplyr::mutate(...)
     10. ├─dplyr:::mutate.data.frame(...)
     11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     12. │ ├─base::withCallingHandlers(...)
     13. │ └─mask$eval_all_mutate(quo)
     14. ├─purrr::map2(...)
     15. │ └─aba .f(.x[[i]], .y[[i]], ...)
     16. │ ├─... %>% mutate(term = tolower(term))
     17. │ ├─aba:::aba_glance(model, basic_model)
     18. │ └─aba:::aba_glance.lm(model, basic_model)
     19. ├─dplyr::mutate(., term = tolower(term))
     20. ├─dplyr::arrange(., match(term, metric_vars))
     21. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     22. ├─dplyr::filter(., term %in% metric_vars)
     23. ├─base::loadNamespace(x)
     24. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     25. │ │ └─base withOneRestart(expr, restarts[[1L]])
     26. │ │ └─base doWithOneRestart(return(expr), restart)
     27. │ └─base::stop(cond)
     28. └─dplyr `<fn>`(`<pckgNtFE>`)
     29. └─rlang::abort(...)
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.0.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [119s/188s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (2)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─ancova_model %>% summary()
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─... %>% aba_summary()
     8. ├─aba::aba_summary(.)
     9. │ └─object %>% calculate_metrics(control)
     10. ├─aba:::calculate_metrics(., control)
     11. │ └─r %>% ...
     12. ├─dplyr::mutate(...)
     13. ├─dplyr:::mutate.data.frame(...)
     14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. │ ├─base::withCallingHandlers(...)
     16. │ └─mask$eval_all_mutate(quo)
     17. ├─purrr::map2(...)
     18. │ └─aba .f(.x[[i]], .y[[i]], ...)
     19. │ ├─... %>% mutate(term = tolower(term))
     20. │ ├─aba:::aba_glance(model, basic_model)
     21. │ └─aba:::aba_glance.lm(model, basic_model)
     22. ├─dplyr::mutate(., term = tolower(term))
     23. ├─dplyr::arrange(., match(term, metric_vars))
     24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. ├─dplyr::filter(., term %in% metric_vars)
     26. ├─base::loadNamespace(x)
     27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. │ │ └─base withOneRestart(expr, restarts[[1L]])
     29. │ │ └─base doWithOneRestart(return(expr), restart)
     30. │ └─base::stop(cond)
     31. └─dplyr `<fn>`(`<pckgNtFE>`)
     32. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     ▆
     1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.0.9
Check: examples
Result: ERROR
    Running examples in ‘aba-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: stat_ancova
    > ### Title: Create an ancova stat object.
    > ### Aliases: stat_ancova
    >
    > ### ** Examples
    >
    > # filter to 24 month visit; calculate change in cognition to use as outcome;
    > # assume abeta status as "treatment" variable.
    > # The goal is to see if "treatment" has an effect on 2y cognitive decline
    > data <- adnimerge %>%
    + dplyr::filter(
    + VISCODE == 'm24',
    + DX_bl %in% c('MCI', 'AD'),
    + !is.na(CSF_ABETA_STATUS_bl)
    + ) %>%
    + dplyr::mutate(
    + CDRSB = CDRSB - CDRSB_bl,
    + ADAS13 = ADAS13 - ADAS13_bl,
    + TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
    + labels=c('Placebo','Treatment'))
    + )
    >
    > # fit model. note that baseline outcome will be added based on the suffix.
    > # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
    > ancova_model <- data %>% aba_model() %>%
    + set_outcomes(CDRSB, ADAS13) %>%
    + set_covariates(AGE, GENDER, EDUCATION) %>%
    + set_stats(
    + stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
    + ) %>%
    + fit()
    >
    > # summarise model. treatment effect will be shown in the treatment coefficient
    > ancova_summary <- ancova_model %>% summary()
    Error in `mutate()`:
    ! Problem while computing `metrics = purrr::map2(...)`.
    Caused by error in `loadNamespace()`:
    ! there is no package called ‘psychometric’
    Backtrace:
     ▆
     1. ├─ancova_model %>% summary()
     2. ├─base::summary(.)
     3. ├─aba:::summary.abaModel(.)
     4. │ └─object %>% aba_summary(...)
     5. ├─aba::aba_summary(., ...)
     6. │ └─object %>% calculate_metrics(control)
     7. ├─aba:::calculate_metrics(., control)
     8. │ └─r %>% ...
     9. ├─dplyr::mutate(...)
     10. ├─dplyr:::mutate.data.frame(...)
     11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     12. │ ├─base::withCallingHandlers(...)
     13. │ └─mask$eval_all_mutate(quo)
     14. ├─purrr::map2(...)
     15. │ └─aba .f(.x[[i]], .y[[i]], ...)
     16. │ ├─... %>% mutate(term = tolower(term))
     17. │ ├─aba:::aba_glance(model, basic_model)
     18. │ └─aba:::aba_glance.lm(model, basic_model)
     19. ├─dplyr::mutate(., term = tolower(term))
     20. ├─dplyr::arrange(., match(term, metric_vars))
     21. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     22. ├─dplyr::filter(., term %in% metric_vars)
     23. ├─base::loadNamespace(x)
     24. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     25. │ │ └─base withOneRestart(expr, restarts[[1L]])
     26. │ │ └─base doWithOneRestart(return(expr), restart)
     27. │ └─base::stop(cond)
     28. └─dplyr `<fn>`(`<pckgNtFE>`)
     29. └─rlang::abort(...)
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.0.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [186s/232s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (2)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─ancova_model %>% summary()
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─... %>% aba_summary()
     8. ├─aba::aba_summary(.)
     9. │ └─object %>% calculate_metrics(control)
     10. ├─aba:::calculate_metrics(., control)
     11. │ └─r %>% ...
     12. ├─dplyr::mutate(...)
     13. ├─dplyr:::mutate.data.frame(...)
     14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. │ ├─base::withCallingHandlers(...)
     16. │ └─mask$eval_all_mutate(quo)
     17. ├─purrr::map2(...)
     18. │ └─aba .f(.x[[i]], .y[[i]], ...)
     19. │ ├─... %>% mutate(term = tolower(term))
     20. │ ├─aba:::aba_glance(model, basic_model)
     21. │ └─aba:::aba_glance.lm(model, basic_model)
     22. ├─dplyr::mutate(., term = tolower(term))
     23. ├─dplyr::arrange(., match(term, metric_vars))
     24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. ├─dplyr::filter(., term %in% metric_vars)
     26. ├─base::loadNamespace(x)
     27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. │ │ └─base withOneRestart(expr, restarts[[1L]])
     29. │ │ └─base doWithOneRestart(return(expr), restart)
     30. │ └─base::stop(cond)
     31. └─dplyr `<fn>`(`<pckgNtFE>`)
     32. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     ▆
     1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.0.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [193s/265s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (2)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─ancova_model %>% summary()
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─... %>% aba_summary()
     8. ├─aba::aba_summary(.)
     9. │ └─object %>% calculate_metrics(control)
     10. ├─aba:::calculate_metrics(., control)
     11. │ └─r %>% ...
     12. ├─dplyr::mutate(...)
     13. ├─dplyr:::mutate.data.frame(...)
     14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. │ ├─base::withCallingHandlers(...)
     16. │ └─mask$eval_all_mutate(quo)
     17. ├─purrr::map2(...)
     18. │ └─aba .f(.x[[i]], .y[[i]], ...)
     19. │ ├─... %>% mutate(term = tolower(term))
     20. │ ├─aba:::aba_glance(model, basic_model)
     21. │ └─aba:::aba_glance.lm(model, basic_model)
     22. ├─dplyr::mutate(., term = tolower(term))
     23. ├─dplyr::arrange(., match(term, metric_vars))
     24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. ├─dplyr::filter(., term %in% metric_vars)
     26. ├─base::loadNamespace(x)
     27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. │ │ └─base withOneRestart(expr, restarts[[1L]])
     29. │ │ └─base doWithOneRestart(return(expr), restart)
     30. │ └─base::stop(cond)
     31. └─dplyr `<fn>`(`<pckgNtFE>`)
     32. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     ▆
     1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.0.9
Check: package dependencies
Result: ERROR
    Packages required but not available:
     'purrr', 'dplyr', 'broom', 'tibble', 'ggplot2', 'glue', 'magrittr',
     'stringr', 'rlang', 'tidyr', 'generics'
    
    Packages suggested but not available for checking:
     'covr', 'knitr', 'plotly', 'rmarkdown', 'testthat', 'tidyselect',
     'yardstick', 'pins', 'MuMIn', 'broom.mixed', 'emmeans', 'ggpubr',
     'pROC', 'progress', 'OptimalCutpoints', 'tableone', 'longpower',
     'withr', 'reactable', 'psychometric', 'readr', 'writexl'
    
    VignetteBuilder package required for checking but not installed: 'knitr'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavor: r-devel-windows-x86_64-new-TK

Version: 0.0.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [152s/172s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (2)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─ancova_model %>% summary()
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─... %>% aba_summary()
     8. ├─aba::aba_summary(.)
     9. │ └─object %>% calculate_metrics(control)
     10. ├─aba:::calculate_metrics(., control)
     11. │ └─r %>% ...
     12. ├─dplyr::mutate(...)
     13. ├─dplyr:::mutate.data.frame(...)
     14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. │ ├─base::withCallingHandlers(...)
     16. │ └─mask$eval_all_mutate(quo)
     17. ├─purrr::map2(...)
     18. │ └─aba .f(.x[[i]], .y[[i]], ...)
     19. │ ├─... %>% mutate(term = tolower(term))
     20. │ ├─aba:::aba_glance(model, basic_model)
     21. │ └─aba:::aba_glance.lm(model, basic_model)
     22. ├─dplyr::mutate(., term = tolower(term))
     23. ├─dplyr::arrange(., match(term, metric_vars))
     24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. ├─dplyr::filter(., term %in% metric_vars)
     26. ├─base::loadNamespace(x)
     27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. │ │ └─base withOneRestart(expr, restarts[[1L]])
     29. │ │ └─base doWithOneRestart(return(expr), restart)
     30. │ └─base::stop(cond)
     31. └─dplyr `<fn>`(`<pckgNtFE>`)
     32. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     ▆
     1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.0.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [156s/187s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(aba)
     >
     >
     > test_check("aba")
     Stratified by DX_bl
     level Overall
     n 2347 24
     AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
     GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
     EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
     ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
     PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
     PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
     Stratified by DX_bl
     AD CU MCI
     n 405 846 1072
     AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
     GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
     EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
     ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
     CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
     PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
     PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
     Stratified by DX_bl
     p test
     n
     AGE (mean (SD)) <0.001
     GENDER (mean (SD)) <0.001
     EDUCATION (mean (SD)) <0.001
     ConvertedToAlzheimers (mean (SD)) NA
     CSF_ABETA_STATUS_bl (mean (SD)) <0.001
     PLASMA_PTAU181_bl (mean (SD)) <0.001
     PLASMA_NFL_bl (mean (SD)) <0.001
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (2)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
     `ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─ancova_model %>% summary()
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─... %>% aba_summary()
     8. ├─aba::aba_summary(.)
     9. │ └─object %>% calculate_metrics(control)
     10. ├─aba:::calculate_metrics(., control)
     11. │ └─r %>% ...
     12. ├─dplyr::mutate(...)
     13. ├─dplyr:::mutate.data.frame(...)
     14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     15. │ ├─base::withCallingHandlers(...)
     16. │ └─mask$eval_all_mutate(quo)
     17. ├─purrr::map2(...)
     18. │ └─aba .f(.x[[i]], .y[[i]], ...)
     19. │ ├─... %>% mutate(term = tolower(term))
     20. │ ├─aba:::aba_glance(model, basic_model)
     21. │ └─aba:::aba_glance.lm(model, basic_model)
     22. ├─dplyr::mutate(., term = tolower(term))
     23. ├─dplyr::arrange(., match(term, metric_vars))
     24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     25. ├─dplyr::filter(., term %in% metric_vars)
     26. ├─base::loadNamespace(x)
     27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     28. │ │ └─base withOneRestart(expr, restarts[[1L]])
     29. │ │ └─base doWithOneRestart(return(expr), restart)
     30. │ └─base::stop(cond)
     31. └─dplyr `<fn>`(`<pckgNtFE>`)
     32. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
     `... <- NULL` threw an unexpected error.
     Message: Problem while computing `metrics = purrr::map2(...)`.
     Caused by error in `loadNamespace()`:
     ! there is no package called 'psychometric'
     Class: dplyr:::mutate_error/rlang_error/error/condition
     Backtrace:
     ▆
     1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
     2. │ └─testthat:::expect_condition_matching(...)
     3. │ └─testthat:::quasi_capture(...)
     4. │ ├─testthat .capture(...)
     5. │ │ └─base::withCallingHandlers(...)
     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
     8. ├─base::summary(.)
     9. ├─aba:::summary.abaModel(.)
     10. │ └─object %>% aba_summary(...)
     11. ├─aba::aba_summary(., ...)
     12. │ └─object %>% calculate_metrics(control)
     13. ├─aba:::calculate_metrics(., control)
     14. │ └─r %>% ...
     15. ├─dplyr::mutate(...)
     16. ├─dplyr:::mutate.data.frame(...)
     17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
     18. │ ├─base::withCallingHandlers(...)
     19. │ └─mask$eval_all_mutate(quo)
     20. ├─purrr::map2(...)
     21. │ └─aba .f(.x[[i]], .y[[i]], ...)
     22. │ ├─... %>% mutate(term = tolower(term))
     23. │ ├─aba:::aba_glance(model, basic_model)
     24. │ └─aba:::aba_glance.lm(model, basic_model)
     25. ├─dplyr::mutate(., term = tolower(term))
     26. ├─dplyr::arrange(., match(term, metric_vars))
     27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
     28. ├─dplyr::filter(., term %in% metric_vars)
     29. ├─base::loadNamespace(x)
     30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     31. │ │ └─base withOneRestart(expr, restarts[[1L]])
     32. │ │ └─base doWithOneRestart(return(expr), restart)
     33. │ └─base::stop(cond)
     34. └─dplyr `<fn>`(`<pckgNtFE>`)
     35. └─rlang::abort(...)
     ── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
     Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
     Backtrace:
     ▆
     1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
     5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
    
     [ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64