cardx 0.3.2

cardx 0.3.1.9001

cardx 0.3.1

• Added the ard_emmeans_emmeans() function. (#317)

• Renamed ard_emmeans_mean_difference() to ard_emmeans_contrast() to align with function naming conventions.

• The ard_complex() function has been renamed to ard_mvsummary().

cardx 0.3.0

New Features and Updates

• Added function ard_tabulate_abnormal() to calculate ARDs for abnormality analyses. (#310)

• Adding strata argument to ard_tabulate_max(). (#445, @jtalboys)

• Added function ard_incidence_rate() to calculate ARDs for incidence rate estimation. (#234)

Lifecycle Changes

• The following functions have been renamed.

  • ard_continuous() to ard_summary()
  • ard_categorical() to ard_tabulate()
  • ard_dichotomous() to ard_tabulate_value()
  • ard_categorical_max() to ard_tabulate_max()

• Updating any fmt_fn references to fmt_fun for consistency.

  • Any function with an argument cardx::foo(fmt_fn) has been updated to cardx::foo(fmt_fun). The old syntax will continue to function, but with a deprecation warning to users.

  • Importantly, the ARD column named "fmt_fn" has been updated to "fmt_fun". This change cannot be formally deprecated. For users who were accessing the ARD object directly to modify this column instead of using functions like cards::update_ard_fmt_fun(), this will be a breaking change.

Bug Fixes

• Fix in ard_survival_survfit.data.frame() method where the stratifying variable was not correctly converted back to its original type.

• Fix in ard_total_n.survey.design() to use update() instead of dplyr::mutate(), which sometimes caused a downstream issue.

cardx 0.2.4

New Features and Updates

• Added function ard_stats_mantelhaen_test() to calculate ARDs for Cochran-Mantel-Haenszel test results using stats::mantelhaen.test(). (#238)

• Added a ard_regression.data.frame() S3 method. Also converted ard_regression_basic() to an S3 generic and added a ard_regression_basic.data.frame() method (#287)

• Specifying ard_survfit_survfit.data.frame(variables=NULL) now creates an unstratified survfit() model, where previously variables argument could not be empty. (#277)

• The ard_survfit_survfit.data.frame(variables) now accepts tidyselect input. (#278)

• Added conf.level and conf.type to ard_survival_survfit() results. (#218)

• Added cards::as_cards_fun() to ard_emmeans_mean_difference() so when an error occurs the user gets an ARD with the expected ARD structure. (#132)

cardx 0.2.3

New Features and Updates

• Added function ard_categorical_max() to calculate categorical occurrence rates by maximum level per unique ID. (#240)

Other Updates

• Little n is now returned with the results of the proportion_ci_*() functions, which then flows into the results of ard_proportion_ci(). (#256)

• Added as_cards_fun() to ard_categorical_ci() so when there is an error, the user gets an ARD with the expected ARD structure. (#262)

• Update in ard_categorical.survey.design() for factor variables that are all missing. These variables can now be tabulated, where previously this resulted in an error.

• Update in ard_missing.survey.design() where we can now tabulate the missing rate of design variables, such as the weights.

Bug Fixes

• Fixed a bug in ard_survival_survfit() causing an error when “=” character is present in stratification variable level labels. (#252)

• Bug fix in ard_categorical_ci(denominator='cell') when missing values were present in the by variable.

cardx 0.2.2

• Added a data.frame method to ard_survival_survfit().

• Added a warning for incorrect formula type to ard_survival_survfit(). (#223)

• Implemented summary(extend=TRUE) in ard_survival_survfit() to return results for time points out of bounds. (#224)

• Methods in the {survey} and {survival} packages do not retain inputs variables types in their outputs. We now are able retain these variable types in ARDs returned by ard_continuous.survey.design(), ard_categorical.survey.design(), ard_continuous_ci.survey.design(), ard_categorical_ci.survey.design(), and ard_survival_survfit.data.frame() (and notably, not in ard_survival_survfit.survfit()).

• Added function ard_stats_mantelhaen_test() for calculating ARDs for Cochran-Mantel-Haenszel test results using stats::mantelhaen.test(). (#238)

cardx 0.2.1

New Features and Updates

• Added S3 method ard_total_n.survey.design() which returns an ARD with both the survey-weighted and unweighted total sample size.

• Added warning and error columns to ard_regression() output. (#148)

• Implemented cards::as_card() where needed in the package to convert data frames to class ‘card’. (#200)

Bug Fixes

• Bug fix in ard_categorical.survey.design() where all unweighted statistics were returned, even in the case where they were explicitly not requested.

Lifecycle Changes

• The bt(pattern), reformulate2(pattern_term), reformulate2(pattern_response) arguments have been deprecated and are now ignored. We now use make.names() to determine whether a column name needs to be wrapped in backticks. (#192)

cardx 0.2.0

Breaking Changes

• Updated function names to follow the pattern ard_<pkgname>_<fnname>(). This change is immediate: previous functions names have not been deprecated. (#106)

ard_ttest()             -> ard_stats_t_test()
ard_paired_ttest()      -> ard_stats_paired_t_test()
ard_wilcoxtest()        -> ard_stats_wilcox_test()
ard_paired_wilcoxtest() -> ard_stats_paired_wilcox_test()
ard_chisqtest()         -> ard_stats_chisq_test()
ard_fishertest()        -> ard_stats_fisher_test()
ard_kruskaltest()       -> ard_stats_kruskal_test()
ard_mcnemartest()       -> ard_stats_mcnemar_test()
ard_moodtest()          -> ard_stats_mood_test()

New Features

• The ard_categorical_ci(value) argument has been added. Previously, only binary variables (0/1 or TRUE/FALSE) could be summarized. When a value is not supplied, each level of the variable is summarized independently. By default, binary variables will have the 1/TRUE level summarized.

• Added the following functions for calculating Analysis Results Datasets (ARDs).

  • ard_stats_aov() for calculating ANOVA results using stats::aov(). (#3)
  • ard_stats_anova() for calculating ANOVA results using stats::anova(). (#12)
  • ard_stats_mcnemar_test_long() for McNemar’s test from long data using stats::mcnemar.test().
  • ard_stats_prop_test() for tests of proportions using stats::prop.test(). (#64)
  • ard_stats_t_test_onesample() for calculating one-sample results.
  • ard_stats_wilcox_test_onesample() for calculating one-sample results.
  • ard_stats_oneway_test() for calculating ANOVA results using stats::oneway.test(). (#3)
  • ard_aod_wald_test() for calculating Wald Tests for regression models using aod::wald.test(). (#84)
  • ard_car_anova() for calculating ANOVA results using car::Anova(). (#3)
  • ard_car_vif() for calculating the variance inflation factor using car::vif(). (#10)
  • ard_effectsize_cohens_d(), ard_effectsize_paired_cohens_d(), ard_effectsize_hedges_g(), and ard_effectsize_paired_hedges_g() for standardized differences using effectsize::cohens_d() and effectsize::hedges_g(). (#50)
  • ard_emmeans_mean_difference() for calculating the least-squares mean differences using the {emmeans} package. (#34)
  • ard_smd_smd() for calculating standardized mean differences using smd::smd(). (#4)
  • ard_survival_survfit() for survival analyses using survival::survfit(). (#43)
  • ard_continuous.survey.design() for calculating univariate summary statistics from weighted/survey data using many functions from the {survey} package. (#68)
  • ard_categorical.survey.design() for tabulating summary statistics from weighted/survey data using many functions from the {survey} package. (#140)
  • ard_dichotomous.survey.design() for tabulating dichotomous summary statistics from weighted/survey data using many functions from the {survey} package. (#2)
  • ard_missing.survey.design() for tabulating missing summary statistics from weighted/survey data using many functions from the {survey} package. (#2)
  • ard_attributes.survey.design() for summarizing labels and attributes from weighted/survey data using many functions from the {survey} package.
  • ard_survey_svychisq() for weighted/survey chi-squared test using survey::svychisq(). (#72)
  • ard_survey_svyttest() for weighted/survey t-tests using survey::svyttest(). (#70)
  • ard_survey_svyranktest() for weighted/survey rank tests using survey::svyranktest(). (#71)
  • ard_survival_survdiff() for creating results from survival::survdiff(). (#113)
  • ard_regression_basic() for basic regression models. The function focuses on matching model terms to underlying variables names. (#46)

• Updated functions ard_stats_t_test(), ard_stats_paired_t_test(), ard_stats_wilcox_test(), ard_stats_paired_wilcox_test(), ard_stats_chisq_test(), ard_stats_fisher_test(), ard_stats_kruskal_test(), ard_stats_mcnemar_test(), and ard_stats_mood_test() to accept multiple variables at once. Independent tests are calculated for each variable. The variable argument is renamed to variables. (#77)

• Updated ard_stats_t_test() and ard_stats_wilcox_test() to no longer require the by argument, which yields central estimates with their confidence intervals. (#82)

• Added model construction helpers, construct_model(), reformulate2(), bt(), and bt_strip().

• Imported cli call environment functions from https://github.com/ddsjoberg/standalone/blob/main/R/standalone-cli_call_env.R and implemented set_cli_abort_call in user-facing functions. (#111)

cardx 0.1.0

• Initial release.