rename functions with new package conventions. (#110)

**What changes are proposed in this pull request?**
Functions are renamed according to new conventions:
`ard_<pkgname>_<fnname>()` if a package specific function is used
If a `.` appears in a function name it will be replaced with a `_` in
the ard_*() function name.

closes #106  @ayogasekaram 


--------------------------------------------------------------------------------

Pre-review Checklist (if item does not apply, mark is as complete)
- [x] **All** GitHub Action workflows pass with a ✅
- [x] PR branch has pulled the most recent updates from master branch:
`usethis::pr_merge_main()`
- [x] If a bug was fixed, a unit test was added.
- [x] If a new `ard_*()` function was added, it passes the ARD
structural checks from `cards::check_ard_structure()`.
- [x] Code coverage is suitable for any new functions/features
(generally, 100% coverage for new code): `devtools::test_coverage()`
- [x] Request a reviewer

Reviewer Checklist (if item does not apply, mark is as complete)

- [x] If a bug was fixed, a unit test was added.
- [x] Run `pkgdown::build_site()`. Check the R console for errors, and
review the rendered website.
- [x] Code coverage is suitable for any new functions/features:
`devtools::test_coverage()`

When the branch is ready to be merged:
- [x] Update `NEWS.md` with the changes from this pull request under the
heading "`# cards (development version)`". If there is an issue
associated with the pull request, reference it in parentheses at the end
update (see `NEWS.md` for examples).
- [ ] **All** GitHub Action workflows pass with a ✅
- [ ] Approve Pull Request
- [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

Author: ayogasekaram

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,16 +14,14 @@ Pre-review Checklist (if item does not apply, mark is as complete)
 - [ ] If a bug was fixed, a unit test was added.
 - [ ] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`.
 - [ ] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()`
-- [ ] Request a reviewer
 
 Reviewer Checklist (if item does not apply, mark is as complete)
 
 - [ ] If a bug was fixed, a unit test was added.
-- [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website.
 - [ ] Code coverage is suitable for any new functions/features: `devtools::test_coverage()`
 
 When the branch is ready to be merged:
-- [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# cards (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
+- [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# cardx (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
 - [ ] **All** GitHub Action workflows pass with a :white_check_mark:
 - [ ] Approve Pull Request
 - [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".

NAMESPACE

@@ -4,33 +4,33 @@ S3method(ard_regression,default)
 export("%>%")
 export(all_of)
 export(any_of)
-export(ard_aov)
 export(ard_car_anova)
-export(ard_chisqtest)
-export(ard_cohens_d)
-export(ard_fishertest)
-export(ard_hedges_g)
-export(ard_kruskaltest)
-export(ard_mcnemartest)
-export(ard_moodtest)
-export(ard_onewaytest)
-export(ard_paired_cohens_d)
-export(ard_paired_hedges_g)
-export(ard_paired_ttest)
-export(ard_paired_wilcoxtest)
+export(ard_car_vif)
+export(ard_effectsize_cohens_d)
+export(ard_effectsize_hedges_g)
+export(ard_effectsize_paired_cohens_d)
+export(ard_effectsize_paired_hedges_g)
 export(ard_proportion_ci)
-export(ard_proptest)
 export(ard_regression)
 export(ard_regression_basic)
-export(ard_smd)
-export(ard_survfit)
-export(ard_svychisq)
-export(ard_svycontinuous)
-export(ard_svyranktest)
-export(ard_svyttest)
-export(ard_ttest)
-export(ard_vif)
-export(ard_wilcoxtest)
+export(ard_smd_smd)
+export(ard_stats_aov)
+export(ard_stats_chisq_test)
+export(ard_stats_fisher_test)
+export(ard_stats_kruskal_test)
+export(ard_stats_mcnemar_test)
+export(ard_stats_mood_test)
+export(ard_stats_oneway_test)
+export(ard_stats_paired_t_test)
+export(ard_stats_paired_wilcox_test)
+export(ard_stats_prop_test)
+export(ard_stats_t_test)
+export(ard_stats_wilcox_test)
+export(ard_survey_svychisq)
+export(ard_survey_svycontinuous)
+export(ard_survey_svyranktest)
+export(ard_survey_svyttest)
+export(ard_survival_survfit)
 export(contains)
 export(ends_with)
 export(everything)

NEWS.md

@@ -1,5 +1,23 @@
 # cardx 0.1.0.9011
 
+### Breaking Changes
+
+* Updated function names have been updated to follow the pattern `ard_<pkgname>_<fnname>()`. Former functions names have _not_ been deprecated. (#106)
+
+```r
+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
+
 * Added the following functions for calculating Analysis Results Data (ARD).
   - `ard_aov()` for calculating ANOVA results using `stats::aov()`. (#3)
   - `ard_car_anova()` for calculating ANOVA results using `car::Anova()`. (#3)
@@ -15,9 +33,9 @@
   - `ard_svyranktest()` for weighted/survey rank tests using `survey::svyranktest()`. (#71)
   - `ard_vif()` for calculating the variance inflation factor using `car::vif()`. (#10)
 
-* Updated functions `ard_ttest()`, `ard_paired_ttest()`, `ard_wilcoxtest()`, `ard_paired_wilcoxtest()`, `ard_chisqtest()`, `ard_fishertest()`, `ard_kruskaltest()`, `ard_mcnemartest()`, and `ard_moodtest()` to accept multiple variables at once. Independent tests are calculated for each variable. The `variable` argument is renamed to `variables`. (#77)
+* 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_ttest()` and `ard_wilcoxtest()` to no longer require the `by` argument, which yields central estimates with their confidence intervals. (#82)
+* 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)
 
 # cardx 0.1.0
 

R/ard_vif.R R/ard_car_vif.RR/ard_vif.R renamed to R/ard_car_vif.R

@@ -10,14 +10,14 @@
 #' @param ... arguments passed to `car::vif(...)`
 #'
 #' @return data frame
-#' @name ard_vif
-#' @rdname ard_vif
+#' @name ard_car_vif
+#' @rdname ard_car_vif
 #' @export
 #'
 #' @examples
 #' lm(AGE ~ ARM + SEX, data = cards::ADSL) |>
-#'   ard_vif()
-ard_vif <- function(x, ...) {
+#'   ard_car_vif()
+ard_car_vif <- function(x, ...) {
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)
 

R/ard_cohens_d.R R/ard_effectsize_cohens_d.RR/ard_cohens_d.R renamed to R/ard_effectsize_cohens_d.R

@@ -16,13 +16,13 @@
 #' @param ... arguments passed to `effectsize::cohens_d(...)`
 #'
 #' @return ARD data frame
-#' @name ard_cohens_d
+#' @name ard_effectsize_cohens_d
 #'
 #' @details
-#' For the `ard_cohens_d()` function, the data is expected to be one row per subject.
+#' For the `ard_effectsize_cohens_d()` function, the data is expected to be one row per subject.
 #' The data is passed as `effectsize::cohens_d(data[[variable]]~data[[by]], data, paired = FALSE, ...)`.
 #'
-#' For the `ard_paired_cohens_d()` function, the data is expected to be one row
+#' For the `ard_effectsize_paired_cohens_d()` function, the data is expected to be one row
 #' per subject per by level. Before the effect size is calculated, the data are
 #' reshaped to a wide format to be one row per subject.
 #' The data are then passed as
@@ -31,7 +31,7 @@
 #' @examplesIf cards::is_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
 #' cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
-#'   ard_cohens_d(by = ARM, variables = AGE)
+#'   ard_effectsize_cohens_d(by = ARM, variables = AGE)
 #'
 #' # constructing a paired data set,
 #' # where patients receive both treatments
@@ -41,12 +41,12 @@
 #'   dplyr::arrange(USUBJID, ARM) |>
 #'   dplyr::group_by(USUBJID) |>
 #'   dplyr::filter(dplyr::n() > 1) |>
-#'   ard_paired_cohens_d(by = ARM, variables = AGE, id = USUBJID)
+#'   ard_effectsize_paired_cohens_d(by = ARM, variables = AGE, id = USUBJID)
 NULL
 
-#' @rdname ard_cohens_d
+#' @rdname ard_effectsize_cohens_d
 #' @export
-ard_cohens_d <- function(data, by, variables, ...) {
+ard_effectsize_cohens_d <- function(data, by, variables, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
 
@@ -85,9 +85,9 @@ ard_cohens_d <- function(data, by, variables, ...) {
 }
 
 
-#' @rdname ard_cohens_d
+#' @rdname ard_effectsize_cohens_d
 #' @export
-ard_paired_cohens_d <- function(data, by, variables, id, ...) {
+ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed("effectsize", reference_pkg = "cardx")
   cards::check_pkg_installed("parameters", reference_pkg = "cardx")

R/ard_hedges_g.R R/ard_effectsize_hedges_g.RR/ard_hedges_g.R renamed to R/ard_effectsize_hedges_g.R

@@ -16,13 +16,13 @@
 #' @param ... arguments passed to `effectsize::hedges_g(...)`
 #'
 #' @return ARD data frame
-#' @name ard_hedges_g
+#' @name ard_effectsize_hedges_g
 #'
 #' @details
-#' For the `ard_hedges_g()` function, the data is expected to be one row per subject.
+#' For the `ard_effectsize_hedges_g()` function, the data is expected to be one row per subject.
 #' The data is passed as `effectsize::hedges_g(data[[variable]]~data[[by]], data, paired = FALSE, ...)`.
 #'
-#' For the `ard_paired_hedges_g()` function, the data is expected to be one row
+#' For the `ard_effectsize_paired_hedges_g()` function, the data is expected to be one row
 #' per subject per by level. Before the effect size is calculated, the data are
 #' reshaped to a wide format to be one row per subject.
 #' The data are then passed as
@@ -31,7 +31,7 @@
 #' @examplesIf cards::is_pkg_installed(c("effectsize", "parameters", "withr"), reference_pkg = "cardx")
 #' cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
-#'   ard_hedges_g(by = ARM, variables = AGE)
+#'   ard_effectsize_hedges_g(by = ARM, variables = AGE)
 #'
 #' # constructing a paired data set,
 #' # where patients receive both treatments
@@ -41,12 +41,12 @@
 #'   dplyr::arrange(USUBJID, ARM) |>
 #'   dplyr::group_by(USUBJID) |>
 #'   dplyr::filter(dplyr::n() > 1) |>
-#'   ard_paired_hedges_g(by = ARM, variables = AGE, id = USUBJID)
+#'   ard_effectsize_paired_hedges_g(by = ARM, variables = AGE, id = USUBJID)
 NULL
 
-#' @rdname ard_hedges_g
+#' @rdname ard_effectsize_hedges_g
 #' @export
-ard_hedges_g <- function(data, by, variables, ...) {
+ard_effectsize_hedges_g <- function(data, by, variables, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed(c("effectsize", "parameters", "withr"), reference_pkg = "cardx")
 
@@ -89,9 +89,9 @@ ard_hedges_g <- function(data, by, variables, ...) {
     dplyr::bind_rows()
 }
 
-#' @rdname ard_hedges_g
+#' @rdname ard_effectsize_hedges_g
 #' @export
-ard_paired_hedges_g <- function(data, by, variables, id, ...) {
+ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed("effectsize", reference_pkg = "cardx")
   cards::check_pkg_installed("parameters", reference_pkg = "cardx")

R/ard_smd.R R/ard_smd_smd.RR/ard_smd.R renamed to R/ard_smd_smd.R

@@ -17,9 +17,9 @@
 #' @export
 #'
 #' @examplesIf cards::is_pkg_installed("smd", reference_pkg = "cardx")
-#' ard_smd(cards::ADSL, by = ARM, variables = AGE, std.error = TRUE)
-#' ard_smd(cards::ADSL, by = ARM, variables = AGEGR1, std.error = TRUE)
-ard_smd <- function(data, by, variables, ...) {
+#' ard_smd_smd(cards::ADSL, by = ARM, variables = AGE, std.error = TRUE)
+#' ard_smd_smd(cards::ADSL, by = ARM, variables = AGEGR1, std.error = TRUE)
+ard_smd_smd <- function(data, by, variables, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed("smd", reference_pkg = "cardx")
 

R/ard_aov.R R/ard_stats_aov.RR/ard_aov.R renamed to R/ard_stats_aov.R

@@ -11,8 +11,8 @@
 #' @export
 #'
 #' @examplesIf cards::is_pkg_installed(c("broom.helpers"), reference_pkg = "cardx")
-#' ard_aov(AGE ~ ARM, data = cards::ADSL)
-ard_aov <- function(formula, data, ...) {
+#' ard_stats_aov(AGE ~ ARM, data = cards::ADSL)
+ard_stats_aov <- function(formula, data, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed(c("broom.helpers"), reference_pkg = "cardx")
 

R/ard_chisqtest.R R/ard_stats_chisq_test.RR/ard_chisqtest.R renamed to R/ard_stats_chisq_test.R

@@ -19,8 +19,8 @@
 #'
 #' @examplesIf cards::is_pkg_installed("broom", reference_pkg = "cardx")
 #' cards::ADSL |>
-#'   ard_chisqtest(by = "ARM", variables = "AGEGR1")
-ard_chisqtest <- function(data, by, variables, ...) {
+#'   ard_stats_chisq_test(by = "ARM", variables = "AGEGR1")
+ard_stats_chisq_test <- function(data, by, variables, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed("broom", reference_pkg = "cardx")
 

R/ard_fishertest.R R/ard_stats_fisher_test.RR/ard_fishertest.R renamed to R/ard_stats_fisher_test.R

@@ -19,8 +19,8 @@
 #'
 #' @examplesIf cards::is_pkg_installed("broom", reference_pkg = "cardx")
 #' cards::ADSL[1:30, ] |>
-#'   ard_fishertest(by = "ARM", variables = "AGEGR1")
-ard_fishertest <- function(data, by, variables, ...) {
+#'   ard_stats_fisher_test(by = "ARM", variables = "AGEGR1")
+ard_stats_fisher_test <- function(data, by, variables, ...) {
   # check installed packages ---------------------------------------------------
   cards::check_pkg_installed("broom", reference_pkg = "cardx")