reduce the amount of spelling issues / WORDLIST (#207)

The follow-up after insightsengineering/coredev-tasks#235 The final output of `spelling::spell_check_package()` Most terms that are left, like chot, houx, Hous, liaoc etc are either names or GitHub nicknames of authors. ```{R} WORD FOUND IN chot tm_g_patient_profile.Rd:234 ci name_ci.Rd:5,12,15,17 dichotomization tm_g_butterfly.Rd:39,41 NEWS.md:99 Forkers README.md:41,51,53 Hou tm_g_patient_profile.Rd:232 houx tm_g_patient_profile.Rd:232 tm_g_waterfall.Rd:149 liaoc tm_g_butterfly.Rd:157 tm_g_spiderplot.Rd:122 lil tm_g_events_term_id.Rd:90 Lil tm_g_ae_sub.Rd:85 pre argument_convention.Rd:15 tm_g_ae_oview.Rd:26 tm_g_ae_sub.Rd:26 tm_g_events_term_id.Rd:26,29 qit tm_g_patient_profile.Rd:238 tm_g_swimlane.Rd:151 tm_g_waterfall.Rd:147 repo README.md:11,17,49,53 TLG title:1 TLGs description:1 UI plot_decorate_output.Rd:5 ui_g_decorate.Rd:5 Xuefeng tm_g_patient_profile.Rd:232 zhanc quick_filter.Rd:23 tm_g_butterfly.Rd:155 tm_g_spiderplot.Rd:120 ```
insightsengineering · Jun 29, 2023 · d1016b5 · d1016b5
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diff --git a/NEWS.md b/NEWS.md
@@ -21,7 +21,7 @@
 
 ### Enhancements
 * Added `teal.reporter` to all modules.
-* Updated `shiny::validate` calls to `shinyvalidate` for better UI overview.
+* Updated `shiny::validate` calls to `shinyvalidate` for better `UI` overview.
 * Implemented `nestcolor` with slight refactoring to `tm_g_swimlane`. Added `nestcolor` in examples.
 
 ### Miscellaneous
@@ -59,7 +59,7 @@
 * Updated `tm_g_ae_sub` so that it no longer displays label inputs for group variables with no values selected.
 
 ### Bug fixes
-* Fixed a bug in `tm_g_waterfall` so that the `Tumor Burden Parameter` UI element is now respected.
+* Fixed a bug in `tm_g_waterfall` so that the `Tumor Burden Parameter` `UI` element is now respected.
 
 ### Miscellaneous
 * Updated R version requirement to `R >= 3.6`.
@@ -92,7 +92,7 @@
 
 ### New features
 * Added new `teal` module `tm_g_heat_bygrade` for a heatmap by grade plot.
-* Added new `teal` module `tm_g_ae_sub` for an AE by subgroups plot.
+* Added new `teal` module `tm_g_ae_sub` for an `AE` by subgroups plot.
 
 ### Bug fixes
 * Fixed misleading validate message in `tm_g_ae_oview` when either Control or Treatment variable is filtered out.
@@ -119,9 +119,9 @@
 
 ### Miscellaneous
 * Retired the following `teal` modules due to duplication in `teal.modules.clinical`:
-  - Teal module for AE overview summary table - can be replaced with `teal.modules.clinical::tm_t_events_summary`.
-  - Teal module for AE summary table by preferred terms - can be replaced with `teal.modules.clinical::tm_t_events`.
-  - Teal module for AE summary table by highest NCI-CTCAE grade - can be replaced with `teal.modules.clinical::tm_t_events_by_grade`.
+  - Teal module for `AE` overview summary table - can be replaced with `teal.modules.clinical::tm_t_events_summary`.
+  - Teal module for `AE` summary table by preferred terms - can be replaced with `teal.modules.clinical::tm_t_events`.
+  - Teal module for `AE` summary table by highest `NCI-CTCAE` grade - can be replaced with `teal.modules.clinical::tm_t_events_by_grade`.
   - Teal module for Disposition table - can be replaced with `teal.modules.clinical::tm_t_summary`.
 * Moved `code` argument to `cdisc_dataset` (from `cdisc_data`) in examples.
 
@@ -136,7 +136,7 @@
 
 *  Added new `teal` modules:
   - Teal module for events by term summary plot.
-  - Teal module for AE overview summary plot.
+  - Teal module for `AE` overview summary plot.
   - Teal module for patient profile plot
 
 # teal.osprey 0.1.4
@@ -163,10 +163,10 @@
 # teal.osprey 0.1.0
 
 * First versioned release of teal.osprey package, which include the following seven new functions to create `teal` modules for analysis functions in `osprey` v0.1.0:
-  - Teal module for AE overview summary table.
-  - Teal module for AE summary table by preferred terms.
-  - Teal module for AE summary table by highest NCI-CTCAE grade.
+  - Teal module for `AE` overview summary table.
+  - Teal module for `AE` summary table by preferred terms.
+  - Teal module for `AE` summary table by highest `NCI-CTCAE` grade.
   - Teal module for Disposition table.
-  - Teal module for AE butterfly plot.
-  - Teal module for Swimlane plot.
+  - Teal module for `AE` butterfly plot.
+  - Teal module for `Swimlane` plot.
   - Teal module for Spider plot.
diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R
@@ -1,9 +1,9 @@
-#' Teal module for the AE overview
+#' Teal module for the `AE` overview
 #'
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' Display the AE overview plot as a shiny module
+#' Display the `AE` overview plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention

diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R
@@ -1,9 +1,9 @@
-#' teal module for the AE by subgroups
+#' teal module for the `AE` by subgroups
 #'
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' Display the AE by subgroups plot as a teal module
+#' Display the `AE` by subgroups plot as a teal module
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention

diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R
@@ -29,7 +29,7 @@
 #'   \code{filter_var_choices} is expected to contain values of either "Y" or
 #'   "N". If multiple variables are selected as \code{filter_var}, only
 #'   observations with "Y" value in each and every selected variables will be
-#'   used for subsequent analysis. Flag variables (from ADaM datasets) can be
+#'   used for subsequent analysis. Flag variables (from `ADaM` datasets) can be
 #'   used directly as filter.
 #'
 #' @inherit argument_convention return

diff --git a/R/tm_g_decorate.R b/R/tm_g_decorate.R
@@ -85,7 +85,7 @@ srv_g_decorate <- function(id,
   })
 }
 
-#' Helper function to plot decorated output ui
+#' Helper function to plot decorated output UI
 #'
 #' @description
 #' `r lifecycle::badge("stable")`

diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R
@@ -23,7 +23,7 @@
 #'               leave unspecified or set to \code{NULL} if exposure data is not available
 #' @param ae_var (\code{choices_selected}) adverse event variable to plot as each line \cr
 #'               leave unspecified or set to \code{NULL} if adverse events data is not available
-#' @param ae_line_col_var (\code{choices_selected}) variable for coloring AE lines \cr
+#' @param ae_line_col_var (\code{choices_selected}) variable for coloring `AE` lines \cr
 #'                        leave unspecified or set to \code{NULL} if adverse events data is not available
 #' @param ae_line_col_opt aesthetic values to map color values
 #'                        (named vector to map color values to each name).

diff --git a/R/tm_g_swimlane.R b/R/tm_g_swimlane.R
@@ -1,14 +1,14 @@
-#' Teal Module for Swimlane Plot
+#' Teal Module for `Swimlane` Plot
 #'
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' This is teal module that generates a swimlane plot (bar plot with markers) for ADaM data
+#' This is teal module that generates a `swimlane` plot (bar plot with markers) for `ADaM` data
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
 #' @param dataname analysis data used for plotting, needs to be available in the list passed to the \code{data}
-#' argument of \code{\link[teal]{init}}. If no markers are to be plotted in the module, "ADSL" should be
+#' argument of \code{\link[teal]{init}}. If no markers are to be plotted in the module, `"ADSL"` should be
 #' the input. If markers are to be plotted, data name for the marker data should be the input
 #' @param bar_var (\code{\link[teal.transform]{choices_selected}}) subject-level numeric variable from dataset
 #' to plot as the bar length

diff --git a/R/tm_g_waterfall.R b/R/tm_g_waterfall.R
@@ -3,7 +3,7 @@
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' This is teal module that generates a waterfall plot for ADaM data
+#' This is teal module that generates a waterfall plot for `ADaM` data
 #'
 #' @inheritParams teal.widgets::standard_layout
 #' @inheritParams argument_convention
@@ -13,7 +13,7 @@
 #' be available in the list passed to the \code{data} argument of \code{\link[teal]{init}}
 #' @param bar_paramcd (\code{choices_selected}) parameter in tumor burden data that will be plotted as
 #' bar height
-#' @param bar_var (\code{choices_selected}) numeric variable from dataset to plot the bar height, e.g., PCHG
+#' @param bar_var (\code{choices_selected}) numeric variable from dataset to plot the bar height, e.g., `PCHG`
 #' @param bar_color_var (\code{choices_selected}) color by variable (subject level), \code{None} corresponds
 #' to \code{NULL}
 #' @param bar_color_opt aesthetic values to map color values (named vector to map color values to each name).

diff --git a/R/utils.R b/R/utils.R
@@ -8,7 +8,7 @@
 #' @param plot_width optional, (\code{numeric}) a vector of length three with \code{c(value, min, max)}. Specifies
 #'   the width of the main plot and renders a slider on the plot to interactively adjust the plot width.
 #' @param label (\code{character}) module label in the teal app. Please note that this module is developed based on
-#' ADaM data structure and ADaM variables.
+#' `ADaM` data structure and `ADaM` variables.
 #'
 #' @name shared_params
 #' @keywords internal
@@ -35,7 +35,7 @@ quick_filter <- function(filter_opt, ANL) { # nolint
   return(ANL)
 }
 
-#' Automatically switch variable labels for standard AE variables in AE osprey functions
+#' Automatically switch variable labels for standard `AE` variables in `AE` osprey functions
 #' `r lifecycle::badge("stable")`
 #'
 #' @param x variable key

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/teal.osprey/_xml_coverage_reports/data/main/badge.svg)](https://insightsengineering.github.io/teal.osprey/main/coverage-report/)
 
 ![GitHub forks](https://img.shields.io/github/forks/insightsengineering/teal.osprey?style=social)
-![GitHub Repo stars](https://img.shields.io/github/stars/insightsengineering/teal.osprey?style=social)
+![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/teal.osprey?style=social)
 
 ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/teal.osprey)
 ![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/teal.osprey)
@@ -26,7 +26,7 @@ This enables `teal` app developers to easily create applications making use of t
 
 ## Installation
 
-For releases from August 2022 it is recommended that you [create and use a Github PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following:
+For releases from August 2022 it is recommended that you [create and use a GitHub PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following:
 
 ```r
 Sys.setenv(GITHUB_PAT = "your_access_token_here")

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,15 +1,6 @@
-ADSL
-ADaM
-AE
-CTCAE
 Forkers
-Github
 Hou
 Lil
-NCI
-PCHG
-Repo
-Swimlane
 TLG
 TLGs
 UI
@@ -23,6 +14,4 @@ lil
 pre
 qit
 repo
-swimlane
-ui
 zhanc
diff --git a/man/label_aevar.Rd b/man/label_aevar.Rd
diff --git a/man/plot_decorate_output.Rd b/man/plot_decorate_output.Rd
diff --git a/man/shared_params.Rd b/man/shared_params.Rd
diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd
diff --git a/man/tm_g_ae_sub.Rd b/man/tm_g_ae_sub.Rd
diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd
diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd
diff --git a/man/tm_g_swimlane.Rd b/man/tm_g_swimlane.Rd
diff --git a/man/tm_g_waterfall.Rd b/man/tm_g_waterfall.Rd