insightsengineering · m7pr · Jun 30, 2023 · Jun 30, 2023 · Jun 30, 2023 · Jun 30, 2023
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -27,6 +27,7 @@ jobs:
     with:
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
+        _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10
         NOT_CRAN=true
       additional-r-cmd-check-params: --as-cran
   coverage:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,6 +53,7 @@ Imports:
     teal.widgets (>= 0.2.0),
     tern (>= 0.7.10)
 Suggests:
+    BiocStyle,
     covr,
     dplyr,
     globals,

diff --git a/NEWS.md b/NEWS.md
@@ -21,7 +21,7 @@
 * Rewrote modules to use `moduleServer` and updated call to `plot_with_settings_srv` after changes in `teal.devel`.
 * Replaced calls to `teal::root_modules` with `teal::modules` following deprecation of `teal::root_modules`.
 * Added basic logging to the modules.
-* Fixed the `geneSpecInput` so that the hermes app doesn't fail anymore (on chrome) on an experiment with no genes.
+* Fixed the `geneSpecInput` so that the `hermes` app doesn't fail anymore (on chrome) on an experiment with no genes.
 
 # teal.modules.hermes 0.1.1
 

diff --git a/R/adtteSpec.R b/R/adtteSpec.R
@@ -1,4 +1,4 @@
-#' Data Preprocessing for ADTTE Module
+#' Data Preprocessing for `ADTTE` Module
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
@@ -88,11 +88,11 @@ h_km_mae_to_adtte <- function(adtte,
   )
 }
 
-#' Module Input for ADTTE Specification
+#' Module Input for `ADTTE` Specification
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
-#' This defines the input for the ADTTE specification.
+#' This defines the input for the `ADTTE` specification.
 #'
 #' @inheritParams module_arguments
 #' @param label_paramcd (`string`)\cr label for the endpoint (`PARAMCD`) selection.
@@ -114,12 +114,12 @@ adtteSpecInput <- function(inputId, # nolint
   )
 }
 
-#' Module Server for ADTTE Specification
+#' Module Server for `ADTTE` Specification
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
-#' This defines the server part for the ADTTE specification. The resulting data
-#' set `binned_adtte_subset` contains the subset of ADTTE selected by the time-to-event
+#' This defines the server part for the `ADTTE` specification. The resulting data
+#' set `binned_adtte_subset` contains the subset of `ADTTE` selected by the time-to-event
 #' endpoint, joined together with the gene information extracted from specified assay
 #' and experiment, as numeric and factor columns. The factor column is created by binning
 #' the numeric column according to the quantile cutoffs specified in `probs`.
@@ -133,7 +133,7 @@ adtteSpecInput <- function(inputId, # nolint
 #'   into.
 #'
 #' @return List with the following elements:
-#'   - `binned_adtte_subset`: reactive containing the joined ADTTE and gene data.
+#'   - `binned_adtte_subset`: reactive containing the joined `ADTTE` and gene data.
 #'   - `gene_col`: reactive containing the string with the column name of the original
 #'        numeric gene variable.
 #'   - `gene_factor`: string with the variable name for the binned gene data.

diff --git a/R/argument_convention.R b/R/argument_convention.R
@@ -13,9 +13,9 @@
 #' @param inputId (`string`)\cr
 #'   the ID used to call the module input.
 #' @param adtte_name (`string`)\cr
-#'   name of the ADTTE dataset.
+#'   name of the `ADTTE` dataset.
 #' @param adtte_vars (named `list` of `string`)\cr
-#'   names of the variables to use in the ADTTE dataset. It should comprise elements:
+#'   names of the variables to use in the `ADTTE` dataset. It should comprise elements:
 #'   - `aval`: the numeric time-to-event variable.
 #'   - `avalu`: the variable holding the unit of `aval`.
 #'   - `is_event`: the logical event variable. It needs to be `TRUE`
@@ -63,7 +63,7 @@ NULL
 #' @param add (`AssertCollection` or `NULL`)\cr collection to store
 #'   assertion messages, see [`checkmate::AssertCollection`].
 #' @param info (`string`)\cr extra information to be included in the
-#'   message for the testthat reporter, see [testthat::expect_that()].
+#'   message for the `testthat` reporter, see [testthat::expect_that()].
 #' @param label (`string`)\cr name of the checked object to print in
 #'   messages. Defaults to the heuristic implemented in [checkmate::vname()].
 #'

diff --git a/R/checkmate.R b/R/checkmate.R
@@ -120,11 +120,11 @@ assert_summary_funs <- function(x, null.ok = FALSE) { # nolint
 
 # assert_adtte_vars ----
 
-#' Check for ADTTE Variables
+#' Check for `ADTTE` Variables
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
-#' Check whether `x` is a list of ADTTE variables.
+#' Check whether `x` is a list of `ADTTE` variables.
 #'
 #' @inheritParams assertion_arguments
 #' @seealso [`assertions`] for more details.

diff --git a/R/km.R b/R/km.R
@@ -3,7 +3,7 @@
 #' @description `r lifecycle::badge("experimental")`
 #'
 #' This teal module produces a grid style Kaplan-Meier plot for data with
-#' ADaM structure.
+#' `ADaM` structure.
 #'
 #' @inheritParams module_arguments
 #'

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 [![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/coverage.xml)
 
 ![GitHub forks](https://img.shields.io/github/forks/insightsengineering/teal.modules.hermes?style=social)
-![GitHub Repo stars](https://img.shields.io/github/stars/insightsengineering/teal.modules.hermes?style=social)
+![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/teal.modules.hermes?style=social)
 
 ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/teal.modules.hermes)
 ![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/teal.modules.hermes)
@@ -24,21 +24,21 @@
 ### What is `teal`?
 
 `teal` is a shiny-based interactive exploration framework for analyzing clinical trials data. `teal` currently provides a dynamic filtering facility and diverse data viewers. `teal` shiny applications are built using standard [shiny modules](https://shiny.rstudio.com/articles/modules.html).
-See [github](https://insightsengineering.github.io/teal) for more details.
+See [`teal` page](https://insightsengineering.github.io/teal) for more details.
 
 ### What is `hermes`?
 
 `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data.
-The core functionality is built on the BioConductor ecosystem, especially the `SummarizedExperiment` class from which the `HermesData` class inherits.
+The core functionality is built on the `BioConductor` ecosystem, especially the `SummarizedExperiment` class from which the `HermesData` class inherits.
 See the [vignette](https://insightsengineering.github.io/hermes/articles/hermes.html) for more details.
 
 ### So what is then `teal.modules.hermes`?
 
-`teal.modules.hermes` provides `teal` modules (which can be used as part of any `teal` app), for interactive RNA-seq data analysis using `hermes`. Again it is heavily built on the BioConductor classes, in particular `MultiAssayExperiment` (MAE) which is expected to contain the `HermesData` experiments.
+`teal.modules.hermes` provides `teal` modules (which can be used as part of any `teal` app), for interactive RNA-seq data analysis using `hermes`. Again it is heavily built on the `BioConductor` classes, in particular `MultiAssayExperiment` (MAE) which is expected to contain the `HermesData` experiments.
 
 ## 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
@@ -1,22 +1,14 @@
-ADTTE
-ADaM
-BioConductor
 Bové
 Forkers
-Github
-hoc
 Hoffmann
 Kaplan
 Lyndsee
 Midori
 RNAseq
-Repo
 Sabanés
 UI
 funder
-github
 hermes
 pre
 reactives
 repo
-testthat
diff --git a/man/adtteSpecInput.Rd b/man/adtteSpecInput.Rd
diff --git a/man/adtteSpecServer.Rd b/man/adtteSpecServer.Rd
diff --git a/man/assert_adtte_vars.Rd b/man/assert_adtte_vars.Rd
diff --git a/man/assertion_arguments.Rd b/man/assertion_arguments.Rd
diff --git a/man/check_tag.Rd b/man/check_tag.Rd
diff --git a/man/h_km_mae_to_adtte.Rd b/man/h_km_mae_to_adtte.Rd
diff --git a/man/module_arguments.Rd b/man/module_arguments.Rd
diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd
diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd
diff --git a/tests/testthat/setup-skip_if_too_deep.R b/tests/testthat/setup-skip_if_too_deep.R
@@ -22,7 +22,7 @@ testing_depth <- function() { # nolint # nousage
   testing_depth
 }
 
-#' Skipping tests in the testthat pipeline under specific scope
+#' Skipping tests in the `testthat` pipeline under specific scope
 #' @description This function should be used per each \code{testthat::test_that} call.
 #'   Each of the call should specify an appropriate depth value.
 #'   The depth value will set the appropriate scope so more/less time consuming tests could be recognized.