From 44380c09d38812d301d06f2d0281499ba6c71516 Mon Sep 17 00:00:00 2001 From: "Stock,Dr.,Christian (MED BDS) BIP-DE-I" Date: Sat, 7 Oct 2023 15:28:53 +0200 Subject: [PATCH] Addressed formatting issues from lintr::lint_package() --- R/brm_package.R | 4 +- vignettes/comparison.Rmd | 95 +++++++++++++++++++++++----------------- 2 files changed, 56 insertions(+), 43 deletions(-) diff --git a/R/brm_package.R b/R/brm_package.R index 2e385e9e..6aca7fcc 100644 --- a/R/brm_package.R +++ b/R/brm_package.R @@ -18,8 +18,8 @@ #' in Longitudinal Clinical Trials. #' Ther Innov Regul Sci, 42, 303–319. #' doi:10.1177/009286150804200402 -#' * Mallinckrodt C and Lipkovich I (2017). Analyzing Longitudinal Trial Data -- -#' A Practical Guide. Chapman `&` Hall/ CRC Biostatistics Series. +#' * Mallinckrodt C and Lipkovich I (2017). Analyzing Longitudinal Trial +#' Data -- A Practical Guide. Chapman `&` Hall/ CRC Biostatistics Series. #' @family help #' @importFrom brms brm brmsformula get_prior prior unstr #' @importFrom coda as.mcmc diff --git a/vignettes/comparison.Rmd b/vignettes/comparison.Rmd index 62d5667c..5b6bf4ab 100644 --- a/vignettes/comparison.Rmd +++ b/vignettes/comparison.Rmd @@ -18,15 +18,23 @@ editor_options: wrap: 72 --- -```{r setup, eval=T, include=F, warning=F, message=F} +```{r setup, eval=TRUE, include=FALSE, warning=FALSE, message=FALSE} rm(list = ls()) library(knitr) -knitr::opts_chunk$set( - echo = T, collapse = T, warning = F, message = F, - prompt = T, comment = NA, size = "scriptsize", - fig.height = 5, fig.width = 6, dpi = 320, - fig.align = "center", fig.path="figures/" - ) +knitr::opts_chunk$set( + echo = TRUE, + collapse = TRUE, + warning = FALSE, + message = FALSE, + prompt = TRUE, + comment = NA, + size = "scriptsize", + fig.height = 5, + fig.width = 6, + dpi = 320, + fig.align = "center", + fig.path = "figures/" +) ``` # About {.unnumbered} @@ -37,32 +45,29 @@ This vignette provides an exemplary comparison of Bayesian MMRM fits, obtained b Load general packages: -```{r load_gen_pkgs, eval=T, echo=T, class.source = NULL} +```{r load_gen_pkgs, eval=TRUE, echo=TRUE, class.source = NULL} packages <- c("tidyr", "dplyr", "tibble", "ggplot2", "gt", "gtsummary") -invisible(lapply(packages, library, character.only = T)) +invisible(lapply(packages, library, character.only = TRUE)) ``` Load packages providing example datasets: -```{r load_dat_pkgs, eval=T, echo=T, class.source = NULL} +```{r load_dat_pkgs, eval=TRUE, echo=TRUE, class.source = NULL} library("Hmisc") library("HSAUR3") ``` Load MMRM packages: -```{r load_mmrm_pkgs, eval=T, echo=T, class.source = NULL} -#if (!require("remotes")) {install.packages("remotes")} -#remotes::install_github("openpharma/brms.mmrm") +```{r load_mmrm_pkgs, eval=TRUE, echo=TRUE, class.source = NULL} library(brms.mmrm) -#remotes::install_github("openpharma/mmrm") library(mmrm) library(emmeans) ``` Set seed: -```{r set_seed, eval=T, echo=T, class.source = NULL} +```{r set_seed, eval=TRUE, echo=TRUE, class.source = NULL} set.seed(123L) ``` @@ -80,14 +85,17 @@ TWSTRS-total scores from 109 patients with cervical dystonia: First 35 subjects ## Data pre-processing -```{r cdystonia1, eval=T, echo=T, class.source = NULL} +```{r cdystonia1, eval=TRUE, echo=TRUE, class.source = NULL} Hmisc::getHdata(cdystonia) cdystonia1 <- cdystonia |> dplyr::filter(treat %in% c("10000U", "Placebo")) |> # restrict to two arms droplevels() |> - dplyr::mutate_all(~{attr(., "label") <- NULL; .})|> + dplyr::mutate_all(~ { + attr(., "label") <- NULL + . + }) |> dplyr::mutate( - week = paste0("w", sprintf("%02d", week)), + week = paste0("w", sprintf("%02d", week)), id = paste0(site, "-", sprintf("%02d", id)) ) |> dplyr::select(-c(site)) |> @@ -106,49 +114,54 @@ cdystonia1 <- cdystonia |> dplyr::filter(!is.na(delta)) ``` -```{r cdystonia2, eval=T, echo=T, class.source = NULL} +```{r cdystonia2, eval=TRUE, echo=TRUE, class.source = NULL} head(cdystonia1) |> gt::gt() ``` ## Descriptive statistics -```{r cdystonia3a, eval=T, echo=T, class.source = 'fold-hide'} -cdystonia1 |> dplyr::select(treat, age, sex, baseline) |> +```{r cdystonia3a, eval=TRUE, echo=TRUE, class.source = 'fold-hide'} +cdystonia1 |> + dplyr::select(treat, age, sex, baseline) |> dplyr::distinct() |> gtsummary::tbl_summary( - by = c(treat), + by = c(treat), statistic = list( all_continuous() ~ "{mean} ({sd})", - all_categorical() ~ "{n} / {N} ({p}%)") - ) |> + all_categorical() ~ "{n} / {N} ({p}%)" + ) + ) |> gtsummary::modify_caption("**Baseline characteristics.**") ``` -```{r cdystonia3b, eval=T, echo=T, class.source = 'fold-hide'} -unique(cdystonia1$week) |> sort() |> +```{r cdystonia3b, eval=TRUE, echo=TRUE, class.source = 'fold-hide'} +unique(cdystonia1$week) |> + sort() |> purrr::map( .f = ~ cdystonia1 |> - dplyr::filter(week %in% .x)|> + dplyr::filter(week %in% .x) |> gtsummary::tbl_summary( - by = treat, + by = treat, include = delta, type = delta ~ "continuous2", - statistic = delta ~ c("{mean} ({sd})", "{median} ({p25}, {p75})", "{min}, {max}"), + statistic = delta ~ c("{mean} ({sd})", + "{median} ({p25}, {p75})", + "{min}, {max}"), label = list(delta = paste("Visit ", .x)) - ) - ) |> - gtsummary::tbl_stack(quiet = T) |> + ) + ) |> + gtsummary::tbl_stack(quiet = TRUE) |> gtsummary::modify_caption("**Change from baseline in total TWSTRS score.**") ``` -```{r cdystonia_boxpl, eval=T, echo=T, fig.align='center', out.width="75%", fig.dim = c(8, 5), fig.fig.keep='all', fig.pos="!ht", fig.cap="Change from baseline in total TWSTRS score"} -cdystonia1 |> dplyr::group_by(treat) |> +```{r cdystonia_boxpl, eval=TRUE, echo=TRUE, fig.align='center', out.width="75%", fig.dim = c(8, 5), fig.fig.keep='all', fig.pos="!ht", fig.cap="Change from baseline in total TWSTRS score"} +cdystonia1 |> + dplyr::group_by(treat) |> ggplot2::ggplot(aes(x = week, y = delta, fill = factor(treat))) + - ggplot2::geom_boxplot() + - ggplot2::labs( - x = "Visit", - y = "Change from baseline in total TWSTRS score", - fill = "Treatment" ) + + ggplot2::geom_boxplot() + + ggplot2::labs(x = "Visit", + y = "Change from baseline in total TWSTRS score", + fill = "Treatment") + ggplot2::theme_bw() ``` @@ -157,7 +170,7 @@ cdystonia1 |> dplyr::group_by(treat) |> ### Function `mmrm::mmrm()` -```{r cdystonia4a, eval=T, echo=T, class.source = 'fold-hide'} +```{r cdystonia4a, eval=TRUE, echo=TRUE, class.source = 'fold-hide'} cdystonia2 <- cdystonia1 |> dplyr::mutate( treat = factor(treat), @@ -220,6 +233,6 @@ summary(cdystonia_mmrm) ## Session info {.unnumbered} -```{r citation_session, echo=T, eval=T, message=F} +```{r citation_session, echo=TRUE, eval=TRUE, message=FALSE} sessionInfo() ```