In ddsjoberg/bstfun: Functions for the MSK Biostatistics Department

knitr::opts_chunk$set(echo = TRUE)

set.seed({{format(Sys.Date(), format = "%Y%m%d")}})

Analytic Data Import

library(biostatR)
library(tidyverse)

# setting MSK ggplot theme and color palette
theme_set(mskRvis::theme_biostat())
mskRvis::set_msk_palette()
{{(ifelse(tolower(Sys.info()[["user"]]) %in% eval(as.list(bstfun::theme_gtsummary_msk)$name), glue::glue("
# Set custom gtsummary theme if exists in the bstfun::theme_gtsummary_msk
bstfun::theme_gtsummary_msk('{tolower(Sys.info()[['user']])}')
"), ""))}}
# importing master analytic data set
df_main <- readRDS(file = here_data("df_main.Rds"))

gt theme

my_theme <- list(
  "pkgwide-fn:pvalue_fun" = function(x) gtsummary::style_pvalue(x, digits = 2),
  "pkgwide-fn:prependpvalue_fun" = function(x) gtsummary::style_pvalue(x, digits = 2, prepend_p = TRUE),
  "tbl_summary-fn:percent_fun" = function(x) paste0(round(x*100)),
  "tbl_summary-str:categorical_stat" = "{n} ({p}%)",
  "tbl_summary-str:continuous_stat" = "{median} [{min} \U2013 {max}]",
  "tbl_summary-arg:missing_text" = "Missing"
)
set_gtsummary_theme(my_theme)

Analysis

Save results

# list result objects here. save only those needed for the final report
save(object,
     file = here::here(path_data,"020-analysis.RData"))

ddsjoberg/bstfun documentation built on June 1, 2024, 11:46 p.m.