In ddsjoberg/bstfun: Functions for the MSK Biostatistics Department

# set chunk defaults
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
set.seed({{format(Sys.Date(), format = "%Y%m%d")}})

knitr::opts_chunk$set(fig.width=8, fig.height=10)

library(biostatR)
library(tidyverse)
library(captioner)

# 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_master <-
  readRDS(
    file = here::here(path_data, "df_master.Rds")
  )

# Import analysis result objects here
load(here::here(path_data,"020-analysis.RData"))

# define complex inline-reporting objects here

## Setting up Table and Fig numberings ------------------
tbl_cap = captioner(prefix = "Table")
fig_cap = captioner(prefix = "Figure")

## table captions --------------
  tbl_cap("tab_table1", "Patient Characteristics")

## figure captions ------------------------------------
  fig_cap("fig_ROCgrade", "Grade ROC")

## To refer to table/fig in the text ------------------------------------
  # Function to reference table in text
  f.ref <- function(x) {
    stringr::str_extract(tbl_cap(x), "[^:]*")
  }
  # example: **`r table_nums("tab_table1", display = "cite")`**

  # Function to reference figure in text
  f.ref.fig <- function(x) {
    stringr::str_extract(fig_cap(x), "[^:]*")
  }
  # example: **`r f.ref("fig_ROCgrade")`**