knitr::opts_chunk$set(echo = TRUE) set.seed({{format(Sys.Date(), format = "%Y%m%d")}})
library(biostatR) library(tidyverse) library(here) library(styler) library(labelled) library(xlsx) {{(ifelse(tolower(Sys.info()[["user"]]) %in% eval(as.list(bstfun::theme_gtsummary_msk)$name), glue::glue(" # Set custom gtsummary theme if exists in the bstfun::theme_gtsummary_msk bstfun::theme_gtsummary_msk('{tolower(Sys.info()[['user']])}') "), ""))}} # example code for importing excel file df_raw_data <- readxl::read_excel( path = here_data("Raw Data from PI.xlsx") ) %>% janitor::clean_names(case = "all_caps") %>% # uppercase col names mutate(across(where(lubridate::is.POSIXt), lubridate::as_date)) %>% # use lubridates mutate_if(is.logical, as.numeric)
# Import data dictionary df_dict <- readxl::read_excel( path = here::here("secure_data", "_data-dictionary.xlsx") ) # Only include variables in the datasets that I want to label vars_tolabel <- colnames(df_drvd) df_dict_tolabel <- df_dict %>% filter(variable %in% vars_tolabel) # Create label lists label_list <- as.list(df_dict_tolabel$label) names(label_list) <- as.list(df_dict_tolabel$variable) # Apply labels to analytic datasets labelled::var_label(df_drvd) <- label_list
# overview of master analytic dataset skimr::skim(df_master) # saving master analytic data set saveRDS( object = df_drvd, file = here::here(path_data, "df_master.Rds") )
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