#### Global chunk options ----------------------------- knitr::opts_chunk$set( eval = TRUE, # whether to run code in code chunk include = TRUE, # whether to include the chunk output echo = FALSE, # Whether to show code chunk in final output error = TRUE, # whether to display error messages message = FALSE, # whether to preserve messages warning = FALSE, # whether to preserve warnings comment = NA, # a character string to append at start of each line of # results in final document tidy = FALSE, # whether to tidy code chunks for display dpi = 96, # dots per inch in graphics when applicable fig.width = 8, # consistent width for figures fig.asp = 0.618, # the golden ratio, can be adjusted in individual chunks out.width = "90%", # controls the output size fig.align = "center", # give plot room to breathe # fig.path = "figures/somedir/" # file path to store plots R.options = list(width = 70), NULL ) #### Other options -------------------------------- ## Width for code chunks ---------------- options(width = 120) ## Scientific notation --------------- # Find out what it is set to # getOption("scipen") # Turn off scientific notation options(scipen = 999) ## define format ---------------- # If you don't define format here, you'll need put `format = "html"` in # every kable function. options(knitr.table.format = "html") # use this option when knitting html # options(knitr.table.format = "latex") # use this option when knitting pdf ## Options for printing and saving ---------------- # Use these with if statements later on to control whether files or plots get # saved/re-written. Basically, a safety measure. save_plots <- TRUE write_files <- TRUE #### Packages -------------------------------------- # Load the packages to be used. ## Define the repository for packages ---------------- options(repos = c(CRAN = "https://cran.rstudio.com")) ## universally useful packages ---------------- # if (!require("pacman")) {install.packages("pacman")} # if (!require("devtools")) {install.packages("devtools")} ## github packages ---------------- # if (!require("lamisc")) {devtools::install_github("emilelatour/lamisc")} ## Load the list of packages ---------------- pacman::p_load( Hmisc, # contains many functions useful for data analysis psych, # a general purpose toolbox tidyverse, # packages ggplot2, tibble, tidyr, readr, purrr, and dplyr forcats, # functions for factors, forcats is an anagram for factors broom, # functions tidy(), glance(), augment() magrittr, # includes the %<>% assignment-pipe (%>% is loaded from dplyr) rlang, # For use in tidyevaluation readxl, # read in excel files writexl, # write excel files, zero dependency # xlsx, # read, write, format Excel files openxlsx, # read, write and edit XLSX files janitor, # for working with dirty data lubridate, # for working with dates and times stringr, # handy string operations tableone, # Create Table 1 to Describe Baseline Characteristics labelled, # Work with labelled data mice, # Multivariate Imputation by Chained Equations DT, # render R objects as HTML tables knitr, # A General-Purpose Package for Dynamic Report Generation in R kableExtra, # Enahced table functions flextable, # easily create tables for reporting and publications officer, # Used by flextable formattable, # Create formattable vectors and data frames extrafont, # Tools for using fonts ggthemes, # Extra Themes, Scales and Geoms for 'ggplot2' ggsci, # Scientific journal themed color palettes for 'ggplot2' gt, # information-rich, publication-quality tables from R scales, # Scale Functions for Visualization survival, # core survival analysis routines survminer, # drawing survival curves humaniformat, # a parser for human names hrbrthemes, # ggplot themes visdat, # Preliminary data visualisation naniar, # structures, summaries, and visualisations for missing data here, # Constructs paths to your project's files glue, # Glue strings to data in R fs, # Cross-platform interface to file system operations varhandle, # Functions for robust variable handling rel, # reliability coefficients irr, # reliability and agreement coefficients vcd, # visualizing categorical data install = FALSE ) #### Other packages ----------------------------- library(lamisc) # devtools::install_github("emilelatour/lamisc") library(latable) # devtools::install_github("emilelatour/latable") library(laviz) # devtools::install_github("emilelatour/laviz") library(purposeful) # devtools::install_github("emilelatour/purposeful") library(redcaptools) # devtools::install_github("emilelatour/redcaptools") #### Some resources --------------------------- #### Themes and colors ------------------------------- #### Load fonts -------------------------------- # extrafont::fonts() # Vector of font family names # extrafont::fonttable() # Show entire table # extrafont::font_import() # imports fonts installed on the system extrafont::loadfonts(device = "pdf", quiet = TRUE)
devtools::session_info()
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