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R Markdown Analysis With Example
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--- | |
title: "your_title_goes_here" | |
author: "your_name_goes_here" | |
date: "`r Sys.Date()`" | |
output: | |
bookdown::html_document2: | |
number_sections: false | |
bibliography: [references.bib, packages.bib] | |
csl: the-new-england-journal-of-medicine.csl | |
--- | |
```{r setup, echo=FALSE} | |
knitr::opts_chunk$set( | |
########## set global options ############ | |
echo = FALSE, # don't show code | |
collapse = TRUE, # keep code from blocks together (if shown) | |
message = TRUE, # show messages | |
warning = TRUE, # show warnings | |
error = TRUE, # show error messages | |
comment = "", # don't show ## with printed output | |
dpi = 100, # image resolution (typically 300 for publication) | |
fig.width = 6.5, # figure width | |
fig.height = 4.0 # figure height | |
) | |
# R's default rounding is to show 7 digits. This rounds results to 3 digits. | |
options(digits = 3) | |
``` | |
```{r tidyverse-tidymodels, echo=FALSE} | |
library(conflicted) | |
suppressPackageStartupMessages(library(tidymodels)) | |
tidymodels_prefer() | |
suppressPackageStartupMessages(library(tidyverse)) | |
# suppress "`summarise()` has grouped output by " messages | |
options(dplyr.summarise.inform = FALSE) | |
``` | |
```{r other-packages} | |
library(glue) # for glue() | |
library(rUM) # needed for the bibliography to include the package | |
library(rio) # for import() | |
# gtsummary for tbl_summary(), add_n(), add_p(), modify_header(), bold_labels() | |
suppressPackageStartupMessages(library(gtsummary)) | |
``` | |
```{r load-data} | |
# If you want to import a dataset which is not an R file, put its name inside | |
# the "" below. For example: | |
# raw_data <- import("the_excel.xlsx") | |
# If your datasets is an Excel file saved in the data folder, add a path like: | |
# raw_data <- import("data/the_excel.xlsx") | |
``` | |
```{r make-analysis} | |
# preprocess your data and ultimately make a dataset called analysis | |
analysis <- mtcars |> | |
mutate(auto_man = if_else(am == 0, "Automatic", "Manual")) |> | |
select(mpg, auto_man) | |
``` | |
# Abstract | |
# Introduction | |
# Methods | |
Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `gtsummary` (`r packageVersion("gtsummary")`) packages used to preprocess and summarize data. [@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-gtsummary] | |
# Results | |
```{r table-1} | |
# To learn how to use tbl_summary look https://www.danieldsjoberg.com/gtsummary/ | |
analysis |> | |
tbl_summary( | |
include = c(everything()), # choose your variables here | |
# change auto_man to the name of your column variable or delete by = auto_man | |
by = auto_man, # split table by group | |
missing = "no" # don't list missing data separately | |
) %>% | |
# add_n() %>% # add column with total number of non-missing observations | |
# add_p() %>% # test for a difference between groups | |
modify_header(label = "") %>% # update the column header to be blank | |
bold_labels() |> | |
modify_caption( | |
"Cross references to tables start with tab: then the code chunk label." | |
) | |
``` | |
As can be seen in Table \@ref(tab:table-1) or [Table 1](#tab:table-1) | |
```{r figure1} | |
#| fig.cap: "Your real caption belongs here. Remember figure references begin with #fig:" | |
# To learn how to use ggplot start here: https://ggplot2.tidyverse.org/#learning-ggplot2 | |
analysis |> | |
ggplot() + | |
labs( | |
title = "Your short title goes here.", | |
caption = "Your data sources/citation goes here." | |
) + | |
geom_blank() | |
# remove geom_blank() and add details here | |
``` | |
See Figure \@ref(fig:figure1) or [Figure 1](#fig:figure1) | |
# Discussion | |
# References {-} | |
```{r include=FALSE} | |
# automatically create a bib database for loaded R packages & rUM | |
knitr::write_bib( | |
c( | |
.packages(), | |
"rUM" | |
), | |
"packages.bib" | |
) | |
``` |
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add figure width and hight and DPI. Tweaked figure caption message