Quarto Analysis with Examples

analysis_with_example.qmd

---
title: "your_title_goes_here"
author: "your_name_goes_here"
date: last-modified
format:
  html:
    self-contained: true
knitr:
  opts_chunk:        ############ set global options ############
    collapse: true   # keep code from blocks together (if shown)
    echo: false      # don't show code
    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.options:    
      digits: 3    # round to three digits
editor: visual
bibliography: [references.bib, packages.bib]
csl: the-new-england-journal-of-medicine.csl
---

```{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
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 tbl-table1}
#| tbl-cap: |
#|   Your real caption belongs here.  Remember that cross references to tables 
#|   use labels for the code chunk starting with tbl-.

# 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()
```

As can be seen in @tbl-table1 ....

```{r fig-figure-1}
#| fig-cap: |
#|   Your real caption belongs here.  Remember that cross references to figures 
#|   use labels for the code chunk starting 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
```

As can be seen in @fig-figure-1 ...

# Discussion

# References {.unnumbered}

```{r}
#| include: false

# automatically create a bib database for loaded R packages & rUM
knitr::write_bib(
  c(
    .packages(),
    "rUM"
  ),
  "packages.bib"
)
```

move labels into {r}

improve load-data block

change date to last-modified, drop table1, add learn more, change ggplot

drop library(table1)

change label on make-analysis code block

change fig and tab caption advice, add fig size and dpi