prettypublisher

prettypublisher is an R package that aims to improve your workflow by allowing an easier transition from literate code to a paper draft ready for journal submission. The core functionality is a set of functions that aim to speed up the reporting of descriptive statistics and effect estimates. It also wraps the captioner package for figure and table referencing, although you may want to use the functionality provided by bookdown. Finally a simple interface is provided for both pander::pandoc.table and knitr::kable, with some additional features to speed up post production table editing in word, although hopefully this functionality will become redundant as packages provide improved table functionality in word.

Installation

You can install prettypublisher from GitHub with:

# install.packages("devtools")
devtools::install_github("seabbs/prettypublisher")

At this time there are no plans to publish prettypublisher to CRAN as some package functionality (for example pretty_captioner) adds a captioning function to the users workspace, which is not allowed by CRAN.

Quick start.

Whilst examples are provided for each function (see here for a list of functions included in the package) the following example, using the iris data-set, outlines some of the functionality the package provides.

Load the dplyr for data manipulation, knitr for tables, broom for model manipulation and prettypublisher.

library(prettypublisher)
library(dplyr)
library(knitr)
library(broom) 

Show the first several rows of the data.

head(iris)
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1          5.1         3.5          1.4         0.2  setosa
#> 2          4.9         3.0          1.4         0.2  setosa
#> 3          4.7         3.2          1.3         0.2  setosa
#> 4          4.6         3.1          1.5         0.2  setosa
#> 5          5.0         3.6          1.4         0.2  setosa
#> 6          5.4         3.9          1.7         0.4  setosa

Add some summary statistics for the number of species, make into a table, and add a caption with a reference (table 1).

iris %>% 
  count(Species) %>% 
  add_count(wt = n) %>% 
  group_by(Species) %>% 
  mutate(per_species = pretty_percentage(n, nn, digits = 1)) %>% 
  select(-nn) %>% 
  pretty_table(label = "per-species",
               col_names = c("Species", "Number of samples", "Proportion of total (%)"),
               caption = "Breakdown of the number of samples per Species in the iris data-set",
               tab_fun = kable)

Table 1: Breakdown of the number of samples per Species in the iris data-set

Species	Number of samples	Proportion of total (%)
setosa	50	33.3% (50/150)
versicolor	50	33.3% (50/150)
virginica	50	33.3% (50/150)

Estimate the association between Species (limiting the data to setosa and versicolor) and sepal length using logistic regression.

iris_model <- glm(Species ~ Sepal.Length, 
                  data = filter(iris, Species %in% c("setosa", "versicolor")),
                  family = binomial("logit"),
                  na.action = na.exclude)

or_df <- iris_model %>% 
  tidy(conf.int = TRUE, 
       conf.level = 0.95,
       exponentiate = TRUE) %>% 
  mutate(or = pretty_ci(estimate, conf.low, conf.high)) %>%
  mutate(per_effect = pretty_per_effect(estimate, conf.low, conf.high)) %>% 
  mutate(p_value = format(p.value, digits = 3, scientific = TRUE)) %>% 
  select(term, or, per_effect, p_value) %>% 
  slice(-1) 

or_df %>% 
  pretty_table(label = "glm",
               caption = "Results table for the association between Species and Sepal length.",
               col_names = c("Variable", "OR", "Percentage Effect (%)", "P value"))

Table 2: Results table for the association between Species and Sepal length.

Variable	OR	Percentage Effect (%)	P value
Sepal.Length	170.77 (30.62 to 1661.55)	16977% (2962% to 166055%)	3.28e-07

Table 2 shows commonly reported summary statistics for logistic regressions. For use in line we can also add additional information as follows;

pretty_inline_ci(or_df$or)
#> [1] "170.77 (95% CI 30.62 to 1661.55)"

Additional Features

This package is a work in progress, although the core features and arguements will remain fixed. Additional functions will be added as I find that they are required in my academic work. If there are functions that fit the package aims, that you use regularly when formatting analysis, then please consider adding them to the package via a pull request.

Docker Development Enviroment

This package has been developed in docker based on the rocker/tidyverse image, to access the development environment enter the following at the command line (with an active docker daemon running),

docker pull seabbs/prettypublisher
docker run -d -p 8787:8787 -e USER=prettypublisher -e PASSWORD=prettypublisher --name prettypublisher seabbs/prettypublisher

The rstudio client can be accessed on port 8787 at localhost (or your machines ip). The default username is prettypublisher and the default password is prettypublisher.