README.md

In JMLuther/tabletools: Helpful Tools to Make html Tables

tabletools

The goal of tabletools is to provide functions which are helpful for generating summary html tables. For details on the functions, please see help documentation in the package.

Installation

Install from Github: devtools::install_github("JMLuther/tabletools", build_vignettes = TRUE)

These functions are most useful in conjunction with an html table generating package::functions such as:

• htmlTable::htmlTable Tables with htmlTable and some alternatives
• knitr::kable see Create Awesome HTML Table with knitr::kable and kableExtra
• formattable

my_summary custom summary

This summary function is customized to my preferences, and should provide enough data to pipe into ggplot or a simple summary table. Just provides a summary for a single continuous variable.

Table:

mtcars %>% 
  group_by(cyl) %>% 
  my_summary(mpg, digits = 1) %>% # override the default 2 decimal point rounding
  htmlTable::htmlTable(rnames=F, align = "c",
                       css.cell = rbind(rep("padding-left: .5em; padding-right: .5em;",times=ncol(.)),
                                        matrix("padding:0 5px 0 5px;", ncol=ncol(.), nrow=nrow(.))))

cyl mpg_n mpg_mean mpg_sd mpg_sem mpg_median mpg_ci_025 mpg_ci_975 4 11 26.7 4.5 1.4 26 21.4 33.5 6 7 19.7 1.5 0.5 19.7 17.8 21.3 8 14 15.1 2.6 0.7 15.2 10.4 19

Plot:

mtcars %>% 
  group_by(cyl) %>% 
  my_summary(mpg) %>% 
  ggplot(aes(factor(cyl), mpg_mean,
             ymin = mpg_ci_025, ymax = mpg_ci_975)) +
  geom_linerange() +
  geom_point(color = "red", size=2) +
  labs(x="No. of Cylinders",
       y= "Average MPG",
       title= "Average MPG by number of Cylinders") +
  theme_bw()

Summary text functions

mtcars %>%
  summarise(mean_sd = txt_mean_sd(mpg),
            mean_sem = txt_mean_sem(mpg),
            mean_range = txt_mean_range(mpg),
            median_iqr = txt_median_iqr(mpg),
            pct_fr = txt_pct_fr(vs, 1)
            ) %>% 
  tidyr::gather(txt_f, output) %>% # this is better than using t() which creates a matrix
  htmlTable::htmlTable(rnames=F, align = "l", align.header = "l", 
                       caption = "Example results",
                       css.cell = rbind(rep("padding-left: .5em; padding-right: .5em;",times=ncol(.)),
                                        matrix("padding:0 5px 0 5px;", ncol=ncol(.), nrow=nrow(.))))

Example results txt_f output mean_sd 20.1±6.0 mean_sem 20.1±1.1 mean_range 20.1(10.4-33.9) median_iqr 19.2\[15.4-22.8\] pct_fr 43.8%(14⁄32)

The following functions provide useful # Session Info

 R version 4.2.1 (2022-06-23 ucrt)
 Platform: x86_64-w64-mingw32/x64 (64-bit)
 Running under: Windows 10 x64 (build 19044)

 Matrix products: default

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     

 other attached packages:
 [1] tidyr_1.2.1      tabletools_0.1.0 htmlTable_2.4.1  ggplot2_3.3.6   
 [5] dplyr_1.0.10    
 

To cite R in publications use:

R Core Team (2022). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.

To cite the ggplot2 package in publications use:

Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.

JMLuther/tabletools documentation built on July 1, 2024, 2:01 p.m.