scriptResume

scriptResume is a R addin package that aims to facilitate the coding process. It comes especially handy after combined with keyboard short cuts. Currently, there are two section of functions implemented - editing functions and script reading functions.

Editing functions

These addin functions help to facilitate coding process.

Objects to quoted text
Remove row ID
Upper case
Lower case
Roxygen comment
Roxygen uncomment
Roxygen quote
to bullet point
to table

Object to quoted text transforms a chunk of selected text with comma separator into a string vector. For example, from

a, b, c, d

c("a", "b", "c", "d")

Remove row ID remove the row IDs from the text copied from the console.

 [1] "1 m = 722"   "10 m = 584"  "11 m = 427"  "12 m = 380"
 [5] "13 m = 243"  "14 m = 211"  "15 m = 321"  "16 m = 316"
 [9] "17 m = 220"  "18 m = 152"  "19 m = 1906" "2 m = 737"
[13] "20 m = 164"  "21 m = 108"  "22 m = 269"  "3 m = 507"
[17] "4 m = 498"   "5 m = 412"   "6 m = 7836"  "7 m = 569"
[21] "8 m = 379"   "9 m = 297"

  "1 m = 722"   "10 m = 584"  "11 m = 427"  "12 m = 380"
  "13 m = 243"  "14 m = 211"  "15 m = 321"  "16 m = 316"
  "17 m = 220"  "18 m = 152"  "19 m = 1906" "2 m = 737"
 "20 m = 164"  "21 m = 108"  "22 m = 269"  "3 m = 507"
 "4 m = 498"   "5 m = 412"   "6 m = 7836"  "7 m = 569"
 "8 m = 379"   "9 m = 297"

Upper case and Lower case transform the selected text into upper or lower cased format.

Roxygen formatting features

These features are used in the R script instead of R Markdown files. They will transform the selected text into Roxygen format comment or quoted text in Roxygen format. Alternatively it can back-tranform a chunk of Roxygen comment format text back to text in R script.

Roxygen comment: e.g. from This is my comment. to #' This is my comment.

Roxygen uncomment: e.g. from #' Recommenting to Recommenting

Roxygen quote: e.g. from Some quotes to #' > Some quotes

to bullet point transforms selected text into bullet points. The selected text has to be separated by \n.

point 1
point 2
point 3

point 1
point 2
point 3

to table transforms selected text, which is colon separated entry into md table format. For example,

a:b:c
1:2:3
4:5:6

a	b	c
1	2	3
4	5	6

Script reading functions

These addin functions read through the currently active script and summarize the script. The functions include:

Insert unique libraries
Insert header

Unique libraries

This function reads through the script and collects the libraries used throughout the script. The function will collect libraries called by library(), require(), lib:: and insert these libraries at current cursor position. It will automatically remove duplicated usage of the same library. For example,

require(abc)
libraries(abc)
xyz::xyz()

library(abc)
library(knitr)
library(lib)
library(rmarkdown)
library(xyz)

The other libraries are used in this Rmd file but not shown in this example. You will find this function handy when reading a messy script that the libraries are imported from every possible random place.

a header summary of a script

This function read through the currently active R script and summarize the script with following information of the current computing enviroment, hence the name of the package scriptResume.

# ******************************************************************************
# Property of company
# Program name     : scriptResume.R
# Description      :
# Author           : author
# Compound number  : SAR
# Study code       :
# Analysis code    : BMK-
# Date created     : 2023-05-16
# Input files      : data/file1.csv,
#                    data/file2.Rds,
#                    data/file3.Rda
# Input programs   : src/preprocess.R
# Packages needed  : abc,
#                    knitr,
#                    lib,
#                    rmarkdown,
#                    xyz
# Outputs created  : data/file2.csv,
#                    data/file3.Rds
# R version        : R version 4.1.0 (2021-05-18)
# Platform         : Linux-4.4.0-19041-Microsoft
# ******************************************************************************
# Modification status :
# In progress | 2023-05-16 | author
# Description:
# ******************************************************************************

Files imported with funcitons read*(), load(), source() will be collected

data1 <- read.csv("data/file1.csv")
data2 <- readRDS("data/file2.Rds")
load("data/file3.Rda")
source("src/preprocess.R")

Files exported with functions write*(), save*() will be collected.

write.csv(data2, "data/file2.csv")
saveRDS(file3, "data/file3.Rds")

Since this function is targeted at pharma industry, it will automatically read the current working directory and output the triplet information. This illustration is tested in local so this function is not shown in the output above.

Below is an example for a dummy directory. Since I’m always working on biomarker analysis, the analysis code always starts with BMK.

# Author           : e123456
# Compound number  : SAR123
# Study code       : LPS123
# Analysis code    : BMK-CSR

R markdown theme

Starting from version 0.1.5, An Addin function, make css will be available for generating a predefined-themed css file. To use this function, put the cursor in the any open R script or any type of file, which defines currently active document, then click on the make css button. A css file named theme.css will be generated in the directory of the current active document.

created: 2023-05-16, updated: 2023-07-27, version 0.1.5