README.md

In rafaelsommer1/emocempr: Functions for analyzing EMOCEMP data

emocempR Package

About emocempr

This is a package for internal use by the Multicentric Study of Pediatric Multiple Sclerosis (EMOCEMP) investigators. Here, we provide functions that facilitate manipulating data directly extracted from qualtrics in the .csv numeric format. Moreover, this functions are used to generate reproducible and automated analysis, as well as an automated dashboard for the purpose of investigator consult.

The emocempR package depends on fuctions from other libraries, so it is recommended that you have installed the following packages: - data.table - stringr - dplyr - lubridate - irr

This can be accomplished with this simple code:

packages <- c("data.table","irr","dplyr","stringr","lubridate")
for (i in packages){
        if(!require(i)){
                install.packages(i)
        }
} 

You are not required to install all this dependencies, since the emocempr package should import the needed functions. However, since it is a package in development, it is recomended that you have all of them in your R library to prevent any kind of importation errors.

How to install

To install the emocempr package type the following code in your R console.

if (!require("devtools")){
        install.packages("devtools")}

devtools::install_github("rafaelsommer1/emocempr")

We suggest you update from the source code each time you wish to use the package, since it is a project on development. For that, code as following:

if (!require("dtupdate")){
        devtools::install_github("hrbrmstr/dtupdate")}

dtupdate::github_update()

Common applications

All functions are based on exported data from qualtrics forms with this configuration (csv numeric)

After that, you can start using the package functions. Usually, all data exported from qualtrics needs to be cleaned so it can be analyzed. The package provides functions which perform for in basically all EMOCEMP forms, so for eg, given a Visit 1 form:

library(emocempr)

v1 <- clean_v1("file.csv")

This read the .csv file downloaded from qualtrics, clean it and store the results in a new R object: v1. You can perform analysis directly in R using this object or write a new .csv file with the cleaned data in order to analyze data in other packages such as GraphPad, SPSS, Excel...

If this is inteded, something like:

write.csv2(v1, "filename")

Should do it.

Further, there are package functions that allow for data manipulation. So, in case you wanted to bind multiple visits data you can use the merge_visits function, which select a minor group of variables

v1 <- clean_v1("fileV1.csv")
v2 <- clean_v2("fileV2.csv")
v3 <- clean_v3("fileV3.csv")
merged <- merge_visits(v1,v2,v3, mode = "long", all.patients=FALSE)

This will use CLEANED data from visits 1, 2 and 3, combine them into a "long" format (each observation as a line) using only patients who have data collected from all 3 visits (all.patients=FALSE), and store the results into the merged object.

As before, one may convert this object into a .csv file for analyzing in other software or carry on the analysis whitin R.

rafaelsommer1/emocempr documentation built on Aug. 31, 2020, 4:38 p.m.