NCC

Neurocysticercosis Project

https://github.com/LiNk-NY/NCC

Instructions for Reproducibility

1. Run the R/loadPackages.R script interactively. Make sure that you have all packages installed on your system.

2. The R/helperData.R script creates data objects for cleaning and parsing the column names in the datasets. This is not to be modified unless you are familiar with the datasets.

3. To download the resources from Dropbox, run the R/download.R script interactively. This requires a GitHub package download karthik/rdrop2 to connect to the Dropbox API. Note that folder access is required in order to be able to download the data. Alternatively, you may download and place the data files in the data folder. The code written will work with data placed inside the NCC/data folder.

4. If you do not have the serialized version of the dataset, run the R/readCleanMerge.R script with the SAV files downloaded from Dropbox. The SPSS (SAV) files can be obtained from Dropbox with folder permissions. This script will then save the datasets in a serialized rds, sav, or csv format.

5. Run the R/validation.R script for obtaining some helper functions to validate and recode the data.

6. Open R/reshapeToLong.R and run the script to change the data from wide to long format. Note: this script will source the previous scripts. This is useful if you have already saved the wide format rds file previously.

7. Open the R/ncc_msm_analysis.R script and run the analysis interactively. Note that BiocParallel is a Bioconductor package and should be be installed as indicated in the script.

Issues

Submit any issues at our GitHub repository issue tracker: https://github.com/LiNk-NY/NCC/issues