00_chmi_structure_readme.md

In mvazquezs/chmitools: Package to manage & obtain results of the CHMI Study

Structure

The chmitools package contains 3 most common parts of a devtools packages (R, test, projects). * R folder: contains R language code. * test folder: ensures the integrity of the code, based in the testthat code. * projects folder: include all results of the aims analysed, based in the R markdown code.

The chmitools data have been stored in the following local folders. * backup data (in google drive): ~/datasets_backup/ (shared folder with ruizolalla git user). * local data to work: ~/datasets/chmiddbb (see complete info in the chmi.dirs.R file).

The chmitools R folder contains the following files. * chmi.dirs.R: contains all the local folder location for the CHMI Study data. * chmi.phen.R: contains chmi.phen() function (see how it works in 00_chmi_r_readme file). * chmi.01_phen.update_dat_imp.R: manages, cleans and modifies common data files. * chmi.02_phen.argument_data_type.R: manages the join to clinical and the several type data. * chmi.03_phen.argument_aims.R: manages and loads the data by aims. * chmi.03_phen.argument_clinical_tr.R: manages list of variables for the clinical data. * chmi.04_phen.argument_fold.R: manages original clean data to obtain the fold_change data. * chmi.06.list_traits.id_in.alert.R: manages alerts in individuals info. * chmi.07_list_traits.R: contains all information of the variables. * chmi.07_list_traits.descriptions.R: contains all descriptives of the variables. * chmi.07_list_traits.source_files.R: contains all information about the original source files. * chmi.07_list_traits.units_ranges.R: contains all units and ranges of the variables. * chmi.08_list_names.R: contains all names and classes of variables, as well as list of antigens and analytes. * chmi.stat.R: contains a list of functions to obtain results (see how it works in 00_chmi_r_readme file). * chmi.stat_lm.R: contains a list of functions to obtain results (see how it works in 00_chmi_r_readme file). * chmi.stat_plots.R: contains a list of functions to obtain results (see how it works in 00_chmi_r_readme file). * chmi.stat_summary.R: contains a list of functions to obtain results (see how it works in 00_chmi_r_readme file). * chmi.stat_tools.R: contains a list of functions to manage data (see how it works in 00_chmi_r_readme file).

The chmitools projects folder contains the original Hector code in r_old folder and the new one to obtain the results.

The chmitools test folder contains double checks to ensure that devtools-like package works well. * needs to be re-done.

Vignettes

For further information (see 19.07.05_devtools_github talk).

mvazquezs/chmitools documentation built on May 1, 2020, 2:06 a.m.