diff --git a/README.md b/README.md index ff3c5f4f27949b8bae249c6d1995ed40a68fe3a2..4dc474a2729716fa65e6d650ff41cca2c72aa4d0 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ Generally speaking, you should not be sourcing or editing manually [INVENTORY_00 * [INVENTORY_00_R_environment.R](<01_INVENTORY/INVENTORY_00_R_environment.R>): load all required packages (or complain they are missing) and sets global variables for the 01_INVENTORY project. * [INVENTORY_00_R_functions.R](<01_INVENTORY/INVENTORY_00_R_functions.R>): custom R functions developed for the 01_INVENTORY project. -* [INVENTORY_01_dump_REDCap_database.R](<01_INVENTORY/INVENTORY_01_dump_REDCap_database.R>): extract database from the REDCap server that is passed into the `RCON_INVENTORY` variable. Very minor tweaks are conducted on the data: manual GPS coordinates are propagated into the `gps_lat` and `gps_lon` fields, and a validity flag is creaated based on expected boundaries for GPS locations. +* [INVENTORY_01_dump_REDCap_database.R](<01_INVENTORY/INVENTORY_01_dump_REDCap_database.R>): extract database from the REDCap servers passed into the `RCON_INVENTORY` variable. Very minor tweaks are conducted on the data: manual GPS coordinates are propagated into the `gps_lat` and `gps_lon` fields, and a validity flag is creaated based on expected boundaries for GPS locations. #### Outputs @@ -130,12 +130,44 @@ Set of methods used to explore and analyze the content of the **Observational St #### Scripts involed * [OBSERVATIONAL_00_R_environment.R](<02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R>): load all required packages (or complain they are missing) and sets global variables for the 02_OBSERVATIONAL project. -* [OBSERVATIONAL_01_dump_REDCap_database.R](<02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R>): extract database from the REDCap server that is passed into the `RCON_OBSERVATIONAL` variable. +* [OBSERVATIONAL_01_dump_REDCap_database.R](<02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R>): extract database from the REDCap servers passed into the `RCON_OBSERVATIONAL` variable. #### Outputs * `dat_observational_raw`: the raw database from REDCap. +### Curation of raw data dumps + +#### Scripts involed + +* [OBSERVATIONAL_02_curate_REDCap_raw_data.R](<02_OBSERVATIONAL/OBSERVATIONAL_02_curate_REDCap_raw_data.R>): process the `dat_observational_raw` into `dat_observational_curated` by correcting some inconsistencies introduced by REDCap bugs. This script does **not** correct erroneous data resulting from incorrect data entry. + +#### Outputs + +* `dat_observational_curated`: the curated database from REDCap. + +### QC steps for data consistency + +TO BE WRITTEN (& CODED) + +## INTERVENTIONAL_M0 + +Set of scripts and methods to process and analyze the data collected as part of the PvSTATEM Intervention study, where clusters have been randomized into the two study arms. + +### R environment setup and database extraction + +#### Scripts involed + +* [INTERVENTIONAL_M0_00_R_environment.R](<03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R>): load all required packages (or complain they are missing) and sets global variables for the 03_INTERVENTIONAL_M0 project. +* [INTERVENTIONAL_M0_01_dump_REDCap_database.R](<03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_01_dump_REDCap_database.R>): extract database from the REDCap servers passed in the `RCON_INTERVENTIONAL_M0` and `RCON_INTERVENTIONAL_PCD` variables. + +#### Outputs + +* `dat_interventional_m0_raw`: the raw database from REDCap for the Active Follow-Up dataset. +* `dat_interventional_pcd_raw`: the raw database from REDCap for the Passive Case Detection dataset. + +--- + ## README.md template The README.md should respect the following conventions: