run_rmarkdown_reportonly: Run Rmarkdown files
In Thaliehln/timci: Data management and visualisation for the TIMCI project

run_rmarkdown_reportonly

R Documentation

Run Rmarkdown files

Description

This function runs several Rmarkdown files to generate standardised automated reports for the Tools for Integrated Management of Childhood Illnesses (TIMCI) project.

Usage

run_rmarkdown_reportonly(
  rctls_pid,
  rctls_pp,
  spa_pid,
  qpid,
  qual_pp,
  research_facilities,
  report_dir,
  participant_zip,
  mdb_dir,
  fu_dir,
  qc_dir,
  lock_dir,
  qualcg_dir,
  qualhcp_dir,
  spa_db_dir,
  path_dir,
  start_date = NULL,
  end_date = NULL,
  spa_pid2 = NULL,
  spa_start_date = NULL,
  lock_date = NULL,
  cost_pid = NULL,
  cost_dir = NULL,
  qualkii_dir = NULL,
  qualos_dir = NULL,
  sample_size = 1e+05,
  is_test = FALSE,
  operational_reports = TRUE,
  is_pilot = FALSE,
  dm_pid = NULL
)

Arguments

`rctls_pid`	Numeric value that refers to the ID of the RCT/LS ODK Central project
`rctls_pp`	Encryption passphrase associated with the RCT/LS ODK ODK Central project
`spa_pid`	Numeric value that refers to the ID of the SPA / time-flow / process mapping project on the ODK Central server
`qpid`	Numeric ID of the qualitative ODK Central project
`qual_pp`	Encryption passphrase associated with the qualitative ODK Central project
`research_facilities`	Dataframe that contains the research facilities
`report_dir`	Path to the output folder for the generated Rmarkdown reports
`participant_zip`	Path to the encrypted zip archive that stores participant data
`mdb_dir`	Path to the output folder for the RCT / LS database exports
`fu_dir`	Path to the output folder for the follow-up exports
`qc_dir`	Path to the output folder that contains the quality check findings
`lock_dir`	Path to the output folder that contains the cleaned datasets
`qualcg_dir`	Path to the output folder for the caregiver in-depth interview exports
`qualhcp_dir`	Path to the output folder for the healthcare provider in-depth interview exports
`spa_db_dir`	Path to the output folder for the SPA / time-flow / process mapping database exports
`path_dir`	Path to the output folder for the M&E exports to be shared with PATH
`start_date`	RCT/LS data collection start date (optional)
`end_date`	RCT/LS data collection end date (optional)
`spa_pid2`	Numeric value (optional) that refers to another ID of the SPA / time-flow / process mapping project on the ODK Central server if data have been split between 2 projects
`spa_start_date`	SPA data collection start date (optional)
`lock_date`	RCT/LS data collection cleaning end date for database lock (optional)
`cost_pid`	Numeric value (optional) that refers to the ID of the cost and cost-effectiveness project on the ODK Central server
`cost_dir`	Path to the output folder for the cost and cost effectiveness database exports (optional)
`qualkii_dir`	Path to the output folder for the key informant interview exports (optional)
`qualos_dir`	Path to the output folder for the online survey exports (optional)
`sample_size`	Numeric value, sample size for RCT/LS enrolment
`is_test`	Boolean that enables to export and process a small subset of data for running technical tests (optional, default set to FALSE)
`operational_reports`	Boolean that enables to generate operational reports (optional, default set to TRUE)
`is_pilot`	Boolean that enables to select the pilot mode for Tanzania and India (optional, default set to FALSE)
`dm_pid`	Numeric value that refers to the ID of the Data Management (DM) ODK Central project