Updated doc

NAMESPACE

@@ -29,7 +29,6 @@ export(delete_users)
 export(fresh_install)
 export(get_domain)
 export(get_ont)
-export(import_data)
 export(list_concepts)
 export(list_ont)
 export(list_projects)

man/add_encounters.Rd

@@ -4,16 +4,13 @@
 \alias{add_encounters}
 \title{Add encounters to the CRC cell}
 \usage{
-add_encounters(encounters, project, patient_mapping = "", host = "",
-  admin = "", pass = "")
+add_encounters(encounters, project, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{encounters}{A dataframe of patients}
 
 \item{project}{The project to add the patients to}
 
-\item{patient_mapping}{The patient mapping table}
-
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/add_observations.Rd

@@ -4,23 +4,22 @@
 \alias{add_observations}
 \title{Add observations to the CRC cell}
 \usage{
-add_observations(observations, project, patient_mapping = "",
-  encounter_mapping = "", host = "", admin = "", pass = "")
+add_observations(observations, project, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{observations}{A dataframe of observation facts}
 
 \item{project}{The name of the project}
 
-\item{patient_mapping}{The patient mapping table}
-
-\item{encounter_mapping}{The encounter mapping table}
-
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}
 
 \item{pass}{The password for the admin account}
+
+\item{patient_mapping}{The patient mapping table}
+
+\item{encounter_mapping}{The encounter mapping table}
 }
 \description{
 Add observations to the CRC cell

man/add_patients_demodata.Rd

@@ -25,5 +25,5 @@ The patients dataframe must contain the following columns:
 - patient_ide: the original patient ID
 - birth_date: as a Date object
 - death_date: as a Date object
-- gender (F or M)
+- sex_cd (F or M)
 }

man/import_data.Rd

@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/import.R
-\name{import_data}
-\alias{import_data}
-\title{Import data into i2b2}
-\usage{
-import_data(data, project, host = "", admin = "", pass = "")
-}
-\arguments{
-\item{data}{A dataframe of observation facts}
-
-\item{project}{The project to which to add the patients and their data}
-
-\item{host}{The host to connect to}
-
-\item{admin}{The admin account for the PostgreSQL database}
-
-\item{pass}{The password for the admin account}
-}
-\description{
-Import data from a data frame into i2b2
-}
-\details{
-The data dataframe must contain the following columns:
-- encounter_ide: the original encounter ID
-- patient_ide: the original patient ID
-- start_date: the start date of the encounter, as Date object
-- concept_cd: the concept to insert
-- provider_id: the provider
-- modifier_cd: optionnal modifier for the concept
-Other observation fact columns can optionnaly be included,
-such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
-
-The function creates and updates the corresponding patients and encounters,
-inserts the new observations, and finally rebuilds the indexes in the database.
-}