Updated documentation

NAMESPACE

@@ -25,7 +25,12 @@ export(delete_ont)
 export(delete_ontology)
 export(delete_users)
 export(fresh_install)
+export(get_ont)
 export(import_data)
+export(list_ont)
+export(list_schemes)
+export(list_user_roles)
+export(list_users)
 export(populate_concept)
 export(populate_ont)
 export(populate_provider)

R/utils.R

@@ -45,7 +45,7 @@ dbPush <- function(df, con, table)
   RPostgreSQL::dbGetQuery(conn = con, .)
 }
 
-#' Udpdate a dataframe into a database table
+#' Update a dataframe into a database table
 #'
 #' @param df Dataframe to update into the database
 #' @param con Database connection
@@ -88,6 +88,12 @@ clear_table <- function(db, table, host = "", admin = "", pass = "")
   RPostgreSQL::dbDisconnect(con)
 }
 
+#' Upserta dataframe into a database table
+#'
+#' @param df Dataframe to upsert into the database
+#' @param con Database connection
+#' @param table Table in the database in which to push the dataframe
+#' @param PK Character vector of the primary key(s)
 dbUpsert <- function(df, con, table, PK)
 {
   columns <- setdiff(names(df), PK)

man/add_encounters.Rd

@@ -4,20 +4,21 @@
 \alias{add_encounters}
 \title{Add encounters to the CRC cell}
 \usage{
-add_encounters(host, admin, pass, encounters, project, patient_mapping)
+add_encounters(encounters, project, patient_mapping, host = "", admin = "",
+  pass = "")
 }
 \arguments{
-\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{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}
+
+\item{pass}{The password for the admin account}
 }
 \value{
 An encounter mapping dataframe for the encounters

man/add_observations.Rd

@@ -4,21 +4,21 @@
 \alias{add_observations}
 \title{Add observations to the CRC cell}
 \usage{
-add_observations(host, admin, pass, observations, patient_mapping,
-  encounter_mapping)
+add_observations(observations, patient_mapping, encounter_mapping, host = "",
+  admin = "", pass = "")
 }
 \arguments{
-\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{observations}{A dataframe of observation facts}
 
 \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}
 }
 \description{
 Add observations to the CRC cell

man/add_ont.Rd

@@ -4,18 +4,18 @@
 \alias{add_ont}
 \title{Add an ontology to metadata}
 \usage{
-add_ont(host, admin, pass, name, scheme)
+add_ont(name, scheme, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{name}{The name of the new ontology}
+
+\item{scheme}{The scheme to use for this ontology}
+
 \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{name}{The name of the new ontology}
-
-\item{scheme}{The scheme to use for this ontology}
 }
 \description{
 Add an empty ontology space

man/add_ontology.Rd

@@ -4,16 +4,10 @@
 \alias{add_ontology}
 \title{Add an ontology to i2b2}
 \usage{
-add_ontology(host = "127.0.0.1", admin, pass, name, scheme, ont,
-  modi = NULL, include_code = T)
+add_ontology(name, scheme, ont, modi = NULL, include_code = T, host = "",
+  admin = "", pass = "")
 }
 \arguments{
-\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{name}{The name of the new ontology}
 
 \item{scheme}{The scheme to use for this ontology}
@@ -23,6 +17,12 @@ add_ontology(host = "127.0.0.1", admin, pass, name, scheme, ont,
 \item{modi}{The modifiers to insert}
 
 \item{include_code}{Whether to include the code in the label or not}
+
+\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{
 Add an ontology into i2b2

man/add_patients_demodata.Rd

@@ -4,18 +4,18 @@
 \alias{add_patients_demodata}
 \title{Add patients to the CRC cell}
 \usage{
-add_patients_demodata(host, admin, pass, patients, project)
+add_patients_demodata(patients, project, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{patients}{A dataframe of patients}
+
+\item{project}{The project to add the patients to}
+
 \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{patients}{A dataframe of patients}
-
-\item{project}{The project to add the patients to}
 }
 \value{
 A patient mapping dataframe for the patients

man/add_patients_imdata.Rd

@@ -4,18 +4,18 @@
 \alias{add_patients_imdata}
 \title{Add patients to the IM cell}
 \usage{
-add_patients_imdata(host, admin, pass, patients, project)
+add_patients_imdata(patients, project, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{patients}{A vector of patients IDs to insert}
+
+\item{project}{The project to add the patients to}
+
 \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{patients}{A vector of patients IDs to insert}
-
-\item{project}{The project to add the patients to}
 }
 \description{
 Add patients to the IM cell, generate new encrypted IDs,

man/clear_default_demodata.Rd

@@ -4,7 +4,7 @@
 \alias{clear_default_demodata}
 \title{Clear the default demodata tables}
 \usage{
-clear_default_demodata(host, admin, pass)
+clear_default_demodata(host = "", admin = "", pass = "")
 }
 \arguments{
 \item{host}{The host to connect to}

man/clear_default_imdata.Rd

@@ -4,7 +4,7 @@
 \alias{clear_default_imdata}
 \title{Clear the default imdata tables}
 \usage{
-clear_default_imdata(host, admin, pass)
+clear_default_imdata(host = "", admin = "", pass = "")
 }
 \arguments{
 \item{host}{The host to connect to}

man/clear_default_metadata.Rd

@@ -4,7 +4,7 @@
 \alias{clear_default_metadata}
 \title{Clear the default metadata tables}
 \usage{
-clear_default_metadata(host, admin, pass)
+clear_default_metadata(host = "", admin = "", pass = "")
 }
 \arguments{
 \item{host}{The host to connect to}

man/clear_table.Rd

@@ -4,7 +4,7 @@
 \alias{clear_table}
 \title{Clear a database table}
 \usage{
-clear_table(db, table, host, admin, pass)
+clear_table(db, table, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{db}{Name of the database}

man/dbUpdate.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/utils.R
 \name{dbUpdate}
 \alias{dbUpdate}
-\title{Udpdate a dataframe into a database table}
+\title{Update a dataframe into a database table}
 \usage{
 dbUpdate(df, con, table, PK)
 }
@@ -16,5 +16,5 @@ dbUpdate(df, con, table, PK)
 \item{PK}{Character vector of the primary key(s)}
 }
 \description{
-Udpdate a dataframe into a database table
+Update a dataframe into a database table
 }

man/dbUpsert.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{dbUpsert}
+\alias{dbUpsert}
+\title{Upserta dataframe into a database table}
+\usage{
+dbUpsert(df, con, table, PK)
+}
+\arguments{
+\item{df}{Dataframe to upsert into the database}
+
+\item{con}{Database connection}
+
+\item{table}{Table in the database in which to push the dataframe}
+
+\item{PK}{Character vector of the primary key(s)}
+}
+\description{
+Upserta dataframe into a database table
+}

man/delete_concept.Rd

@@ -4,16 +4,16 @@
 \alias{delete_concept}
 \title{Delete concepts}
 \usage{
-delete_concept(host, admin, pass, scheme)
+delete_concept(scheme, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{scheme}{The scheme to delete from the concepts}
+
 \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{scheme}{The scheme to delete from the concepts}
 }
 \description{
 Delete concepts from concept_dimension

man/delete_modifier.Rd

@@ -4,16 +4,16 @@
 \alias{delete_modifier}
 \title{Delete modifiers}
 \usage{
-delete_modifier(host, admin, pass, scheme)
+delete_modifier(scheme, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{scheme}{The scheme to delete from the concepts}
+
 \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{scheme}{The scheme to delete from the concepts}
 }
 \description{
 Delete modifiers from modifier_dimension

man/delete_ont.Rd

@@ -4,16 +4,16 @@
 \alias{delete_ont}
 \title{Delete an ontology from metadata}
 \usage{
-delete_ont(host, admin, pass, scheme)
+delete_ont(scheme, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{scheme}{The scheme to use for this ontology}
+
 \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{scheme}{The scheme to use for this ontology}
 }
 \description{
 Delete an existing ontology from metadata

man/delete_ontology.Rd

@@ -4,16 +4,16 @@
 \alias{delete_ontology}
 \title{Delete an ontology from i2b2}
 \usage{
-delete_ontology(host = "127.0.0.1", admin, pass, scheme)
+delete_ontology(scheme, host = "", admin = "", pass = "")
 }
 \arguments{
+\item{scheme}{The scheme to use for this ontology}
+
 \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{scheme}{The scheme to use for this ontology}
 }
 \description{
 Delete an existing ontology from metadata

man/get_ont.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{get_ont}
+\alias{get_ont}
+\title{Fetch an ontology}
+\usage{
+get_ont(ont, host = "", admin = "", pass = "")
+}
+\arguments{
+\item{ont}{The name of the ontology, from the c_table_name column in list_ont()}
+
+\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{
+Fetch an ontology
+}

man/import_data.Rd

@@ -4,18 +4,18 @@
 \alias{import_data}
 \title{Import data into i2b2}
 \usage{
-import_data(host, admin, pass, data, project)
+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}
-
-\item{data}{A dataframe of observation facts}
-
-\item{project}{The project to which to add the patients and their data}
 }
 \description{
 Import data from a data frame into i2b2

man/list_ont.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{list_ont}
+\alias{list_ont}
+\title{List the available ontologies}
+\usage{
+list_ont(host = "", admin = "", pass = "")
+}
+\arguments{
+\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{
+List the available ontologies
+}

man/list_schemes.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{list_schemes}
+\alias{list_schemes}
+\title{List the available schemes}
+\usage{
+list_schemes(host = "", admin = "", pass = "")
+}
+\arguments{
+\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{
+List the available schemes
+}

man/list_user_roles.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{list_user_roles}
+\alias{list_user_roles}
+\title{List user roles}
+\usage{
+list_user_roles(user, host = "", admin = "", pass = "")
+}
+\arguments{
+\item{user}{An user id}
+
+\item{host}{The host to connect to}
+
+\item{admin}{The admin account for the PostgreSQL database}
+
+\item{pass}{The password for the database admin}
+}
+\description{
+Delete i2b2 users from the instance
+}

man/list_users.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{list_users}
+\alias{list_users}
+\title{List users}
+\usage{
+list_users(host = "", admin = "", pass = "")
+}
+\arguments{
+\item{host}{The host to connect to}
+
+\item{admin}{The admin account for the PostgreSQL database}
+
+\item{pass}{The password for the database admin}
+}
+\description{
+Delete i2b2 users from the instance
+}

man/populate_concept.Rd

@@ -4,15 +4,10 @@
 \alias{populate_concept}
 \title{Populate the concept_dimension}
 \usage{
-populate_concept(host, admin, pass, ont, modi, name, scheme)
+populate_concept(ont, modi, name, scheme, host = "", admin = "",
+  pass = "")
 }
 \arguments{
-\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{ont}{The ontology to insert}
 
 \item{modi}{The modifiers to insert}
@@ -20,6 +15,12 @@ populate_concept(host, admin, pass, ont, modi, name, scheme)
 \item{name}{The name of the new ontology}
 
 \item{scheme}{The scheme to use for this ontology}
+
+\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{
 Populate the concept_dimension with new concepts

man/populate_ont.Rd

@@ -4,16 +4,10 @@
 \alias{populate_ont}
 \title{Populate an empty ontology table}
 \usage{
-populate_ont(host, admin, pass, ont, modi = NULL, name, scheme,
-  include_code = T)
+populate_ont(ont, modi = NULL, name, scheme, include_code = T, host = "",
+  admin = "", pass = "")
 }
 \arguments{
-\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{ont}{The ontology to insert}
 
 \item{modi}{The modifiers to insert}
@@ -23,6 +17,12 @@ populate_ont(host, admin, pass, ont, modi = NULL, name, scheme,
 \item{scheme}{The scheme to use for this ontology}
 
 \item{include_code}{Whether to include the code in the label or not}
+
+\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{
 Populate an empty ontology table

man/populate_provider.Rd

@@ -4,20 +4,20 @@
 \alias{populate_provider}
 \title{Populate the provider_dimension}
 \usage{
-populate_provider(host, admin, pass, ont, name, scheme)
+populate_provider(ont, name, scheme, host = "", admin = "", pass = "")
 }
 \arguments{
-\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{ont}{The ontology to insert}
 
 \item{name}{The name of the new ontology}
 
 \item{scheme}{The scheme to use for this ontology}
+
+\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{
 Populate the provider_dimension with new providers

man/rebuild_indexes_demodata.Rd

@@ -4,7 +4,7 @@
 \alias{rebuild_indexes_demodata}
 \title{Rebuild the indexes}
 \usage{
-rebuild_indexes_demodata(host, admin, pass)
+rebuild_indexes_demodata(host = "", admin = "", pass = "")
 }
 \arguments{
 \item{host}{The host to connect to}