From 6f2cb827b2ac8627926b4f6a23120304b0897229 Mon Sep 17 00:00:00 2001
From: Jennifer Thom <jennifer.thom@phs.scot>
Date: Tue, 26 Sep 2023 12:42:02 +0100
Subject: [PATCH] update documentation

---
 NAMESPACE                         |  1 -
 man/add_nsu_cohort.Rd             |  3 ++-
 man/add_ppa_flag.Rd               |  3 ++-
 man/apply_cost_uplift.Rd          |  3 ++-
 man/correct_cij_vars.Rd           | 11 +++-----
 man/create_cohort_lookups.Rd      | 11 +++-----
 man/create_cost_inc_dna.Rd        | 11 +++-----
 man/create_episode_file.Rd        | 16 +++++++++++
 man/fill_missing_cij_markers.Rd   | 11 +++-----
 man/join_cohort_lookups.Rd        | 34 +++++++++++++++++------
 man/link_delayed_discharge_eps.Rd |  3 ++-
 man/load_ep_file_vars.Rd          | 11 +++-----
 man/lookup_uplift.Rd              |  3 ++-
 man/run_episode_file.Rd           | 45 -------------------------------
 man/store_ep_file_vars.Rd         | 13 +++------
 15 files changed, 71 insertions(+), 108 deletions(-)
 delete mode 100644 man/run_episode_file.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 3e631047f..b5436d21e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -156,7 +156,6 @@ export(read_sc_all_alarms_telecare)
 export(read_sc_all_care_home)
 export(read_sc_all_home_care)
 export(read_sc_all_sds)
-export(run_episode_file)
 export(setup_keyring)
 export(start_fy)
 export(start_fy_quarter)
diff --git a/man/add_nsu_cohort.Rd b/man/add_nsu_cohort.Rd
index 0673c3bf3..43118a087 100644
--- a/man/add_nsu_cohort.Rd
+++ b/man/add_nsu_cohort.Rd
@@ -28,11 +28,12 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/add_ppa_flag.Rd b/man/add_ppa_flag.Rd
index a067188b6..f19f81009 100644
--- a/man/add_ppa_flag.Rd
+++ b/man/add_ppa_flag.Rd
@@ -24,11 +24,12 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/apply_cost_uplift.Rd b/man/apply_cost_uplift.Rd
index 2802eb8b2..5461d15be 100644
--- a/man/apply_cost_uplift.Rd
+++ b/man/apply_cost_uplift.Rd
@@ -22,11 +22,12 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/correct_cij_vars.Rd b/man/correct_cij_vars.Rd
index be6c550e5..5fd265d22 100644
--- a/man/correct_cij_vars.Rd
+++ b/man/correct_cij_vars.Rd
@@ -1,24 +1,18 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{correct_cij_vars}
 \alias{correct_cij_vars}
 \title{Correct the CIJ variables}
 \usage{
-correct_cij_vars(data)
-
 correct_cij_vars(data)
 }
 \arguments{
 \item{data}{The in-progress episode file data.}
 }
 \value{
-The data with CIJ variables corrected.
-
 The data with CIJ variables corrected.
 }
 \description{
-Correct the CIJ variables
-
 Correct the CIJ variables
 }
 \seealso{
@@ -28,11 +22,12 @@ Other episode_file:
 \code{\link{apply_cost_uplift}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/create_cohort_lookups.Rd b/man/create_cohort_lookups.Rd
index 1e9ac5b13..934354375 100644
--- a/man/create_cohort_lookups.Rd
+++ b/man/create_cohort_lookups.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{create_cohort_lookups}
 \alias{create_cohort_lookups}
 \title{Create the cohort lookups}
 \usage{
-create_cohort_lookups(data, year, update = latest_update())
-
 create_cohort_lookups(data, year, update = latest_update())
 }
 \arguments{
@@ -16,13 +14,9 @@ create_cohort_lookups(data, year, update = latest_update())
 \item{update}{The update to use.}
 }
 \value{
-The data unchanged (the cohorts are written to disk)
-
 The data unchanged (the cohorts are written to disk)
 }
 \description{
-Create the cohort lookups
-
 Create the cohort lookups
 }
 \seealso{
@@ -32,11 +26,12 @@ Other episode_file:
 \code{\link{apply_cost_uplift}()},
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/create_cost_inc_dna.Rd b/man/create_cost_inc_dna.Rd
index 304079bd4..d78e9c907 100644
--- a/man/create_cost_inc_dna.Rd
+++ b/man/create_cost_inc_dna.Rd
@@ -1,24 +1,18 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{create_cost_inc_dna}
 \alias{create_cost_inc_dna}
 \title{Create cost total net inc DNA}
 \usage{
-create_cost_inc_dna(data)
-
 create_cost_inc_dna(data)
 }
 \arguments{
 \item{data}{The in-progress episode file data.}
 }
 \value{
-The data with cost including dna.
-
 The data with cost including dna.
 }
 \description{
-Create cost total net inc DNA
-
 Create cost total net inc DNA
 }
 \seealso{
@@ -28,11 +22,12 @@ Other episode_file:
 \code{\link{apply_cost_uplift}()},
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/create_episode_file.Rd b/man/create_episode_file.Rd
index c1ce0e063..3ce6c815d 100644
--- a/man/create_episode_file.Rd
+++ b/man/create_episode_file.Rd
@@ -47,3 +47,19 @@ a \link[tibble:tibble-package]{tibble} containing the episode file
 \description{
 Produce the Source Episode file
 }
+\seealso{
+Other episode_file: 
+\code{\link{add_nsu_cohort}()},
+\code{\link{add_ppa_flag}()},
+\code{\link{apply_cost_uplift}()},
+\code{\link{correct_cij_vars}()},
+\code{\link{create_cohort_lookups}()},
+\code{\link{create_cost_inc_dna}()},
+\code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
+\code{\link{link_delayed_discharge_eps}()},
+\code{\link{load_ep_file_vars}()},
+\code{\link{lookup_uplift}()},
+\code{\link{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/fill_missing_cij_markers.Rd b/man/fill_missing_cij_markers.Rd
index ce654495e..7918329a7 100644
--- a/man/fill_missing_cij_markers.Rd
+++ b/man/fill_missing_cij_markers.Rd
@@ -1,24 +1,18 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{fill_missing_cij_markers}
 \alias{fill_missing_cij_markers}
 \title{Fill any missing CIJ markers for records that should have them}
 \usage{
-fill_missing_cij_markers(data)
-
 fill_missing_cij_markers(data)
 }
 \arguments{
 \item{data}{The in-progress episode file data.}
 }
 \value{
-A data frame with CIJ markers filled in for those missing.
-
 A data frame with CIJ markers filled in for those missing.
 }
 \description{
-Fill any missing CIJ markers for records that should have them
-
 Fill any missing CIJ markers for records that should have them
 }
 \seealso{
@@ -29,10 +23,11 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/join_cohort_lookups.Rd b/man/join_cohort_lookups.Rd
index e674396c6..142a2c1ee 100644
--- a/man/join_cohort_lookups.Rd
+++ b/man/join_cohort_lookups.Rd
@@ -1,12 +1,18 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{join_cohort_lookups}
 \alias{join_cohort_lookups}
 \title{Join cohort lookups}
 \usage{
-join_cohort_lookups(data, year, update = latest_update())
-
-join_cohort_lookups(data, year, update = latest_update())
+join_cohort_lookups(
+  data,
+  year,
+  update = latest_update(),
+  demographic_cohort = read_file(get_demographic_cohorts_path(year, update), col_select =
+    c("chi", "demographic_cohort")),
+  service_use_cohort = read_file(get_service_use_cohorts_path(year, update), col_select =
+    c("chi", "service_use_cohort"))
+)
 }
 \arguments{
 \item{data}{The in-progress episode file data.}
@@ -18,12 +24,24 @@ join_cohort_lookups(data, year, update = latest_update())
 \item{demographic_cohort, service_use_cohort}{The cohort data}
 }
 \value{
-The data including the Demographic and Service Use lookups.
-
 The data including the Demographic and Service Use lookups.
 }
 \description{
 Join cohort lookups
-
-Join cohort lookups
 }
+\seealso{
+Other episode_file: 
+\code{\link{add_nsu_cohort}()},
+\code{\link{add_ppa_flag}()},
+\code{\link{apply_cost_uplift}()},
+\code{\link{correct_cij_vars}()},
+\code{\link{create_cohort_lookups}()},
+\code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
+\code{\link{fill_missing_cij_markers}()},
+\code{\link{link_delayed_discharge_eps}()},
+\code{\link{load_ep_file_vars}()},
+\code{\link{lookup_uplift}()},
+\code{\link{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/link_delayed_discharge_eps.Rd b/man/link_delayed_discharge_eps.Rd
index 9ae86688d..245fa2754 100644
--- a/man/link_delayed_discharge_eps.Rd
+++ b/man/link_delayed_discharge_eps.Rd
@@ -32,10 +32,11 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{load_ep_file_vars}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/load_ep_file_vars.Rd b/man/load_ep_file_vars.Rd
index 393a9c415..965e8bfce 100644
--- a/man/load_ep_file_vars.Rd
+++ b/man/load_ep_file_vars.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{load_ep_file_vars}
 \alias{load_ep_file_vars}
 \title{Load the unneeded episode file variables}
 \usage{
-load_ep_file_vars(data, year)
-
 load_ep_file_vars(data, year)
 }
 \arguments{
@@ -14,13 +12,9 @@ load_ep_file_vars(data, year)
 \item{year}{The year to process, in FY format.}
 }
 \value{
-The full SLF data.
-
 The full SLF data.
 }
 \description{
-Load the unneeded episode file variables
-
 Load the unneeded episode file variables
 }
 \seealso{
@@ -31,10 +25,11 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/lookup_uplift.Rd b/man/lookup_uplift.Rd
index a463aad3b..356a25d4a 100644
--- a/man/lookup_uplift.Rd
+++ b/man/lookup_uplift.Rd
@@ -23,10 +23,11 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
-\code{\link{run_episode_file}()},
 \code{\link{store_ep_file_vars}()}
 }
 \concept{episode_file}
diff --git a/man/run_episode_file.Rd b/man/run_episode_file.Rd
deleted file mode 100644
index cd25908c4..000000000
--- a/man/run_episode_file.Rd
+++ /dev/null
@@ -1,45 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run_episode_file.R
-\name{run_episode_file}
-\alias{run_episode_file}
-\title{Produce the Source Episode file}
-\usage{
-run_episode_file(
-  processed_data_list,
-  year,
-  write_to_disk = TRUE,
-  anon_chi_out = TRUE
-)
-}
-\arguments{
-\item{processed_data_list}{containing data from processed extracts.}
-
-\item{year}{The year to process, in FY format.}
-
-\item{write_to_disk}{(optional) Should the data be written to disk default is
-\code{TRUE} i.e. write the data to disk.}
-
-\item{anon_chi_out}{(Default:TRUE) Should \code{anon_chi} be used in the output
-(instead of chi)}
-}
-\value{
-a \link[tibble:tibble-package]{tibble} containing the episode file
-}
-\description{
-Produce the Source Episode file
-}
-\seealso{
-Other episode_file: 
-\code{\link{add_nsu_cohort}()},
-\code{\link{add_ppa_flag}()},
-\code{\link{apply_cost_uplift}()},
-\code{\link{correct_cij_vars}()},
-\code{\link{create_cohort_lookups}()},
-\code{\link{create_cost_inc_dna}()},
-\code{\link{fill_missing_cij_markers}()},
-\code{\link{link_delayed_discharge_eps}()},
-\code{\link{load_ep_file_vars}()},
-\code{\link{lookup_uplift}()},
-\code{\link{store_ep_file_vars}()}
-}
-\concept{episode_file}
diff --git a/man/store_ep_file_vars.Rd b/man/store_ep_file_vars.Rd
index cab617713..687bdcecb 100644
--- a/man/store_ep_file_vars.Rd
+++ b/man/store_ep_file_vars.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_episode_file.R, R/run_episode_file.R
+% Please edit documentation in R/create_episode_file.R
 \name{store_ep_file_vars}
 \alias{store_ep_file_vars}
 \title{Store the unneeded episode file variables}
 \usage{
-store_ep_file_vars(data, year, vars_to_keep)
-
 store_ep_file_vars(data, year, vars_to_keep)
 }
 \arguments{
@@ -17,13 +15,9 @@ store_ep_file_vars(data, year, vars_to_keep)
 will be stored.}
 }
 \value{
-\code{data} with only the \code{vars_to_keep} kept
-
 \code{data} with only the \code{vars_to_keep} kept
 }
 \description{
-Store the unneeded episode file variables
-
 Store the unneeded episode file variables
 }
 \seealso{
@@ -34,10 +28,11 @@ Other episode_file:
 \code{\link{correct_cij_vars}()},
 \code{\link{create_cohort_lookups}()},
 \code{\link{create_cost_inc_dna}()},
+\code{\link{create_episode_file}()},
 \code{\link{fill_missing_cij_markers}()},
+\code{\link{join_cohort_lookups}()},
 \code{\link{link_delayed_discharge_eps}()},
 \code{\link{load_ep_file_vars}()},
-\code{\link{lookup_uplift}()},
-\code{\link{run_episode_file}()}
+\code{\link{lookup_uplift}()}
 }
 \concept{episode_file}