From 81c21910006c3b6327fddad9686b27cb9d00173a Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Tue, 26 Sep 2023 12:50:19 +0100
Subject: [PATCH] Fix the pkgdown site/job (#804)

* Fix the pkgdown site/job

It generates this site: https://public-health-scotland.github.io/source-linkage-files/ although it hasn't been working for a while since any new function needs to be added to (or captured by) the `_pkgdown.yml` file.

This PR is a pretty minimal fix to get the site working again.

* Update documentation

* Update documentation

* Update `create_episode_file`

* Remove `run_episode_file`

* update documentation

---------

Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com>
Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com>
Co-authored-by: Jennifer Thom <jennifer.thom@phs.scot>
---
 R/add_nsu_cohort.R                |  2 +-
 R/add_ppa_flag.R                  |  2 +-
 R/aggregate_by_chi.R              |  2 ++
 R/cost_uplift.R                   |  2 ++
 R/create_episode_file.R           |  8 +++++
 R/create_individual_file.R        | 38 +++++++++++++++++---
 R/link_delayed_discharge_eps.R    |  2 +-
 _pkgdown.yml                      | 60 ++++++++++++++++++++++++++-----
 man/add_acute_columns.Rd          | 32 +++++++++++++++++
 man/add_ae_columns.Rd             | 32 +++++++++++++++++
 man/add_all_columns.Rd            | 32 +++++++++++++++++
 man/add_at_columns.Rd             | 32 +++++++++++++++++
 man/add_ch_columns.Rd             | 32 +++++++++++++++++
 man/add_cij_columns.Rd            | 32 +++++++++++++++++
 man/add_cmh_columns.Rd            | 32 +++++++++++++++++
 man/add_dd_columns.Rd             | 32 +++++++++++++++++
 man/add_dn_columns.Rd             | 32 +++++++++++++++++
 man/add_gls_columns.Rd            | 32 +++++++++++++++++
 man/add_hc_columns.Rd             | 32 +++++++++++++++++
 man/add_hl1_columns.Rd            | 32 +++++++++++++++++
 man/add_ipdc_cols.Rd              | 35 +++++++++++++++++-
 man/add_mat_columns.Rd            | 32 +++++++++++++++++
 man/add_mh_columns.Rd             | 32 +++++++++++++++++
 man/add_nrs_columns.Rd            | 32 +++++++++++++++++
 man/add_nsu_cohort.Rd             | 16 +++++++--
 man/add_nsu_columns.Rd            | 32 +++++++++++++++++
 man/add_ooh_columns.Rd            | 32 +++++++++++++++++
 man/add_op_columns.Rd             | 32 +++++++++++++++++
 man/add_pis_columns.Rd            | 32 +++++++++++++++++
 man/add_ppa_flag.Rd               | 16 +++++++--
 man/add_sds_columns.Rd            | 32 +++++++++++++++++
 man/add_standard_cols.Rd          | 35 +++++++++++++++++-
 man/aggregate_by_chi.Rd           | 32 +++++++++++++++++
 man/aggregate_ch_episodes.Rd      | 32 +++++++++++++++++
 man/apply_cost_uplift.Rd          | 16 +++++++++
 man/clean_up_ch.Rd                | 32 +++++++++++++++++
 man/condition_cols.Rd             | 32 +++++++++++++++++
 man/correct_cij_vars.Rd           | 16 +++++++++
 man/create_cohort_lookups.Rd      | 16 +++++++++
 man/create_cost_inc_dna.Rd        | 16 +++++++++
 man/create_episode_file.Rd        | 16 +++++++++
 man/create_individual_file.Rd     | 32 +++++++++++++++++
 man/fill_missing_cij_markers.Rd   | 16 +++++++++
 man/join_cohort_lookups.Rd        | 16 +++++++++
 man/link_delayed_discharge_eps.Rd | 16 +++++++--
 man/load_ep_file_vars.Rd          | 16 +++++++++
 man/lookup_uplift.Rd              | 16 +++++++++
 man/max_no_inf.Rd                 |  5 +++
 man/min_no_inf.Rd                 |  5 +++
 man/recode_gender.Rd              | 32 +++++++++++++++++
 man/remove_blank_chi.Rd           | 32 +++++++++++++++++
 man/store_ep_file_vars.Rd         | 16 +++++++++
 52 files changed, 1240 insertions(+), 28 deletions(-)

diff --git a/R/add_nsu_cohort.R b/R/add_nsu_cohort.R
index 00260bb8e..9a3032259 100644
--- a/R/add_nsu_cohort.R
+++ b/R/add_nsu_cohort.R
@@ -7,7 +7,7 @@
 #' @return A data frame containing the Non-Service Users as additional rows
 #' @export
 #'
-#' @family episode file
+#' @family episode_file
 #' @seealso [get_nsu_path()]
 add_nsu_cohort <- function(
     data,
diff --git a/R/add_ppa_flag.R b/R/add_ppa_flag.R
index d0d0c4395..bb99f0543 100644
--- a/R/add_ppa_flag.R
+++ b/R/add_ppa_flag.R
@@ -6,7 +6,7 @@
 #' @param data A data frame
 #'
 #' @return A data frame to use as a lookup of PPAs
-#' @family episode file
+#' @family episode_file
 add_ppa_flag <- function(data) {
   check_variables_exist(
     data,
diff --git a/R/aggregate_by_chi.R b/R/aggregate_by_chi.R
index db12f7a9e..b12fa5710 100644
--- a/R/aggregate_by_chi.R
+++ b/R/aggregate_by_chi.R
@@ -7,6 +7,7 @@
 #' @importFrom data.table .SD
 #'
 #' @inheritParams create_individual_file
+#' @family individual_file
 aggregate_by_chi <- function(episode_file) {
   cli::cli_alert_info("Aggregate by CHI function started at {Sys.time()}")
 
@@ -196,6 +197,7 @@ vars_contain <- function(data, vars, ignore_case = FALSE) {
 #' @description Aggregate CH variables by CHI and CIS.
 #'
 #' @inheritParams create_individual_file
+#' @family individual_file
 aggregate_ch_episodes <- function(episode_file) {
   cli::cli_alert_info("Aggregate ch episodes function started at {Sys.time()}")
 
diff --git a/R/cost_uplift.R b/R/cost_uplift.R
index 2bb1d4c1f..e554c2505 100644
--- a/R/cost_uplift.R
+++ b/R/cost_uplift.R
@@ -3,6 +3,7 @@
 #' @param data episode data
 #'
 #' @return episode data with uplifted costs
+#' @family episode_file
 apply_cost_uplift <- function(data) {
   data <- data %>%
     # attach a uplift scale as the last column
@@ -34,6 +35,7 @@ apply_cost_uplift <- function(data) {
 #' @param data episode data
 #'
 #' @return episode data with a uplift scale
+#' @family episode_file
 lookup_uplift <- function(data) {
   # We have set uplifts to use for 2020/21, 2021/22 and 2022/23,
   # provided by Paul Leak.
diff --git a/R/create_episode_file.R b/R/create_episode_file.R
index 3dc33e193..fad4d4584 100644
--- a/R/create_episode_file.R
+++ b/R/create_episode_file.R
@@ -15,6 +15,7 @@
 #'
 #' @return a [tibble][tibble::tibble-package] containing the episode file
 #' @export
+#' @family episode_file
 create_episode_file <- function(
     processed_data_list,
     year,
@@ -158,6 +159,7 @@ create_episode_file <- function(
 #' @param vars_to_keep a character vector of the variables to keep, all others
 #' will be stored.
 #'
+#' @family episode_file
 #' @return `data` with only the `vars_to_keep` kept
 store_ep_file_vars <- function(data, year, vars_to_keep) {
   tempfile_path <- get_file_path(
@@ -195,6 +197,7 @@ store_ep_file_vars <- function(data, year, vars_to_keep) {
 #' @inheritParams create_episode_file
 #' @inheritParams store_ep_file_vars
 #'
+#' @family episode_file
 #' @return The full SLF data.
 load_ep_file_vars <- function(data, year) {
   tempfile_path <- get_file_path(
@@ -222,6 +225,7 @@ load_ep_file_vars <- function(data, year) {
 #'
 #' @inheritParams store_ep_file_vars
 #'
+#' @family episode_file
 #' @return A data frame with CIJ markers filled in for those missing.
 fill_missing_cij_markers <- function(data) {
   fixable_data <- data %>%
@@ -276,6 +280,7 @@ fill_missing_cij_markers <- function(data) {
 #'
 #' @inheritParams store_ep_file_vars
 #'
+#' @family episode_file
 #' @return The data with CIJ variables corrected.
 correct_cij_vars <- function(data) {
   check_variables_exist(
@@ -317,6 +322,7 @@ correct_cij_vars <- function(data) {
 #'
 #' @inheritParams store_ep_file_vars
 #'
+#' @family episode_file
 #' @return The data with cost including dna.
 create_cost_inc_dna <- function(data) {
   check_variables_exist(data, c("cost_total_net", "attendance_status"))
@@ -341,6 +347,7 @@ create_cost_inc_dna <- function(data) {
 #' @inheritParams store_ep_file_vars
 #' @inheritParams create_demographic_cohorts
 #'
+#' @family episode_file
 #' @return The data unchanged (the cohorts are written to disk)
 create_cohort_lookups <- function(data, year, update = latest_update()) {
   # Use future so the cohorts can be created simultaneously (in parallel)
@@ -377,6 +384,7 @@ create_cohort_lookups <- function(data, year, update = latest_update()) {
 #' @inheritParams get_demographic_cohorts_path
 #' @param demographic_cohort,service_use_cohort The cohort data
 #'
+#' @family episode_file
 #' @return The data including the Demographic and Service Use lookups.
 join_cohort_lookups <- function(
     data,
diff --git a/R/create_individual_file.R b/R/create_individual_file.R
index 436f1c8d7..d4b29eadd 100644
--- a/R/create_individual_file.R
+++ b/R/create_individual_file.R
@@ -8,6 +8,7 @@
 #' @inheritParams create_episode_file
 #'
 #' @return The processed individual file
+#' @family individual_file
 #' @export
 create_individual_file <- function(
     episode_file,
@@ -99,7 +100,7 @@ create_individual_file <- function(
 #' Remove blank CHI
 #'
 #' @description Convert blank strings to NA and remove NAs from CHI column
-#'
+#' @family individual_file
 #' @inheritParams create_individual_file
 remove_blank_chi <- function(episode_file) {
   cli::cli_alert_info("Remove blank CHI function started at {Sys.time()}")
@@ -113,7 +114,7 @@ remove_blank_chi <- function(episode_file) {
 #' Add CIJ-related columns
 #'
 #' @description Add new columns related to CIJ
-#'
+#' @family individual_file
 #' @inheritParams create_individual_file
 add_cij_columns <- function(episode_file) {
   cli::cli_alert_info("Add cij columns function started at {Sys.time()}")
@@ -152,7 +153,7 @@ add_cij_columns <- function(episode_file) {
 #'
 #' @description Add new columns based on SMRType and recid which follow a pattern
 #' of prefixed column names created based on some condition.
-#'
+#' @family individual_file
 #' @inheritParams create_individual_file
 add_all_columns <- function(episode_file) {
   cli::cli_alert_info("Add all columns function started at {Sys.time()}")
@@ -203,6 +204,7 @@ add_all_columns <- function(episode_file) {
 #' @inheritParams create_individual_file
 #' @param prefix Prefix to add to related columns, e.g. "Acute"
 #' @param condition Condition to create new columns based on
+#' @family individual_file
 add_acute_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -213,6 +215,7 @@ add_acute_columns <- function(episode_file, prefix, condition) {
 #' Add Mat columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_mat_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -223,6 +226,7 @@ add_mat_columns <- function(episode_file, prefix, condition) {
 #' Add MH columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_mh_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -233,6 +237,7 @@ add_mh_columns <- function(episode_file, prefix, condition) {
 #' Add GLS columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_gls_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -243,6 +248,7 @@ add_gls_columns <- function(episode_file, prefix, condition) {
 #' Add OP columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_op_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file <- episode_file %>%
@@ -265,6 +271,7 @@ add_op_columns <- function(episode_file, prefix, condition) {
 #' Add AE columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_ae_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -275,6 +282,7 @@ add_ae_columns <- function(episode_file, prefix, condition) {
 #' Add PIS columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_pis_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -285,6 +293,7 @@ add_pis_columns <- function(episode_file, prefix, condition) {
 #' Add OoH columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_ooh_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file <- episode_file %>%
@@ -319,6 +328,7 @@ add_ooh_columns <- function(episode_file, prefix, condition) {
 #' Add DN columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_dn_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   if ("total_no_dn_contacts" %in% names(episode_file)) {
@@ -341,6 +351,7 @@ add_dn_columns <- function(episode_file, prefix, condition) {
 #' Add CMH columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_cmh_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -351,6 +362,7 @@ add_cmh_columns <- function(episode_file, prefix, condition) {
 #' Add DD columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_dd_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   condition_delay <- substitute(condition & primary_delay_reason != "9")
@@ -371,6 +383,7 @@ add_dd_columns <- function(episode_file, prefix, condition) {
 #' Add NSU columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_nsu_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -381,6 +394,7 @@ add_nsu_columns <- function(episode_file, prefix, condition) {
 #' Add NRS columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_nrs_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -391,6 +405,7 @@ add_nrs_columns <- function(episode_file, prefix, condition) {
 #' Add HL1 columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_hl1_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -400,6 +415,7 @@ add_hl1_columns <- function(episode_file, prefix, condition) {
 #' Add CH columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_ch_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -428,6 +444,7 @@ add_ch_columns <- function(episode_file, prefix, condition) {
 #' Add HC columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_hc_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file <- episode_file %>%
@@ -470,6 +487,7 @@ add_hc_columns <- function(episode_file, prefix, condition) {
 #' Add AT columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_at_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -483,6 +501,7 @@ add_at_columns <- function(episode_file, prefix, condition) {
 #' Add SDS columns
 #'
 #' @inheritParams add_acute_columns
+#' @family individual_file
 add_sds_columns <- function(episode_file, prefix, condition) {
   condition <- substitute(condition)
   episode_file %>%
@@ -502,7 +521,9 @@ add_sds_columns <- function(episode_file, prefix, condition) {
 #'
 #' @inheritParams add_acute_columns
 #' @param ipdc_d Whether to create columns based on IPDC = "D" (lgl)
-#' @param elective Whether to create columns based on Elective/Non-Elective cij_pattype (lgl)
+#' @param elective Whether to create columns based on Elective/Non-Elective
+#' cij_pattype (lgl)
+#' @family individual_file
 add_ipdc_cols <- function(episode_file, prefix, condition, ipdc_d = TRUE, elective = TRUE) {
   condition_i <- substitute(eval(condition) & ipdc == "I")
   episode_file <- episode_file %>%
@@ -540,11 +561,13 @@ add_ipdc_cols <- function(episode_file, prefix, condition, ipdc_d = TRUE, electi
 
 #' Add standard columns
 #'
-#' @description Add standard columns (DoB, postcode, gpprac, episodes, cost) to episode file.
+#' @description Add standard columns (DoB, postcode, gpprac, episodes, cost)
+#' to episode file.
 #'
 #' @inheritParams add_acute_columns
 #' @param episode Whether to create prefix_episodes col, e.g. "Acute_episodes"
 #' @param cost Whether to create prefix_cost col, e.g. "Acute_cost"
+#' @family individual_file
 add_standard_cols <- function(episode_file, prefix, condition, episode = FALSE, cost = FALSE) {
   if (episode) {
     episode_file <- dplyr::mutate(episode_file, "{prefix}_episodes" := dplyr::if_else(eval(condition), 1L, NA_integer_))
@@ -560,6 +583,7 @@ add_standard_cols <- function(episode_file, prefix, condition, episode = FALSE,
 #' @description Clean up CH-related columns.
 #'
 #' @inheritParams create_individual_file
+#' @family individual_file
 clean_up_ch <- function(episode_file, year) {
   cli::cli_alert_info("Clean up CH function started at {Sys.time()}")
 
@@ -602,6 +626,7 @@ clean_up_ch <- function(episode_file, year) {
 #' @description Recode gender to 1.5 if 0 or 9.
 #'
 #' @inheritParams create_individual_file
+#' @family individual_file
 recode_gender <- function(episode_file) {
   cli::cli_alert_info("Recode Gender function started at {Sys.time()}")
 
@@ -620,6 +645,7 @@ recode_gender <- function(episode_file) {
 #' @description Returns chr vector of column names
 #' which follow format "condition" and "condition_date" e.g.
 #' "dementia" and "dementia_date"
+#' @family individual_file
 condition_cols <- function() {
   conditions <- slfhelper::ltc_vars
   date_cols <- paste0(conditions, "_date")
@@ -634,6 +660,7 @@ condition_cols <- function() {
 #' are missing (instead returns NA)
 #'
 #' @param x Vector to return max of
+#' @family helper_funs
 max_no_inf <- function(x) {
   dplyr::if_else(all(is.na(x)), NA, max(x, na.rm = TRUE))
 }
@@ -645,6 +672,7 @@ max_no_inf <- function(x) {
 #' are missing (instead returns NA)
 #'
 #' @param x Vector to return min of
+#' @family helper_funs
 min_no_inf <- function(x) {
   dplyr::if_else(all(is.na(x)), NA, min(x, na.rm = TRUE))
 }
diff --git a/R/link_delayed_discharge_eps.R b/R/link_delayed_discharge_eps.R
index fd9b2ea60..5fb19b651 100644
--- a/R/link_delayed_discharge_eps.R
+++ b/R/link_delayed_discharge_eps.R
@@ -7,7 +7,7 @@
 #' @return A data frame with the delayed discharge cohort added and linked
 #' using the `cij_marker`
 #'
-#' @family episode file
+#' @family episode_file
 link_delayed_discharge_eps <- function(
     episode_file,
     year,
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 41517d94a..dd144fe2a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -18,6 +18,7 @@ reference:
     - is_missing
     - check_variables_exist
     - check_year_valid
+    - check_it_reference
 
 
   - title: Years & Dates
@@ -45,6 +46,8 @@ reference:
   - contents:
     - starts_with("clean_up")
     - fill_ch_names
+    - cascade_geographies
+    - correct_demographics
 
 
   - title: Create
@@ -80,13 +83,7 @@ reference:
     - contains("_hscp_to")
     - contains("_chi")
     - contains("lca")
-
-
-  - title: Duplicates
-    desc: Functions to fix duplicates
-  - contents:
-    - contains("_duplicates")
-
+    - la_code_lookup
 
   - title: Writing data
     desc: Functions which mask the typical data write functions to add some nice defaults and importantly fix file permissions.
@@ -101,6 +98,8 @@ reference:
     - ends_with("_period")
     - ends_with("_update")
     - starts_with("it_extract")
+    - gzip_files
+    - make_lowercase_ext
 
 
   - title: Files
@@ -141,10 +140,53 @@ reference:
   - title: Episode file
     desc: Building the episode file
   - contents:
-    - has_concept("episode file")
-  - subtitle: Cohorts
+    - has_concept("episode_file")
+    - fill_geographies
+  - subtitle: Lookups
   - contents:
     - has_concept("Demographic and Service Use Cohort functions")
+    - join_sparra_hhg
+    - join_deaths_data
+    - join_sc_client
+    - match_on_ltcs
+
+
+  - title: Individual file
+    desc: Building the episode file
+  - contents:
+    - has_concept("individual_file")
+  - subtitle: Lookups
+  - contents:
+    - has_concept("Demographic and Service Use Cohort functions")
+    - join_sparra_hhg
+    - join_cohort_lookups
+    - join_deaths_data
+    - join_slf_lookup_vars
+    - match_on_ltcs
+
+  - title: Demographics
+    desc: Things related to demographic lookups
+  - contents:
+    - fill_geographies
+    - get_gpprac_opendata
+    - make_gpprac_lookup
+    - make_postcode_lookup
+    - recode_health_boards
+    - recode_hscp
+    - la_code_lookup
+
+
+  - title: Miscellaneous functions
+    desc: Miscellaneous functions.
+  - subtitle: Homelessness
+  - contents:
+    - fix_east_ayrshire_duplicates
+    - fix_west_dun_duplicates
+    - produce_homelessness_completeness
+  - subtitle: Helper functions
+  - contents:
+    - vars_end_with
+    - has_concept("helper_funs")
 
 
   - title: Testing
diff --git a/man/add_acute_columns.Rd b/man/add_acute_columns.Rd
index c2659f821..801708caf 100644
--- a/man/add_acute_columns.Rd
+++ b/man/add_acute_columns.Rd
@@ -16,3 +16,35 @@ add_acute_columns(episode_file, prefix, condition)
 \description{
 Add Acute columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_ae_columns.Rd b/man/add_ae_columns.Rd
index fdc31b7ff..027a5ebe2 100644
--- a/man/add_ae_columns.Rd
+++ b/man/add_ae_columns.Rd
@@ -16,3 +16,35 @@ add_ae_columns(episode_file, prefix, condition)
 \description{
 Add AE columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_all_columns.Rd b/man/add_all_columns.Rd
index 1d2e587db..eb0b70231 100644
--- a/man/add_all_columns.Rd
+++ b/man/add_all_columns.Rd
@@ -13,3 +13,35 @@ add_all_columns(episode_file)
 Add new columns based on SMRType and recid which follow a pattern
 of prefixed column names created based on some condition.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_at_columns.Rd b/man/add_at_columns.Rd
index af978530a..cddd7dc2d 100644
--- a/man/add_at_columns.Rd
+++ b/man/add_at_columns.Rd
@@ -16,3 +16,35 @@ add_at_columns(episode_file, prefix, condition)
 \description{
 Add AT columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_ch_columns.Rd b/man/add_ch_columns.Rd
index a036a257e..94aca9618 100644
--- a/man/add_ch_columns.Rd
+++ b/man/add_ch_columns.Rd
@@ -16,3 +16,35 @@ add_ch_columns(episode_file, prefix, condition)
 \description{
 Add CH columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_cij_columns.Rd b/man/add_cij_columns.Rd
index c48c1a3ef..a708919fe 100644
--- a/man/add_cij_columns.Rd
+++ b/man/add_cij_columns.Rd
@@ -12,3 +12,35 @@ add_cij_columns(episode_file)
 \description{
 Add new columns related to CIJ
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_cmh_columns.Rd b/man/add_cmh_columns.Rd
index a1cb74abb..b34619fd3 100644
--- a/man/add_cmh_columns.Rd
+++ b/man/add_cmh_columns.Rd
@@ -16,3 +16,35 @@ add_cmh_columns(episode_file, prefix, condition)
 \description{
 Add CMH columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_dd_columns.Rd b/man/add_dd_columns.Rd
index 11e85fdc7..20e956226 100644
--- a/man/add_dd_columns.Rd
+++ b/man/add_dd_columns.Rd
@@ -16,3 +16,35 @@ add_dd_columns(episode_file, prefix, condition)
 \description{
 Add DD columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_dn_columns.Rd b/man/add_dn_columns.Rd
index ffdf59a82..a1450ef6d 100644
--- a/man/add_dn_columns.Rd
+++ b/man/add_dn_columns.Rd
@@ -16,3 +16,35 @@ add_dn_columns(episode_file, prefix, condition)
 \description{
 Add DN columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_gls_columns.Rd b/man/add_gls_columns.Rd
index 6ab7e9645..f724fc28e 100644
--- a/man/add_gls_columns.Rd
+++ b/man/add_gls_columns.Rd
@@ -16,3 +16,35 @@ add_gls_columns(episode_file, prefix, condition)
 \description{
 Add GLS columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_hc_columns.Rd b/man/add_hc_columns.Rd
index a58f226ec..a0dcd3ea7 100644
--- a/man/add_hc_columns.Rd
+++ b/man/add_hc_columns.Rd
@@ -16,3 +16,35 @@ add_hc_columns(episode_file, prefix, condition)
 \description{
 Add HC columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_hl1_columns.Rd b/man/add_hl1_columns.Rd
index 24fc714e9..1af70e711 100644
--- a/man/add_hl1_columns.Rd
+++ b/man/add_hl1_columns.Rd
@@ -16,3 +16,35 @@ add_hl1_columns(episode_file, prefix, condition)
 \description{
 Add HL1 columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_ipdc_cols.Rd b/man/add_ipdc_cols.Rd
index bd630b9d3..c943028bc 100644
--- a/man/add_ipdc_cols.Rd
+++ b/man/add_ipdc_cols.Rd
@@ -15,9 +15,42 @@ add_ipdc_cols(episode_file, prefix, condition, ipdc_d = TRUE, elective = TRUE)
 
 \item{ipdc_d}{Whether to create columns based on IPDC = "D" (lgl)}
 
-\item{elective}{Whether to create columns based on Elective/Non-Elective cij_pattype (lgl)}
+\item{elective}{Whether to create columns based on Elective/Non-Elective
+cij_pattype (lgl)}
 }
 \description{
 Add columns based on value in IPDC column, which can
 be further split by Elective/Non-Elective CIJ.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_mat_columns.Rd b/man/add_mat_columns.Rd
index 5faab0dc1..744c2f528 100644
--- a/man/add_mat_columns.Rd
+++ b/man/add_mat_columns.Rd
@@ -16,3 +16,35 @@ add_mat_columns(episode_file, prefix, condition)
 \description{
 Add Mat columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_mh_columns.Rd b/man/add_mh_columns.Rd
index c587c490a..f103eced7 100644
--- a/man/add_mh_columns.Rd
+++ b/man/add_mh_columns.Rd
@@ -16,3 +16,35 @@ add_mh_columns(episode_file, prefix, condition)
 \description{
 Add MH columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_nrs_columns.Rd b/man/add_nrs_columns.Rd
index b41201a57..47d5a598d 100644
--- a/man/add_nrs_columns.Rd
+++ b/man/add_nrs_columns.Rd
@@ -16,3 +16,35 @@ add_nrs_columns(episode_file, prefix, condition)
 \description{
 Add NRS columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_nsu_cohort.Rd b/man/add_nsu_cohort.Rd
index 4ea9324e0..43118a087 100644
--- a/man/add_nsu_cohort.Rd
+++ b/man/add_nsu_cohort.Rd
@@ -22,8 +22,18 @@ Add NSU cohort to working file
 \seealso{
 \code{\link[=get_nsu_path]{get_nsu_path()}}
 
-Other episode file: 
+Other episode_file: 
 \code{\link{add_ppa_flag}()},
-\code{\link{link_delayed_discharge_eps}()}
+\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{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}
+\concept{episode_file}
diff --git a/man/add_nsu_columns.Rd b/man/add_nsu_columns.Rd
index 5aed481f0..9626686aa 100644
--- a/man/add_nsu_columns.Rd
+++ b/man/add_nsu_columns.Rd
@@ -16,3 +16,35 @@ add_nsu_columns(episode_file, prefix, condition)
 \description{
 Add NSU columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_ooh_columns.Rd b/man/add_ooh_columns.Rd
index f1e6b63f5..345ae89e3 100644
--- a/man/add_ooh_columns.Rd
+++ b/man/add_ooh_columns.Rd
@@ -16,3 +16,35 @@ add_ooh_columns(episode_file, prefix, condition)
 \description{
 Add OoH columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_op_columns.Rd b/man/add_op_columns.Rd
index 9fb8bc158..9749c8f28 100644
--- a/man/add_op_columns.Rd
+++ b/man/add_op_columns.Rd
@@ -16,3 +16,35 @@ add_op_columns(episode_file, prefix, condition)
 \description{
 Add OP columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_pis_columns.Rd b/man/add_pis_columns.Rd
index 836218da0..fc2175b62 100644
--- a/man/add_pis_columns.Rd
+++ b/man/add_pis_columns.Rd
@@ -16,3 +16,35 @@ add_pis_columns(episode_file, prefix, condition)
 \description{
 Add PIS columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_ppa_flag.Rd b/man/add_ppa_flag.Rd
index 8533a09f5..f19f81009 100644
--- a/man/add_ppa_flag.Rd
+++ b/man/add_ppa_flag.Rd
@@ -18,8 +18,18 @@ a combination of diagnostic codes and operation codes, whether an admission
 was preventable or not.
 }
 \seealso{
-Other episode file: 
+Other episode_file: 
 \code{\link{add_nsu_cohort}()},
-\code{\link{link_delayed_discharge_eps}()}
+\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{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}
+\concept{episode_file}
diff --git a/man/add_sds_columns.Rd b/man/add_sds_columns.Rd
index c06b88527..fd9ed0324 100644
--- a/man/add_sds_columns.Rd
+++ b/man/add_sds_columns.Rd
@@ -16,3 +16,35 @@ add_sds_columns(episode_file, prefix, condition)
 \description{
 Add SDS columns
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/add_standard_cols.Rd b/man/add_standard_cols.Rd
index 4392157d2..6dba5de0d 100644
--- a/man/add_standard_cols.Rd
+++ b/man/add_standard_cols.Rd
@@ -24,5 +24,38 @@ add_standard_cols(
 \item{cost}{Whether to create prefix_cost col, e.g. "Acute_cost"}
 }
 \description{
-Add standard columns (DoB, postcode, gpprac, episodes, cost) to episode file.
+Add standard columns (DoB, postcode, gpprac, episodes, cost)
+to episode file.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/aggregate_by_chi.Rd b/man/aggregate_by_chi.Rd
index 1585accbb..ffe7fcf4b 100644
--- a/man/aggregate_by_chi.Rd
+++ b/man/aggregate_by_chi.Rd
@@ -13,3 +13,35 @@ aggregate_by_chi(episode_file)
 Aggregate episode file by CHI to convert into
 individual file.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/aggregate_ch_episodes.Rd b/man/aggregate_ch_episodes.Rd
index 3223e6d25..2d284a2c3 100644
--- a/man/aggregate_ch_episodes.Rd
+++ b/man/aggregate_ch_episodes.Rd
@@ -12,3 +12,35 @@ aggregate_ch_episodes(episode_file)
 \description{
 Aggregate CH variables by CHI and CIS.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/apply_cost_uplift.Rd b/man/apply_cost_uplift.Rd
index 315e154f3..5461d15be 100644
--- a/man/apply_cost_uplift.Rd
+++ b/man/apply_cost_uplift.Rd
@@ -15,3 +15,19 @@ episode data with uplifted costs
 \description{
 Uplift costs
 }
+\seealso{
+Other episode_file: 
+\code{\link{add_nsu_cohort}()},
+\code{\link{add_ppa_flag}()},
+\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{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/clean_up_ch.Rd b/man/clean_up_ch.Rd
index c0c61966d..fda979372 100644
--- a/man/clean_up_ch.Rd
+++ b/man/clean_up_ch.Rd
@@ -14,3 +14,35 @@ clean_up_ch(episode_file, year)
 \description{
 Clean up CH-related columns.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/condition_cols.Rd b/man/condition_cols.Rd
index ba037a609..c8c73921a 100644
--- a/man/condition_cols.Rd
+++ b/man/condition_cols.Rd
@@ -11,3 +11,35 @@ Returns chr vector of column names
 which follow format "condition" and "condition_date" e.g.
 "dementia" and "dementia_date"
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/correct_cij_vars.Rd b/man/correct_cij_vars.Rd
index 558514dc6..5fd265d22 100644
--- a/man/correct_cij_vars.Rd
+++ b/man/correct_cij_vars.Rd
@@ -15,3 +15,19 @@ The data with CIJ variables corrected.
 \description{
 Correct the CIJ variables
 }
+\seealso{
+Other episode_file: 
+\code{\link{add_nsu_cohort}()},
+\code{\link{add_ppa_flag}()},
+\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{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/create_cohort_lookups.Rd b/man/create_cohort_lookups.Rd
index 109869074..934354375 100644
--- a/man/create_cohort_lookups.Rd
+++ b/man/create_cohort_lookups.Rd
@@ -19,3 +19,19 @@ The data unchanged (the cohorts are written to disk)
 \description{
 Create the 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_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{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/create_cost_inc_dna.Rd b/man/create_cost_inc_dna.Rd
index 47c38b176..d78e9c907 100644
--- a/man/create_cost_inc_dna.Rd
+++ b/man/create_cost_inc_dna.Rd
@@ -15,3 +15,19 @@ The data with cost including dna.
 \description{
 Create cost total net inc DNA
 }
+\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_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{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/create_individual_file.Rd b/man/create_individual_file.Rd
index c4502e5ae..2b54de366 100644
--- a/man/create_individual_file.Rd
+++ b/man/create_individual_file.Rd
@@ -32,3 +32,35 @@ The processed individual file
 \description{
 Creates the individual file from the episode file.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{recode_gender}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/fill_missing_cij_markers.Rd b/man/fill_missing_cij_markers.Rd
index 4795eed7a..7918329a7 100644
--- a/man/fill_missing_cij_markers.Rd
+++ b/man/fill_missing_cij_markers.Rd
@@ -15,3 +15,19 @@ A data frame with CIJ markers filled in for those missing.
 \description{
 Fill any missing CIJ markers for records that should have them
 }
+\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{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/join_cohort_lookups.Rd b/man/join_cohort_lookups.Rd
index 3ef549cc3..142a2c1ee 100644
--- a/man/join_cohort_lookups.Rd
+++ b/man/join_cohort_lookups.Rd
@@ -29,3 +29,19 @@ The data including the Demographic and Service Use lookups.
 \description{
 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 49c3e2a75..245fa2754 100644
--- a/man/link_delayed_discharge_eps.Rd
+++ b/man/link_delayed_discharge_eps.Rd
@@ -25,8 +25,18 @@ using the \code{cij_marker}
 Link  Delayed Discharge to WIP episode file
 }
 \seealso{
-Other episode file: 
+Other episode_file: 
 \code{\link{add_nsu_cohort}()},
-\code{\link{add_ppa_flag}()}
+\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{join_cohort_lookups}()},
+\code{\link{load_ep_file_vars}()},
+\code{\link{lookup_uplift}()},
+\code{\link{store_ep_file_vars}()}
 }
-\concept{episode file}
+\concept{episode_file}
diff --git a/man/load_ep_file_vars.Rd b/man/load_ep_file_vars.Rd
index 509b0e00c..965e8bfce 100644
--- a/man/load_ep_file_vars.Rd
+++ b/man/load_ep_file_vars.Rd
@@ -17,3 +17,19 @@ The full SLF data.
 \description{
 Load the unneeded episode file variables
 }
+\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{join_cohort_lookups}()},
+\code{\link{link_delayed_discharge_eps}()},
+\code{\link{lookup_uplift}()},
+\code{\link{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/lookup_uplift.Rd b/man/lookup_uplift.Rd
index f3fb4865c..356a25d4a 100644
--- a/man/lookup_uplift.Rd
+++ b/man/lookup_uplift.Rd
@@ -15,3 +15,19 @@ episode data with a uplift scale
 \description{
 Set uplift scale
 }
+\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{join_cohort_lookups}()},
+\code{\link{link_delayed_discharge_eps}()},
+\code{\link{load_ep_file_vars}()},
+\code{\link{store_ep_file_vars}()}
+}
+\concept{episode_file}
diff --git a/man/max_no_inf.Rd b/man/max_no_inf.Rd
index 79b9a1057..b6b4b0f0c 100644
--- a/man/max_no_inf.Rd
+++ b/man/max_no_inf.Rd
@@ -14,3 +14,8 @@ Custom maximum function which removes
 missing values but doesn't return Inf if all values
 are missing (instead returns NA)
 }
+\seealso{
+Other helper_funs: 
+\code{\link{min_no_inf}()}
+}
+\concept{helper_funs}
diff --git a/man/min_no_inf.Rd b/man/min_no_inf.Rd
index 38029214f..35c187649 100644
--- a/man/min_no_inf.Rd
+++ b/man/min_no_inf.Rd
@@ -14,3 +14,8 @@ Custom minimum function which removes
 missing values but doesn't return Inf if all values
 are missing (instead returns NA)
 }
+\seealso{
+Other helper_funs: 
+\code{\link{max_no_inf}()}
+}
+\concept{helper_funs}
diff --git a/man/recode_gender.Rd b/man/recode_gender.Rd
index aaa28e6eb..2ea26b5cc 100644
--- a/man/recode_gender.Rd
+++ b/man/recode_gender.Rd
@@ -12,3 +12,35 @@ recode_gender(episode_file)
 \description{
 Recode gender to 1.5 if 0 or 9.
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{remove_blank_chi}()}
+}
+\concept{individual_file}
diff --git a/man/remove_blank_chi.Rd b/man/remove_blank_chi.Rd
index b290dd1e7..4e5efa740 100644
--- a/man/remove_blank_chi.Rd
+++ b/man/remove_blank_chi.Rd
@@ -12,3 +12,35 @@ remove_blank_chi(episode_file)
 \description{
 Convert blank strings to NA and remove NAs from CHI column
 }
+\seealso{
+Other individual_file: 
+\code{\link{add_acute_columns}()},
+\code{\link{add_ae_columns}()},
+\code{\link{add_all_columns}()},
+\code{\link{add_at_columns}()},
+\code{\link{add_ch_columns}()},
+\code{\link{add_cij_columns}()},
+\code{\link{add_cmh_columns}()},
+\code{\link{add_dd_columns}()},
+\code{\link{add_dn_columns}()},
+\code{\link{add_gls_columns}()},
+\code{\link{add_hc_columns}()},
+\code{\link{add_hl1_columns}()},
+\code{\link{add_ipdc_cols}()},
+\code{\link{add_mat_columns}()},
+\code{\link{add_mh_columns}()},
+\code{\link{add_nrs_columns}()},
+\code{\link{add_nsu_columns}()},
+\code{\link{add_ooh_columns}()},
+\code{\link{add_op_columns}()},
+\code{\link{add_pis_columns}()},
+\code{\link{add_sds_columns}()},
+\code{\link{add_standard_cols}()},
+\code{\link{aggregate_by_chi}()},
+\code{\link{aggregate_ch_episodes}()},
+\code{\link{clean_up_ch}()},
+\code{\link{condition_cols}()},
+\code{\link{create_individual_file}()},
+\code{\link{recode_gender}()}
+}
+\concept{individual_file}
diff --git a/man/store_ep_file_vars.Rd b/man/store_ep_file_vars.Rd
index 880266d58..687bdcecb 100644
--- a/man/store_ep_file_vars.Rd
+++ b/man/store_ep_file_vars.Rd
@@ -20,3 +20,19 @@ will be stored.}
 \description{
 Store the unneeded episode file variables
 }
+\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{join_cohort_lookups}()},
+\code{\link{link_delayed_discharge_eps}()},
+\code{\link{load_ep_file_vars}()},
+\code{\link{lookup_uplift}()}
+}
+\concept{episode_file}