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 <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennifer Thom <[email protected]>
Public-Health-Scotland · Sep 26, 2023 · 81c2191 · 81c2191
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commit 81c2191
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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,