Merge pull request #41 from NorwegianVeterinaryInstitute/dev

NVIdb v0.11.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.11.0
-Date: 2024-01-24
+Version: 0.11.1
+Date: 2024-02-05
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",

NEWS

@@ -1,9 +1,22 @@
+NVIdb 0.11.1 - (2024-02-05)
+----------------------------------------
+
+New features:
+
+- set_disease_parameters now accepts the arguments purpose, FUN and select_statement.
+
+
+Bug fixes:
+
+- set_disease_parameters now accepts metodekode with 2 digits.
+
+
 NVIdb 0.11.0 - (2024-01-24)
 ----------------------------------------
 
 New features:
 
-- Created `retrieve_PJS_data` to retrieve and standardisation of PJSdata.
+- Created `retrieve_PJS_data` to retrieve and standardise PJSdata.
 
 - Created `transform_code_values` to easy transform few code combinations into other values.
 

R/build_query_one_disease.R

@@ -1,25 +1,41 @@
 #' @title Builds query for selecting data for one disease from PJS
-#' @description Builds the query for selecting all data for one infection/disease within one year from PJS. The input is the analytter
-#'     for the infectious agent and/or disease, the hensikter and metoder specific for the infection and/or disease. The the query is
-#'     written in T-SQL as used by MS-SQL.
+#' @description Builds the query for selecting all data for one
+#'     infection/disease within one year from PJS. The input is the
+#'     analytter for the infectious agent and/or disease, the
+#'     hensikter and metoder specific for the infection and/or
+#'     disease. The the query is written in T-SQL as used by MS-SQL.
 #'
-#' @details The function builds the SQL syntax to select all PJS-journals concerning one infection and/o disease from PJS. This is based
-#'     on selecting all journals with the disease and/or infectious agent analytt in resultat, konklusjon or sakskonklusjon. By this, all
-#'     journals were the examination have been performed and a result has been entered should be selected.
+#' @details The function builds the SQL syntax to select all PJS-journals
+#'     concerning one infection and/o disease from PJS. This is based
+#'     on selecting all journals with the disease and/or infectious
+#'     agent analytt in resultat, konklusjon or sakskonklusjon. By this,
+#'     all journals were the examination have been performed and a
+#'     result has been entered should be selected.
 #'
-#'     One or more specific hensikter may be input to the selection statement. With specific hensikt is meant a hensikt that will imply
-#'     that the sample will be examined for the infectious agent or disease. Thereby, the selection will include samples that haven't
-#'     been set up for examination yet, samples that were unfit for examination and samples for which wrong conclusions have been entered.
+#'     One or more specific hensikter may be input to the selection
+#'     statement. With specific hensikt is meant a hensikt that will
+#'     imply that the sample will be examined for the infectious agent
+#'     or disease. Thereby, the selection will include samples that
+#'     haven't been set up for examination yet, samples that were
+#'     unfit for examination and samples for which wrong conclusions
+#'      have been entered.
 #'
-#'     One or more specific metoder may be input to the selection statement. With specific metode is meant a metode that implies an
-#'     examination that will give one of the input analytter as a result. Thereby, the query will include samples that have been set up
-#'     for examination, but haven't been examined yet, samples that were unfit for examination and samples for which wrong results have
-#'     been entered.
+#'     One or more specific metoder may be input to the selection
+#'     statement. With specific metode is meant a metode that implies
+#'     an examination that will give one of the input analytter as a
+#'     result. Thereby, the query will include samples that have been
+#'     set up for examination, but haven't been examined yet, samples
+#'     that were unfit for examination and samples for which wrong
+#'     results have been entered.
 #'
-#'     To select both the disease analytt and the infectious agent analytt ensures that all journals that have been examined with a result
-#'     is included in the output. The inclusion of specific hensikter and metoder, if exists, ensures that all journals received with the
-#'     purpose of examining for the infectious agent and/or disease will be included even if the examination has not been performed. This
-#'     is important for a full control of all relevant data for an infectious agent and/or disease.
+#'     To select both the disease analytt and the infectious agent
+#'     analytt ensures that all journals that have been examined with
+#'     a result is included in the output. The inclusion of specific
+#'     hensikter and metoder, if exists, ensures that all journals
+#'     received with the purpose of examining for the infectious agent
+#'     and/or disease will be included even if the examination has
+#'     not been performed. This is important for a full control of
+#'     all relevant data for an infectious agent and/or disease.
 #'
 #' @template build_query_year
 #' @param analytt [\code{character}]\cr

R/set_disease_parameters.R

@@ -12,6 +12,12 @@
 #'     a relevant "utbrudds_ID" and/or specific "metoder." These can be used to select
 #'     saker in PJS and/or to structure and simplify the output from PJS.
 #'
+#'     The purpose is a short description of purpose of the selection described by the
+#'     selection parameters for example "ok_svin_virus" that describes the selection
+#'     parameters for the OK programme for virus in swine. The purpose is also used as
+#'     part of the file name for selection_parameters, i.e. "purpose_selection_parameters"
+#'     and in the annual tables for ok_programmer: Kontrolltabeller for yyyy.
+#'
 #'     One or more specific "hensiktkoder" may be input to the selection statement.
 #'     With specific "hensiktkode" is meant a "hensiktkode" that will imply that the sample
 #'     will be examined for specific infectious agent(s) or disease. One or more
@@ -39,9 +45,11 @@
 #'     warning is issued and the input is transferred to \code{include_missing_art} and
 #'     \code{selection_parameters}, respectively.
 #'
+#' @param purpose [\code{character}]\cr
+#' A short description of the purpose of the selection, see details. Defaults to NULL.
 #' @param hensikt2select [\code{character}]\cr
 #' Specific "hensiktkoder" for the "analytt" in question. If sub-codes should
-#'     be included, end the code with \%.Defaults to \code{NULL}.
+#'     be included, end the code with \%. Defaults to \code{NULL}.
 #' @param hensikt2delete [\code{character}]\cr
 #' "hensiktkoder" for which saker should be excluded.
 #'     If sub-codes should be included, end the code with \%. Defaults to \code{NULL}.
@@ -66,6 +74,14 @@
 #' Either the path and file name for an R script that can be sourced and that
 #'     sets the selection parameters or a named list with the selection parameters
 #'     (i.e. equal to the output of this function). Defaults to \code{NULL}.
+#' @param FUN [\code{function}]\cr
+#' Function to build the selection statement, see
+#'     \ifelse{html}{\code{\link{retrieve_PJSdata}}}{\code{retrieve_PJSdata}}).
+#'     Defaults to \code{NULL}.
+#' @param select_statement [\code{character(1)}]\cr
+#' A written select statement, see
+#'     \ifelse{html}{\code{\link{retrieve_PJSdata}}}{\code{retrieve_PJSdata}}).
+#'     Defaults to \code{NULL}.
 #' @param \dots Other arguments to be passed to `set_disease_parameters`.
 #'
 #' @return A named list with selection parameters that can be used to generate
@@ -80,23 +96,28 @@
 #'   hensikt2select = c("0100108018", "0100109003", "0100111003", "0800109"),
 #'   metode2select = c("070070", "070231", "010057", "060265")
 #'   )
-set_disease_parameters <- function(hensikt2select = NULL,
+set_disease_parameters <- function(purpose = NULL,
+                                   hensikt2select = NULL,
                                    hensikt2delete = NULL,
                                    utbrudd2select = NULL,
                                    metode2select = NULL,
                                    analytt2select = NULL,
                                    analytt2delete = NULL,
                                    art2select = NULL,
                                    include_missing_art = NULL,
+                                   FUN = NULL,
+                                   select_statement = NULL,
                                    selection_parameters = NULL,
                                    ...) {
 
   # SET SELECTION PARAMETERS ----
   # Vector with possible selection parameter names
   # missing_art is deprecated
-  var2select_template <- c("hensikt2select", "hensikt2delete", "utbrudd2select",
+  var2select_template <- c("purpose",
+                           "hensikt2select", "hensikt2delete", "utbrudd2select",
                            "metode2select", "analytt2select", "analytt2delete", "art2select",
-                           "include_missing_art", "missing_art")
+                           "include_missing_art", "missing_art",
+                           "FUN", "select_statement")
 
   # PREPARE ARGUMENTS BEFORE CHECKING ----
   if ("file" %in% ...names() & is.null(selection_parameters)) {
@@ -165,11 +186,12 @@ set_disease_parameters <- function(hensikt2select = NULL,
   # checks <- checkmate::makeAssertCollection()
 
   # Perform checks
+  checkmate::assert_string(purpose, null.ok = TRUE, add = checks)
   NVIcheckmate::assert_non_null(list(analytt2select, hensikt2select, utbrudd2select, unlist(selection_parameters)), add = checks)
   checkmate::assert_character(hensikt2select, min.chars = 2, max.chars = 15, any.missing = FALSE, null.ok = TRUE, add = checks)
   checkmate::assert_character(hensikt2delete, min.chars = 2, max.chars = 15, any.missing = FALSE, null.ok = TRUE, add = checks)
   checkmate::assert_character(utbrudd2select, max.chars = 5, any.missing = FALSE, null.ok = TRUE, add = checks)
-  checkmate::assert_character(metode2select, n.chars = 6, any.missing = FALSE, null.ok = TRUE, add = checks)
+  checkmate::assert_character(metode2select, min.chars = 2, max.chars = 6, any.missing = FALSE, null.ok = TRUE, add = checks)
   checkmate::assert_character(analytt2select, min.chars = 2, max.chars = 20, any.missing = FALSE, null.ok = TRUE, add = checks)
   checkmate::assert_character(analytt2delete, min.chars = 2, max.chars = 20, any.missing = FALSE, null.ok = TRUE, add = checks)
   checkmate::assert_character(art2select, min.chars = 2, max.chars = 20, all.missing = FALSE, null.ok = TRUE, add = checks)
@@ -178,17 +200,25 @@ set_disease_parameters <- function(hensikt2select = NULL,
                            choices = c("never", "always", "for_selected_hensikt"),
                            add = checks)
   # }
+  checkmate::assert_function(FUN, null.ok = TRUE, add = checks)
+  checkmate::assert(checkmate::check_list(x = select_statement, null.ok = TRUE),
+                    checkmate::check_string(x = select_statement),
+                    combine = "or",
+                    add = checks)
 
   # Report check-results
   checkmate::reportAssertions(checks)
 
   # CREATE LIST WITH PARAMETER VALUES ----
-  return(list("hensikt2select" = hensikt2select,
+  return(list("purpose" = purpose,
+              "hensikt2select" = hensikt2select,
               "hensikt2delete" = hensikt2delete,
               "utbrudd2select" = utbrudd2select,
               "metode2select" = metode2select,
               "analytt2select" = analytt2select,
               "analytt2delete" = analytt2delete,
               "art2select" = art2select,
-              "include_missing_art" = include_missing_art))
+              "include_missing_art" = include_missing_art,
+              "FUN" = FUN,
+              "select_statement" = select_statement))
 }