Merge pull request #27 from PetterHopp/main

NVIdb v0.10.1 (2023-05-31)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.10.0
-Date: 2023-04-18
+Version: 0.10.1
+Date: 2023-05-31
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",

NEWS

@@ -1,3 +1,26 @@
+NVIdb 0.10.1 - (2023-05-31)
+----------------------------------------
+
+New features:
+
+- add_PJS_code_description is extended so that analytt and kjennelse at sakskonklusjon-level can be translated when using the arguments `PJS_variable_type` = "auto" and `new_column` = "auto". 
+
+
+Bug fixes:
+
+-
+
+
+Other changes:
+
+- Improved help by standardising argument description for a few functions.
+
+
+BREAKING CHANGES:
+
+-
+
+
 NVIdb 0.10.0 - (2023-04-18)
 ----------------------------------------
 

R/add_MT_omrader.R

@@ -91,9 +91,6 @@
 #'                        new_column = c("MT_regionnavn" = "MT_region"))
 #' }
 #'
-# To avoid checking of the variable kommune_fylke as default input argument in the function
-utils::globalVariables("komnr_2_MT_omrader")
-
 add_MT_omrader <- function(data,
                            translation_table = komnr_2_MT_omrader,
                            code_column = c("komnr"),
@@ -155,3 +152,7 @@ add_MT_omrader <- function(data,
 
   return(data)
 }
+
+# To avoid checking of the variable kommune_fylke as default input argument in the function
+utils::globalVariables("komnr_2_MT_omrader")
+

R/add_PJS_code_description.R

@@ -15,7 +15,7 @@
 #'
 #'     \code{add_PJS_code_description} uses the pre made translation table 
 #'     "PJS_codes_2_text.csv". The data need to be loaded by 
-#'     \code{read_PJS_code_registers} before running \code{add_PJS_code_description},
+#'     \code{read_PJS_codes_2_text} before running \code{add_PJS_code_description},
 #'     see example. The file "PJS_codes_2_text.csv" is normally updated every night 
 #'     from PJS.
 #'
@@ -46,9 +46,11 @@
 #'   metode \tab metodekode \tab metode \tab \cr
 #'   metode \tab subund_metodekode \tab submetode \tab \cr
 #'   konkl_type \tab konkl_typekode \tab konkl_type \tab \cr
+#'   kjennelse \tab sakskonkl_kjennelsekode \tab sakskonkl_kjennelse \tab \cr
 #'   kjennelse \tab konkl_kjennelsekode \tab konkl_kjennelse \tab \cr
 #'   kjennelse \tab res_kjennelsekode \tab res_kjennelse \tab \cr
 #'   kjennelse \tab subres_kjennelsekode \tab subres_kjennelse \tab \cr
+#'   analytt \tab sakskonkl_analyttkode \tab sakskonkl_analytt \tab \cr
 #'   analytt \tab konkl_analyttkode \tab konkl_analytt \tab \cr
 #'   analytt \tab res_analyttkode \tab res_analytt \tab \cr
 #'   analytt \tab subres_analyttkode \tab subres_analytt \tab \cr
@@ -85,7 +87,7 @@
 #'     descriptive text strings, there are no unique translation. In these cases, 
 #'     the code value is left empty.
 #'
-#'     \code{read_PJS_code_registers} reads the file "PJS_codes_2_text.csv" into a 
+#'     \code{read_PJS_codes_2_text} reads the file "PJS_codes_2_text.csv" into a 
 #'     data frame that can be used by \code{add_PJS_code_description}. In standard 
 #'     setting will the file read in the latest updated file from NVI's internal 
 #'     network. If changing the \code{from_path}, the function can be used to read 
@@ -101,7 +103,7 @@
 #'     other PJS variables, a data frame with the same column definition can be 
 #'     constructed to translate new variables.
 #'
-#'     \code{copy_PJS_code_registers} copies the file pjsCodeDescriptions.csv to 
+#'     \code{copy_PJS_codes_2_text} copies the file pjsCodeDescriptions.csv to 
 #'     a given directory.
 #'
 #' @param data [\code{data.frame}] \cr
@@ -208,9 +210,6 @@
 #'                                      impute_old_when_missing = TRUE)
 #' }
 #'
-# To avoid checking of the variable kommune_fylke as default input argument in the function
-utils::globalVariables("PJS_codes_2_text")
-
 add_PJS_code_description <- function(data,
                                      translation_table = PJS_codes_2_text,
                                      PJS_variable_type,
@@ -387,3 +386,7 @@ add_PJS_code_description <- function(data,
   }
   return(data)
 }
+
+# To avoid checking of the variable kommune_fylke as default input argument in the function
+utils::globalVariables("PJS_codes_2_text")
+

R/add_kommune_fylke.R

@@ -79,9 +79,6 @@
 #'                                             "kommune" = "gjeldende_kommune"))
 #' }
 #'
-# To avoid checking of the variable kommune_fylke as default input argument in the function
-utils::globalVariables("kommune_fylke")
-
 add_kommune_fylke <- function(data,
                               translation_table = kommune_fylke,
                               code_column = c("komnr"),
@@ -156,3 +153,7 @@ add_kommune_fylke <- function(data,
 
   return(data)
 }
+
+# To avoid checking of the variable kommune_fylke as default input argument in the function
+utils::globalVariables("kommune_fylke")
+

R/add_lokalitet.R

@@ -1,34 +1,62 @@
 #' @title Manage adding extra information to aquaculture sites
-#' @description Function to add a column with current aquaculture zone and/or coordinates. In addition there are
-#'    function to read the translation table.
-#' @details \code{add_lokalitet} can be used to add aquaculture zone to aquaculture sites.
+#' @description Function to add a column with current aquaculture
+#'    zone and/or geo-coordinates. In addition there are function
+#'    to read the translation table.
+#' @details \code{add_lokalitet} can be used to add aquaculture
+#'    zone and/or geo-coordinates to aquaculture sites. The new 
+#'    columns can be one or more of c("sone", "EastUTM_33N_WGS84",
+#'    "NorthUTM_33N_WGS84", "Longitude_WGS84", "Latitude_WGS84").
+#'    If the new columns in the result data frame should have 
+#'    other names, \code{new_column} can be input as a named 
+#'    vector, see examples.
 #'
-#'     \code{position =} is used to give the place if the new columns in the data.frame. For \code{position = "right"} the new variables are
-#'     placed to the right of the code_variable. Likewise, for \code{position = "left"} the new variables are placed to the left of the
-#'     code_variable. If \code{position = "first"} or \code{position = "last"} the new columns are placed first or last, respectively, in the
-#'     data.frame. A special case occurs for \code{position = "keep"} which only has meaning when the new column has the same name as an existing
-#'     column and overwrite = TRUE. In these cases, the existing column will be overwritten with new data and have the same position.
+#' \code{position} is used to give the position if the new columns 
+#'     in the data.frame. For \code{position = "right"} the new 
+#'     variables are placed to the right of the code_variable. 
+#'     Likewise, for \code{position = "left"} the new variables 
+#'     are placed to the left of the code_variable. If 
+#'     \code{position = "first"} or \code{position = "last"} the 
+#'     new columns are placed first or last, respectively, in the
+#'     data frame. A special case occurs for \code{position = "keep"} 
+#'     which only has meaning when the new column has the same name 
+#'     as an existing column and \code{overwrite = TRUE}. In these 
+#'     cases, the existing column will be overwritten with new data 
+#'     and have the same position.
 #'
-#'     \code{read_sonetilhorighet} reads the file "sonetilhorighet.txt" into a data frame that can be used by other routines. Standard setting
-#'     will the file read in the latest updated file from NVI's internal network. If changing the from_path, the function can be used to read
-#'     the translation file from other directories. This can be useful if having a stand alone app with no connection the NVI's internal
-#'     network. In other cases, it should be avoided.
+#' \code{read_sonetilhorighet} reads the file "sonetilhorighet.txt" 
+#'     into a data frame that can be used by other routines. Standard 
+#'     setting will the file read in the latest updated file from 
+#'     NVI's internal network. If changing the from_path, the 
+#'     function can be used to read the translation file from 
+#'     other directories. This can be useful if having a stand 
+#'     alone app with no connection the NVI's internal network. 
+#'     In other cases, it should be avoided.
 #'
-#' @param data Data frame with data with a column with a aquaculture site number ("LokNr")
-#' @param translation_table Data frame with the table for translating from loknr to the property in question.
-#' @param code_column The column with the coded value. Valid values are one of c("LokNr"). If the column in
+#' @param data [\code{data.frame}]\cr  
+#' Data with a column with an aquaculture site number ("LokNr")
+#' @param translation_table [\code{data.frame}]\cr  
+#' Table for translating from loknr to the property in question.
+#' @param code_column [\code{character(1)}]\cr  
+#' The column with the coded value. Valid values are one of c("LokNr"). If the column in
 #'     data has another name, it can be input as a named vector, see examples.
-#' @param new_column The new columns that should be included into the data frame. The new columns can be one ore more of
-#'     c("sone", "EastUTM_33N_WGS84", "NorthUTM_33N_WGS84", "Longitude_WGS84", "Latitude_WGS84"). If the new columns in the result
-#'     data frame should have other names, \code{new_column} can be input as a named vector, see examples.
+#' @param new_column [\code{character}]\cr  
+#' The new columns that should be included into the data frame.
 #' @template position
 #' @template overwrite
-#' @param filename a list with the filenames of the source files with the tables for generating the translation table.
-#' @param from_path Path for the source files for the translation table.
+#' @param filename [\code{list}]\cr  
+#' The filenames of the source files with the tables for generating the translation table.
+#' @param from_path [\code{character(1)}]\cr  
+#' Path for the source files for the translation table.
 #'
-#' @return \code{add_lokalitet} A data frame where the aquaculture zone and / or coordinates have been added in the column to the
+#' @return \code{add_lokalitet}: \code{data.frame} where the aquaculture 
+#'     zone and / or geo-coordinates have been added in the column to the
 #'     right of the column with the LokNr.
 #'
+#' \code{read_sonetilhorighet}: \code{data.frame} with "LokNr", 
+#'     aquaculture zone and geo-coordinates. If not changing standard 
+#'     input to the function, the standard file at NVI's internal 
+#'     network is read.
+#'
 #' @author Petter Hopp Petter.Hopp@@vetinst.no
 #' @export
 #' @examples

R/add_poststed.R

@@ -71,8 +71,6 @@
 #'                         new_column = c("poststed", "postkomnr" = "komnr"))
 #' }
 #'
-# To avoid checking of the variable kommune_fylke as default input argument in the function
-utils::globalVariables("poststed")
 
 add_poststed <- function(data,
                          translation_table = poststed,
@@ -127,3 +125,7 @@ add_poststed <- function(data,
 
   return(data)
 }
+
+
+# To avoid checking of the variable kommune_fylke as default input argument in the function
+utils::globalVariables("poststed")

R/ignore_unused_imports.R

@@ -0,0 +1,14 @@
+# Remove NOTE when running CMD check and checking dependencies
+# Namespaces in Imports field not imported from:
+#   'NVIrpackages' 'rlang' 'rmarkdown' 'shiny' 'tidyr'
+# All declared Imports should be used.
+
+
+ignore_unused_imports <- function() {
+  # Removes NOTE because of packages needed for building vignette: "Contribute to ..."
+  rmarkdown::html_vignette
+  knitr::opts_chunk
+  NVIrpackages::NVIpackages
+  # R.rsp is used when adding the pdf reference manual as a vignette
+  R.rsp::rfile
+}

R/read_eos_data.R

@@ -1,20 +1,30 @@
 #' @title Read EOS data from RaData
 #' @description Reads EOS data from RaData. Includes historical data if these exists.
 #'     It is possible to limit the data to one or more years.
-#' @details read_eos_data uses \code{data.table::fread} to read the data with the 
-#'     settings \code{showProgress = FALSE} and \code{data.table = FALSE}. Other 
-#'     arguments can be passed to \code{data.table::fread} if necessary.
+#' @details read_eos_data uses 
+#'     \ifelse{html}{\code{\link[data.table:fread]{data.table::fread}}}{\code{data.table::fread}}
+#'     to read the data with the settings \code{showProgress = FALSE} and 
+#'     \code{data.table = FALSE}. Other arguments can be passed to  
+#'     \ifelse{html}{\code{\link[data.table:fread]{data.table::fread}}}{\code{data.table::fread}}
+#'     if necessary.
 #'     
-#'     The eos_table name is the same name as the name as in the EOS data base.
+#' The eos_table name is the same name as the name as in the EOS data base.
 #' 
-#' @param from_path Path for raw data from eos_data
-#' @param eos_table The name of the table with eos raw data.
-#' @param year The years to be included in the result. Can be both numeric
+#' @param from_path [\code{character(1)}]\cr
+#'     Path for raw data from eos_data.
+#' @param eos_table [\code{character(1)}]\cr
+#'     The name of the table with eos raw data.
+#' @param year [\code{character} | \code{numeric}]\cr
+#'     The years to be included in the result. Can be both numeric
 #'     or character. Defaults to \code{NULL}, i.e. no selection.
-#' @param colClasses The class of the columns, as in utils::read.table, Defaults to 
-#'     \code{"character"}.
-#' @param encoding The encoding. Defaults to \code{"UTF-8"}.
-#' @param \dots	Other arguments to be passed to \code{data.table::fread}.
+#' @param colClasses [\code{character}]\cr
+#'     The class of the columns, as in  
+#'     \ifelse{html}{\code{\link[utils:read.table]{utils::read.table}}}{\code{utils::read.table}}.
+#'     Defaults to \code{"character"}.
+#' @param encoding [\code{character(1)}]\cr
+#'     The encoding, one of c("UTF-8", "latin1"). Defaults to \code{"UTF-8"}.
+#' @param \dots	Other arguments to be passed to  
+#'     \ifelse{html}{\code{\link[data.table:fread]{data.table::fread}}}{\code{data.table::fread}}.
 #'
 #' @return A data frame with data from EOS.
 #'

R/standardize_eos_data.R

@@ -77,7 +77,7 @@ standardize_eos_data <- function(data,
   # Object to store check-results
   checks <- checkmate::makeAssertCollection()
   # Perform checks
-  checkmate::assert_data_frame(data)
+  checkmate::assert_data_frame(data, add = checks)
   checkmate::assert_character(dbsource, len = 1, min.chars = 1, add = checks)
   checkmate::assert_data_frame(standards, null.ok = TRUE, add = checks)
   checkmate::assert_flag(standardize_colnames, add = checks) 

data-raw/generate_PJS_code_description_colname.R

@@ -3,7 +3,9 @@
 # GENERATE rda-file with the corresponding standard colnames for description to PJS code variables
 
 # GENERATE DATA ----
-PJS_code_description_colname <- as.data.frame(matrix(rbind(c("ansvarlig_seksjon", "seksjon", "ansvarlig_seksjon_navn"),
+PJS_code_description_colname <- as.data.frame(matrix(rbind(c("sakskonkl_kjennelsekode", "kjennelse", "sakskonkl_kjennelse"),
+                                                           c("sakskonkl_analyttkode", "analytt", "sakskonkl_analytt"),
+                                                           c("ansvarlig_seksjon", "seksjon", "ansvarlig_seksjon_navn"),
                                                            c("utf_seksjon", "seksjon", "utforende_seksjon_navn"),
                                                            c("hensiktkode", "hensikt", "hensikt"),
                                                            c("utbruddnr", "utbrudd", "utbrudd"),