Merge pull request #95 from NorwegianVeterinaryInstitute/dev

NVIdb v0.13.0

.Rbuildignore

@@ -5,6 +5,7 @@
 ^nosync$
 ^man-roxygen$
 ^CONTRIBUTING.md
+^LICENSE.md
 ^README\.md
 ^README\.Rmd
 ^NVIdb.Rcheck\vign_test$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.12.0
-Date: 2024-05-22
+Version: 0.13.0
+Date: 2024-12-13
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -14,18 +14,17 @@ Authors@R:
     person(given = "Norwegian Veterinary Institute",
            role = "cph"))
 Description: Provides tools to facilitate downloading and processing of data from 
-    the Norwegian Veterinary Institute's databases, in particular PJS and EOS. The 
-    package comprises several categories of functions: 
+    the Norwegian Veterinary Institute's databases. The package comprises several 
+    categories of functions. 
     1) Manage credentials (i.e. password and username), 
     2) Login functions for database services, 
-    3) Select PJS-data, 
-    4) Initial cleaning of PJS-data,
-    5) Read, copy and update various in-house data registers, 
-    6) Translate codes into descriptions. 
+    3) Read, copy and update various in-house data registers, 
+    4) Translate codes into descriptions. 
     NVIdb is dependant of NVIconfig which has to be installed manually from GitHub.
+    All PJS and EOS related functions are moved to NVIpjsr.
 URL: https://github.com/NorwegianVeterinaryInstitute/NVIdb
 BugReports: https://github.com/NorwegianVeterinaryInstitute/NVIdb/issues
-Depends: R (>= 3.5.0)
+Depends: R (>= 4.1.0)
 License: BSD_3_clause + file LICENSE
 Imports:
     askpass,
@@ -34,7 +33,6 @@ Imports:
     DBI,
     dplyr,
     keyring,
-    magrittr,
     odbc,
     RODBC,
     RPostgreSQL,

LICENSE

@@ -1,29 +1,3 @@
-BSD 3-Clause License
-
-Copyright (c) 2021 - 2024 Norwegian Veterinary Institute
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+YEAR: 2019 - 2024
+COPYRIGHT HOLDER: Norwegian Veterinary Institute
+ORGANIZATION: Norwegian Veterinary Institute

LICENSE.md

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2019 - 2024 Norwegian Veterinary Institute
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(add_MT_omrader)
 export(add_PJS_code_description)
 export(add_kommune_fylke)
@@ -61,4 +60,3 @@ export(standardize_PJSdata)
 export(standardize_columns)
 export(standardize_eos_data)
 export(transform_code_combinations)
-importFrom(magrittr,"%>%")

NEWS.md

@@ -1,8 +1,29 @@
+# NVIdb 0.13.0 - (2024-12-13)
+
+## Bug fixes:
+
+- Fixed `login_by_input` for log in when using `dbinterface = "RPostgreSQL"`.
+
+
+## Other changes:
+
+- Included a meaningful error message for `read_Prodtilskudd` if no versions of Produksjonstilskudd was available for the selected years and months.
+
+- Improved help by standardising parameter description for functions.
+
+- Changed pipe to internal pipe |> and updated dependencies to R 4.1.0.
+
+
+## BREAKING CHANGES:
+
+- Deprecated all functions that have been moved to NVIpjsr, i.e. `add_PJS_code_description`, `build_query_hensikt`, `build_query_one_disease`, `build_query_outbreak`, `build_sql_select_code`, `build_sql_select_year`, `choose_PJS_levels`, `copy_PJS_code_2_text`, `exclude_from_PJSdata`, `login_by_credentials_PJS`, `read_eos_data`, `read_PJS_code_2_text`, `retrieve_PJSdata`, `select_PJSdata_for_value`, `set_disease_parameters`, `standardize_eos_data`, `standardize_PJSdata`, `transform_code_combinations`.
+
+
 # NVIdb 0.12.0 - (2024-05-22)
 
 ## New features:
 
-- Added argument `year` to `add_kommune_fylke`. Kommune and fylke can now be translated to any year from 1077 to current year from previous years. It is not possible to translate from a later year to previous years.
+- Added argument `year` to `add_kommune_fylke`. Kommune and fylke can now be translated to any year from 1977 to current year from previous years. It is not possible to translate from a later year to previous years.
 
 
 # NVIdb 0.11.3 - (2024-05-03)

R/NVIdb-deprecated.R

@@ -39,6 +39,31 @@
 #'     using the old arguments, the input will be transferred to
 #'     \code{selection_parameters}.
 #'
+#' All functions made especially to handle PJS data have been moved to \code{NVIpjsr}
+#'     and were deprecated from v0.##.# released 2024-##-##. Further development
+#'     of these functions will only take place in \code{NVIpjsr}. The following
+#'     functions have been moved:
+#' \itemize{
+#'   \item \code{add_PJS_code_description}
+#'   \item \code{build_query_hensikt}
+#'   \item \code{build_query_one_disease}
+#'   \item \code{build_query_outbreak}
+#'   \item \code{build_sql_select_code}
+#'   \item \code{build_sql_select_year}
+#'   \item \code{choose_PJS_levels}
+#'   \item \code{copy_PJS_code_2_text}
+#'   \item \code{exclude_from_PJSdata}
+#'   \item \code{login_by_credentials_PJS}
+#'   \item \code{read_eos_data}
+#'   \item \code{read_PJS_code_2_text}
+#'   \item \code{retrieve_PJSdata}
+#'   \item \code{select_PJSdata_for_value}
+#'   \item \code{set_disease_parameters}
+#'   \item \code{standardize_eos_data}
+#'   \item \code{standardize_PJSdata}
+#'   \item \code{transform_code_combinations}
+#'   }
+#'
 #' @param \dots (arguments)
 #' @return (results)
 #' @name NVIdb-deprecated
@@ -56,5 +81,24 @@
 #' login_by_input_EOS(...) ### -- use login_by_input("EOS") instead.
 #' login_by_credentials_EOS(...) ### -- use login_by_credentials("EOS") instead.
 #' set_credentials_EOS(...) ### -- use set_credentials("EOS") instead.
+#' login_by_credentials_PJS(...) ### -- use login_by_credentials("PJS") instead
+#' add_PJS_code_description(...) ### -- use NVIpjsr::add_PJS_code_description() instead
+#' build_query_hensikt(...) ### -- use NVIpjsr::build_query_hensikt() instead
+#' build_query_one_disease(...) ### -- use NVIpjsr:build_query_one_disease:() instead
+#' build_query_outbreak(...) ### -- use NVIpjsr::build_query_outbreak() instead
+#' build_sql_select_code(...) ### -- use NVIpjsr::build_sql_select_code() instead
+#' build_sql_select_year(...) ### -- use NVIpjsr::build_sql_select_year() instead
+#' choose_PJS_levels(...) ### -- use NVIpjsr::choose_PJS_levels() instead
+#' copy_PJS_code_2_text(...) ### -- use NVIpjsr::copy_PJS_code_2_text() instead
+#' exclude_from_PJSdata(...) ### -- use NVIpjsr::exclude_from_PJSdata() instead
+#' login_by_credentials_PJS(...) ### -- use login_by_credentials("PJS") instead
+#' read_eos_data(...) ### -- use NVIpjsr::read_eos_data() instead
+#' read_PJS_code_2_text(...) ### -- use NVIpjsr::read_PJS_code_2_text() instead
+#' retrieve_PJSdata(...) ### -- use NVIpjsr::retrieve_PJSdata() instead
+#' select_PJSdata_for_value(...) ### -- use NVIpjsr::select_PJSdata_for_value() instead
+#' set_disease_parameters(...) ### -- use NVIpjsr::set_disease_parameters() instead
+#' standardize_eos_data(...) ### -- use NVIpjsr::standardize_eos_data() instead
+#' standardize_PJSdata(...) ### -- use NVIpjsr::standardize_PJSdata() instead
+#' transform_code_combinations(...) ### -- use NVIpjsr::transform_code_combinations() instead
 #' }
 NULL

R/add_MT_omrader.R

@@ -45,22 +45,29 @@
 #'     available for \code{read_MT_omrader} if they should be read from
 #'     another directory.
 #'
-#' @param data Data frame with data with a column with a komnr.
-#' @param translation_table Data frame with the table for translating from
-#'     komnr to MT_areas.
-#' @param code_column The column with the coded value. Valid values are one
+#' @param data [\code{data.frame}]\cr
+#' Data with a column with kommunenummer (komnr).
+#' @param translation_table [\code{data.frame}]\cr
+#' The translation table for translating komnr to MT-areas. Defaults
+#'     to \code{komnr_2_MT_omrader}.
+#' @param code_column [\code{character(1)}]\cr
+#' The column with the code value. Valid values are one
 #'     of c("komnr", "MT_avdelingnr", "MT_regionnr"). 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 up to c("MT_avdelingnr", "MT_avdeling",
-#'     "MT_regionnr", "MT_region") depending on \code{code_column}.
-#'     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.
+#'     Defaults to "komnr".
+#' @param new_column [\code{character}]\cr
+#' The name(s) of the new column(s) that should be added to the data,
+#'     see examples. Defaults to c("MT_avdelingnr", "MT_avdeling",
+#'     "MT_regionnr", "MT_region").
 #' @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 to_path Path to where the source files for the translation table should be copied.
+#' @param filename [\code{list}]\cr
+#' File names of the source files for the translation table. Defaults to
+#'     list("komnr_2_MT_avdeling.csv", "MT_omrader.csv").
+#' @template from_path_add
+#' @template to_path_add
+#' @param \dots	Other arguments to be passed to
+#'     \ifelse{html}{\code{\link[utils:read.csv2]{utils::read.csv2}}}{\code{utils::read.csv2}}.
 #'
 #' @return \code{add_MT_omrader} A data frame where the MT_avdelingnr has been added in the column to the
 #'     right of the column with the komnr.