Merge pull request #30 from PetterHopp/main

NVIdb v0.11.0

.gitignore

@@ -20,7 +20,6 @@
 # RStudio files
 .Rproj.user/
 
-
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
@@ -40,7 +39,3 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 
-# Directories that shouldn't be syncronized
-nosync/
-Meta
-.Ruserdata

CONTRIBUTING.md

@@ -83,7 +83,7 @@ NVIverse packages</td>
 <tr class="even">
 <td style="text-align: left;">NVIrpackages</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Keeps a table of the R-Packages in
+<td style="text-align: left;">Keeps a table of the R packages in
 NVIverse</td>
 </tr>
 </tbody>
@@ -157,9 +157,11 @@ development guidelines below.
 
 ## Development guidelines
 
-If you want to contribute code, you are welcome to do so. Please try to
-adhere to some principles and style convention used for
-`NVIverse`-packages.
+If you want to contribute code, you are welcome to do so. You will find
+a description of the code conventions, which have been used, in the
+vignette “NVIverse code conventions” in the package `NVIpackager`. A
+summary of the principles and style convention used for
+`NVIverse`-packages is given below.
 
 -   Please limit the number of package dependencies for `NVIdb`. The use
     of base functions is much appreciated.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.10.1
-Date: 2023-05-31
+Version: 0.11.0
+Date: 2024-01-24
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -34,29 +34,27 @@ Imports:
     DBI,
     dplyr,
     keyring,
-    knitr,
     magrittr,
     odbc,
-    remotes,
-    rlang,
-    rmarkdown,
     RODBC,
     RPostgreSQL,
-    R.rsp,
-    shiny,
     snakecase,
     stats,
-    svDialogs,
     utils,
-    NVIcheckmate (>= 0.4.0),
-    NVIrpackages
+    NVIcheckmate (>= 0.7.0)
 Suggests:
     covr,
+    desc,
     devtools,
+    knitr,
+    R.rsp,
+    remotes,
+    rmarkdown,
     spelling,
     testthat,
     tibble,
-    NVIpackager
+    NVIpackager,
+    NVIrpackages
 Remotes: 
     NorwegianVeterinaryInstitute/NVIcheckmate,
     NorwegianVeterinaryInstitute/NVIrpackages,

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Norwegian Veterinary Institute
+Copyright (c) 2021 - 2024 Norwegian Veterinary Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

NAMESPACE

@@ -49,6 +49,8 @@ export(read_sonetilhorighet)
 export(read_varekode)
 export(remove_PAT)
 export(remove_credentials)
+export(retrieve_PJSdata)
+export(select_PJSdata_for_value)
 export(set_PAT)
 export(set_credentials)
 export(set_credentials_EOS)
@@ -58,5 +60,5 @@ export(set_disease_parameters)
 export(standardize_PJSdata)
 export(standardize_columns)
 export(standardize_eos_data)
+export(transform_code_combinations)
 importFrom(magrittr,"%>%")
-importFrom(rlang,.data)

NEWS

@@ -1,41 +1,66 @@
-NVIdb 0.10.1 - (2023-05-31)
+NVIdb 0.11.0 - (2024-01-24)
 ----------------------------------------
 
 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". 
+- Created `retrieve_PJS_data` to retrieve and standardisation of PJSdata.
+
+- Created `transform_code_values` to easy transform few code combinations into other values.
+
+- Created `select_PJSdata_for_values` to perform inclusion/exclusion of rows in PJSdata based on coded values. For codes ending with "%", sub levels are included.
+
+- `read_Prodtilskudd` now accepts the argument `exctracted_date`.
+
+- The PJS- and EOS-wrappers for the login functions `login`, `login_by_credentials` and `login_by_input` now accepts arguments to be passed to the parent functions. Thereby, one may change login information for the databases PJS and EOS by modifying the scripts until a new version of the package `NVIconfig` is available and installed.
 
 
 Bug fixes:
 
--
+- Corrected `read_varekode` so accepts old source files in latin1.
 
 
 Other changes:
 
-- Improved help by standardising argument description for a few functions.
+- Modified help for several functions.
+
+- Modified `set_disease_parameters` to make the name of the input arguments easier to comprehend. New arguments are `analytt2delete`, `include_missing_art` and `selection_parameters`. The argument `selection_parameters` accepts both a "purpose" file and a list (as generated by as `set_disease_parameters`) as input.
 
 
 BREAKING CHANGES:
 
--
+- In `set_disease_parameters` the arguments `missing_art` and `file` is deprecated. These are replaced by `include_missing_art` and `selection_parameters`, respectively. If using the old arguments, the input will be transferred to the new arguments. 
+
+- `set_PAT`, `get_PAT`, and `remove_PAT` was deprecated.These should be replaced by corresponding functions in package `gitcreds`.
+
+
+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". 
+
+
+Other changes:
+
+- Improved help by standardising argument description for a few functions.
 
 
 NVIdb 0.10.0 - (2023-04-18)
 ----------------------------------------
 
 New features:
 
-- Created standardize_eos_data for standardisation of column names etc. in eos-data.
+- Created `standardize_eos_data` for standardisation of column names etc. in eos-data.
 
-- set_dir_NVI now accepts argument `slash`. set `slash = FALSE` to remove ending slash.
+- `set_dir_NVI` now accepts argument `slash`. set `slash = FALSE` to remove ending slash.
 
-- add_PJS_code_description now accepts the argument `impute_old_when_missing`.
+- `add_PJS_code_description` now accepts the argument `impute_old_when_missing`.
 
 
 Bug fixes:
 
-- add_PJS_code_description now performs back translation also in the case that the code has expired ("utg\u00E5tt").
+- `add_PJS_code_description` now performs back translation also in the case that the code has expired ("utg\u00E5tt").
 
 
 Other changes:

R/NVIdb-deprecated.R

@@ -3,14 +3,19 @@
 #'     versions of NVIdb only, and may be defunct as soon as the next release.
 #'     When possible, alternative functions are mentioned. Help pages for
 #'     deprecated functions are available at \code{help("<function>-deprecated")}.
-#' @details \code{add_produsent} was deprecated 2022-05-02 as other properties
+#' @details \code{add_produsent} was deprecated from v0.8.0 released 2022-08-25
+#'     as other properties
 #'     than 'gjeldende_prodnr8' could not be included without breaking backward
 #'     compatibility. Use \code{add_produsent_properties} instead and ensure
 #'     to set the parameter \code{impute_old_when_missing = TRUE} when translating
 #'     from "prodnr8" to "gjeldende_prodnr8" and set the parameter
 #'     \code{impute_old_when_missing = FALSE} when translating from "prodnr8" to
 #'     other properties.
 #'
+#' \code{set_PAT}, \code{get_PAT}, and \code{remove_PAT} was deprecated from
+#'     v0.11.0 released 2023-09-22. The functions were never taken into use.
+#'     Functions from the much better package \code{gitcreds} should be used instead.
+#'
 #' @param \dots (arguments)
 #' @return (results)
 #' @name NVIdb-deprecated
@@ -20,6 +25,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' add_produsent(...) ### -- use \code{\link{add_produsent_properties}}   instead
+#' add_produsent(...) ### -- use \code{\link{add_produsent_properties}} instead.
+#' set_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_set}} instead.
+#' get_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_get}} instead.
+#' remove_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_delete}} instead.
 #' }
 NULL

R/add_MT_omrader.R

@@ -155,4 +155,3 @@ add_MT_omrader <- function(data,
 
 # To avoid checking of the variable kommune_fylke as default input argument in the function
 utils::globalVariables("komnr_2_MT_omrader")
-