Merge pull request #21 from PetterHopp/main

NVIdb v0.10.0 2023-04-18

CONTRIBUTING.md

@@ -29,52 +29,62 @@ data reporting at the Norwegian Veterinary Institute (NVI).
 <tr class="odd">
 <td style="text-align: left;">NVIconfig</td>
 <td style="text-align: left;">Private</td>
-<td style="text-align: left;">Configuration information necessary for some NVIverse functions</td>
+<td style="text-align: left;">Configuration information necessary for
+some NVIverse functions</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">NVIdb</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate the use of NVI’s databases</td>
+<td style="text-align: left;">Tools to facilitate the use of NVI’s
+databases</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">NVIspatial</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate working with spatial data at NVI</td>
+<td style="text-align: left;">Tools to facilitate working with spatial
+data at NVI</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">NVIpretty</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to make R-output pretty in accord with NVI’s graphical profile</td>
+<td style="text-align: left;">Tools to make R-output pretty in accord
+with NVI’s graphical profile</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">NVIbatch</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate the running of R-scripts in batch mode at NVI</td>
+<td style="text-align: left;">Tools to facilitate the running of
+R-scripts in batch mode at NVI</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">OKplan</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate the planning of surveillance programmes for the NFSA</td>
+<td style="text-align: left;">Tools to facilitate the planning of
+surveillance programmes for the NFSA</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">OKcheck</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate checking of data from national surveillance programmes</td>
+<td style="text-align: left;">Tools to facilitate checking of data from
+national surveillance programmes</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">NVIcheckmate</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Extension of checkmate with argument checking adapted for NVIverse</td>
+<td style="text-align: left;">Extension of checkmate with argument
+checking adapted for NVIverse</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">NVIpackager</td>
 <td style="text-align: left;">Public</td>
-<td style="text-align: left;">Tools to facilitate the development of NVIverse packages</td>
+<td style="text-align: left;">Tools to facilitate the development of
+NVIverse packages</td>
 </tr>
 <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 NVIverse</td>
+<td style="text-align: left;">Keeps a table of the R-Packages in
+NVIverse</td>
 </tr>
 </tbody>
 </table>

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.9.0
-Date: 2023-01-16
+Version: 0.10.0
+Date: 2023-04-18
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -28,13 +28,11 @@ BugReports: https://github.com/NorwegianVeterinaryInstitute/NVIdb/issues
 Depends: R (>= 3.5.0)
 License: BSD_3_clause + file LICENSE
 Imports:
-    stats,
-    utils,
+    askpass,
     checkmate,
     data.table,
     DBI,
     dplyr,
-    getPass,
     keyring,
     knitr,
     magrittr,
@@ -47,7 +45,9 @@ Imports:
     R.rsp,
     shiny,
     snakecase,
+    stats,
     svDialogs,
+    utils,
     NVIcheckmate (>= 0.4.0),
     NVIrpackages
 Suggests:

NAMESPACE

@@ -57,5 +57,6 @@ export(set_dir_NVI)
 export(set_disease_parameters)
 export(standardize_PJSdata)
 export(standardize_columns)
+export(standardize_eos_data)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)

NEWS

@@ -1,3 +1,25 @@
+NVIdb 0.10.0 - (2023-04-18)
+----------------------------------------
+
+New features:
+
+- 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.
+
+- 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").
+
+
+Other changes:
+
+- Minor updates of help.
+
+
 NVIdb 0.9.0 - (2023-01-16)
 ----------------------------------------
 
@@ -7,7 +29,7 @@ New features:
 
 - Created `read_varekode` for reading the formatted varekoderegister or the raw data to update the formatted varekoderegister.
 
-- `login`, `login_by_credentials` and `login_by_input` now accept the argument `dbinterface` with the R-package names "RODBC", "odbc" or, "RPostgreSQL" as input.
+- `login`, `login_by_credentials` and `login_by_input` now accept the argument `dbinterface` with the R-package names "RODBC", "odbc" or, "RPostgreSQL" as input.Thanks to @krdean for providing code for logging in by odbc.
 
 - Created `cut_slash` to remove ending slash from path. This is useful if pathnames should be created using `base::file.path`.
 

R/add_MT_omrader.R

@@ -91,6 +91,9 @@
 #'                        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"),