Merge pull request #10 from PetterHopp/main

OKplan v0.5.0

CONTRIBUTING.md

@@ -37,36 +37,41 @@ data reporting at the Norwegian Veterinary Institute (NVI).
 <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>
+</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>
 </tr>
-<tr class="even">
+<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>
 </tr>
-<tr class="odd">
+<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>
 </tr>
-<tr class="even">
+<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>
 </tr>
-<tr class="odd">
+<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>
 </tr>
-<tr class="even">
+<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>
 </tr>
-<tr class="odd">
+<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>
@@ -150,38 +155,43 @@ adhere to some principles and style convention used for
     use of base functions is much appreciated.
 
 -   New code should generally follow the tidyverse [style
-    guide](http://style.tidyverse.org). I recommend to use the
-    [`styler`](https://CRAN.R-project.org/package=styler) package to
-    apply spaces: `styler::style_file(filename, scope = "spaces")`.
-    Please don’t restyle code that has nothing to do with your pull
-    request.
+    guide](http://style.tidyverse.org) with some modifications.
+
+    -   use snake\_case for variable names, column names, function names
+        etc.
+    -   function names should start with a verb and should be
+        descriptive and can be long. Avoid strange abbreviations.
+    -   to indent the code you may use the short cut keys Ctrl+a (select
+        all) and Ctrl+i (indent) when you are in R-studio.
+    -   I recommend to use the
+        [`styler`](https://CRAN.R-project.org/package=styler) package to
+        apply spaces:
+        `styler::style_file(filename, scope = c("spaces", "line_breaks"))`.
+        Please don’t restyle code that has nothing to do with your pull
+        request.
 
 -   You should add a bullet point to `NEWS` motivating the change.
 
 -   You should add yourself as a contributor to the `DESCRIPTION`.
 
--   If you’re adding a new function or new arguments to an existing
-    function, you’ll also need to document them. `NVIverse`-packages use
-    [`roxygen2`](https://cran.r-project.org/package=roxygen2), with
-    [Markdown
-    syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html),
-    for documentation. Make sure to re-run `devtools::document()` on the
-    code before submitting.
+Although not expected from all contributors, it will be highly
+appreciated if you also are willing to suggest:
 
--   `NVIverse`-packages use the assert-functions from
+-   documentation for new functions or new arguments to existing
+    functions The `NVIverse`-packages use
+    [`roxygen2`](https://cran.r-project.org/package=roxygen2) for
+    documentation.
+
+-   argument checking of the function arguments. The `NVIverse`-packages
+    use the assert-functions from the
     [`checkmate`](https://CRAN.R-project.org/package=checkmate) package
-    for argument checking as well as some additional assert\_functions
-    in
+    for argument checking as well as some additional assert-functions in
     [`NVIcheckmate`](https://github.com/NorwegianVeterinaryInstitute/NVIcheckmate).
-    Adding argument checking for new functions and/or arguments will be
-    highly appreciated.
 
--   If you can, also write a test. `NVIverse`-packages use
+-   one or more tests ensuring that the function works as intended. The
+    `NVIverse`-packages use
     [`testthat`](https://cran.r-project.org/package=testthat) for tests.
 
--   Also run `devtools::check()` to make sure your function doesn’t
-    imply downstream errors or warnings.
-
 ### Git commit standards
 
 We follow the commit message style guide maintained within the

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OKplan
 Title: Tools to facilitate the Planning of the annual Surveillance Programmes
-Version: 0.4.2
-Date: 2022-01-20
+Version: 0.5.0
+Date: 2022-12-15
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -24,11 +24,14 @@ Imports:
     knitr,
     magrittr,
     openxlsx,
+    rlang,
     rmarkdown,
     stats,
+    NVIbatch (>= 0.4.0),
     NVIdb (>= 0.3.0),
-    NVIpretty,
-    NVIrpackages
+    NVIpretty (>= 0.4.0),
+    NVIrpackages,
+    OKcheck
 Suggests:
     covr,
     devtools,
@@ -37,10 +40,12 @@ Suggests:
     utils,
     NVIpackager
 Remotes: 
+    NorwegianVeterinaryInstitute/NVIbatch,
     NorwegianVeterinaryInstitute/NVIdb,
     NorwegianVeterinaryInstitute/NVIpretty,
     NorwegianVeterinaryInstitute/NVIpackager,
-    NorwegianVeterinaryInstitute/NVIrpackages
-RoxygenNote: 7.1.2
+    NorwegianVeterinaryInstitute/NVIrpackages,
+    NorwegianVeterinaryInstitute/OKcheck
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Language: en-GB

NAMESPACE

@@ -4,7 +4,9 @@ export(adjust_samples_to_budget)
 export(append_date_generated_line)
 export(append_sum_line)
 export(check_OK_selection)
+export(check_ok_selection)
 export(make_random)
 export(style_sum_line)
 export(write_ok_selection_list)
 importFrom(magrittr,"%>%")
+importFrom(rlang,.data)

NEWS

@@ -1,3 +1,24 @@
+OKplan 0.5.0 - (2022-12-15)
+---------------------------
+
+New features:
+
+- write_ok_selection_list now includes the argument `add_worksheet` that makes it possible to add a new worksheet to an existing workbook.
+
+- adjust_samples_to_budget includes the argument `group` so that sample size can be adjusted per group.
+
+- check_ok_selection now calls an R markdown file, generates a html-report with descriptive statistics and displays the report in the browser. The function is renamed (all lower case letters) and includes several new arguments. check_OK_selection is deprecated.
+
+Other changes:
+
+- README updated with improved installation guide.
+
+
+BREAKING CHANGES:
+
+  - Renamed to check_ok_selection from check_OK_selection. check_OK_selection is deprecated.
+
+
 OKplan 0.4.2 - (2022-01-20)
 ---------------------------
 

R/OKplan-deprecated.R

@@ -0,0 +1,22 @@
+#' @title Deprecated Functions in Package OKplan
+#' @description These functions are provided for compatibility with older
+#'     versions of OKplan 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{check_OK_selection} was deprecated 2022-12-15 to replace it
+#'     with check_ok_selection with a standardised function name with lower case
+#'     letters for OK. Use check_ok_selection with the additional parameters
+#'     \code{purpose =} and \code{plan_aar =}.
+#'
+#' @param \dots (arguments)
+#' @return (results)
+#' @name OKplan-deprecated
+#' @keywords internal
+#'
+#' @author Petter Hopp Petter.Hopp@@vetinst.no
+#'
+#' @examples
+#' \dontrun{
+#' check_OK_selection(...) ### -- use \code{\link{check_ok_selection}} instead.
+#' }
+NULL