Merge pull request #13 from PetterHopp/main

OKplan v0.7.0

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>
@@ -147,9 +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 `OKplan`. The
     use of base functions is much appreciated.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OKplan
 Title: Tools to facilitate the Planning of the annual Surveillance Programmes
-Version: 0.6.1
-Date: 2023-10-09
+Version: 0.7.0
+Date: 2024-01-05
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -21,26 +21,28 @@ LazyData: true
 Imports:
     checkmate,
     dplyr,
-    knitr,
     magrittr,
     openxlsx,
     rlang,
-    rmarkdown,
     stats,
     NVIbatch (>= 0.4.0),
-    NVIcheckmate (>= 0.6.0),
+    NVIcheckmate (>= 0.7.3),
     NVIdb (>= 0.3.0),
     NVIpretty (>= 0.4.0),
-    NVIrpackages,
     OKcheck
 Suggests:
     covr,
     desc,
     devtools,
+    findInFiles,
+    knitr,
+    purrr,
+    rmarkdown,
     testthat,
     usethis,
     utils,
-    NVIpackager
+    NVIpackager,
+    NVIrpackages
 Remotes: 
     NorwegianVeterinaryInstitute/NVIbatch,
     NorwegianVeterinaryInstitute/NVIcheckmate,

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020 - 2023 Norwegian Veterinary Institute
+Copyright (c) 2020 - 2024 Norwegian Veterinary Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

NAMESPACE

@@ -5,6 +5,7 @@ export(append_date_generated_line)
 export(append_sum_line)
 export(check_OK_selection)
 export(check_ok_selection)
+export(get_holiday)
 export(get_tested_herds)
 export(make_random)
 export(style_sum_line)

NEWS

@@ -1,11 +1,34 @@
+OKplan 0.7.0 - (2024-01-05)
+----------------------------------------
+
+New features:
+
+- Created `get_holiday` to get the "non-workdays" or "workdays" within one year.
+
+
+Bug fixes:
+
+- Fixed several bugs in `get_tested_herds`. 
+
+
+Other changes:
+
+- To come.
+
+
+BREAKING CHANGES:
+
+- To come.
+
+
 OKplan 0.6.1 - (2023-10-09)
 ----------------------------------------
 
 Bug fixes:
 
-- the argument `year` in `get_tested_herds` now accepts more than one year as input. 
+- The argument `year` in `get_tested_herds` now accepts more than one year as input. 
 
-- The argument column can now be passed to append_sum_line.
+- `write_ok_selection_list` now accepts the argument `column` which will be passed to `append_sum_line`.
 
 
 Other changes:

R/adjust_samples_to_budget.R

@@ -123,10 +123,13 @@ adjust_samples_to_budget <- function(data,
     dplyr::mutate(total_estimated = sum(dplyr::across(dplyr::all_of(sample_to_adjust)), na.rm = TRUE)) %>%
     dplyr::mutate(included = dplyr::case_when(dplyr::across(dplyr::all_of(sample_to_adjust)) > 0 ~ 1,
                                               TRUE ~ 0)) %>%
-    dplyr::mutate(n_units = sum(.data$included, na.rm = TRUE)) %>%
+    # dplyr::mutate(n_units = sum(.data$included, na.rm = TRUE)) %>%
+    dplyr::mutate(n_units = sum(dplyr::across(dplyr::all_of("included")), na.rm = TRUE)) %>%
     dplyr::mutate(difference = .data$total_estimated - as.numeric(.data$budget)) %>%
+    # dplyr::mutate(difference = as.numeric(dplyr::all_of("total_estimated")) - as.numeric(dplyr::all_of("budget"))) %>% # This don't work
     dplyr::ungroup() %>%
-    dplyr::group_by(dplyr::across(dplyr::all_of(group)), .data$included) %>%
+    # dplyr::group_by(dplyr::across(dplyr::all_of(group)), .data$included) %>%
+    dplyr::group_by(dplyr::across(dplyr::all_of(c(group, "included")))) %>%
     dplyr::mutate(n_seq = 1:dplyr::n()) %>%
     dplyr::ungroup()
 

R/check_ok_selection.R

@@ -108,6 +108,5 @@ check_ok_selection <- function(input = system.file('templates', "check_ok_select
                             intermediates_dir = tempdir(),
                             params = list("data" = data, "purpose" = purpose, "plan_aar" = plan_aar),
                             display = display,
-                            email = FALSE,
                             ...)
 }

R/data.R

@@ -1,11 +1,12 @@
 #' @title Data: Column standards for OK sampling plans.
 #'
-#' @description A data frame with the column standards for data frames and Excel
-#'    sheets produced when planning of the Norwegian surveillance programmes.
-#'    The raw data for the column standards can be edited in the original Excel
-#'    table. The the code for preparing of the data frame is written in
-#'    "./data-raw/generate_OK_column_standards". The \code{OK_column_standards}
-#'    is used as input for
+#' @description A data frame with the column standards for data frames
+#'    and Excel sheets produced when planning the sampling schemes for
+#'    the Norwegian surveillance programmes. The raw data for the column
+#'    standards can be edited in the original Excel table. The code for
+#'    preparing of the data frame is written in
+#'    "./data-raw/generate_OK_column_standards". The
+#'    \code{OK_column_standards} is used as input for
 #'    \ifelse{html}{\code{\link[NVIdb]{standardize_columns}}}{\code{NVIdb::standardize_columns}}.
 #'
 #' @format A data frame with 14 variables: