Merge pull request #10 from mbranca/main

Update bookmarks and fields

.github/workflows/R-CMD-check.yaml

@@ -36,9 +36,9 @@ jobs:
           - {os: windows-latest, r: 'oldrel-1'}
 
           # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel'}
+          #- {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          #- {os: ubuntu-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'oldrel'}
 
 
     env:
@@ -57,6 +57,21 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - name: install freetype2 and imagemagick deps and libreoffice
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+           brew install --cask libreoffice
+
+      - name: install libreoffice for ubuntu
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+           sudo apt install libreoffice
+
+      - name: install libreoffice for windows
+        if: matrix.config.os == 'windows-latest'
+        run: |
+          choco install libreoffice-fresh -y
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck

.github/workflows/R-CMD-release.yaml

@@ -8,6 +8,8 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v2
+      - name: install freetype2 and imagemagick deps and libreoffice
+        run: brew install --cask libreoffice
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "rcmdcheck"))

DESCRIPTION

@@ -1,12 +1,17 @@
 Package: SwissASR
 Title: Automated Completion of the SwissEthics Annual Safety Report
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: 
-    person(given = "Alan G.",
+    c(person(given = "Alan G.",
            family = "Haynes",
            role = c("aut", "cre"),
-           email = "alan.haynes@ctu.unibe.ch",
-           comment = c(ORCID = "0000-0003-1374-081X"))
+           email = "alan.haynes@unibe.ch",
+           comment = c(ORCID = "0000-0003-1374-081X")),
+      person(given = "Mattia",
+           family = "Branca",
+           role = "ctb",
+           email = "mattia.branca@unibe.ch",
+           comment = c(ORCID = "0000-0002-8063-7882")) )
 Description: Completing the SwissEthics Annual Safety Report can be tiresome. This package eases the pain by providing an automated method to fill it out.
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -21,4 +26,5 @@ Imports:
     magrittr,
     officer,
     stringr,
-    tibble
+    tibble, 
+    doconv

NAMESPACE

@@ -5,6 +5,7 @@ export(asr_dataprep)
 export(asr_safety_summary)
 import(flextable)
 import(officer)
+importFrom(doconv,docx_update)
 importFrom(glue,glue)
 importFrom(magrittr,"%>%")
 importFrom(stringr,str_to_lower)

NEWS.md

@@ -1,15 +1,20 @@
-# swissethics 0.3.0
+# SwissASR 0.4.0
+
+* Modified some bookmarks into word fields such that the replacement can still happen in tables and not after them, as per recent update of officer package. This resolves issue #9.
+* The above change requires use of the `doconv` package, which may require **setting some permissions on MAC OS** (for details see [the doconv documentation](https://github.com/ardata-fr/doconv)), and **may not work on Ubuntu** systems.
+
+# SwissASR 0.3.0
 
 * Additional option to include an intervention (random allocation) variable into the line listing (option `var_tx`), which is sometimes requested by ethics bodies.
 * Addition of a logo
 
-# swissethics 0.2.0
+# SwissASR 0.2.0
 
 * Addition of `asr_dataprep` and `asr_safety_summary` functions allowing for production of tables without generation of the MS Word report.
 * Reworking of the internals of `asr` to utilise the above mentioned functions.
 * Addition of demonstration dataset.
 * Line listing pages in the word template set to landscape.
 
-# swissethics 0.1.0
+# SwissASR 0.1.0
 
 * Added a `NEWS.md` file to track changes to the package.

R/asr.R

@@ -122,6 +122,7 @@
 #' @importFrom tibble tribble
 #' @importFrom glue glue
 #' @importFrom stringr str_to_lower str_to_sentence
+#' @importFrom doconv docx_update
 #' @examples
 #'
 #' data(asr_sae)
@@ -202,7 +203,7 @@ asr <- function(data,
                 , report_date = format(Sys.Date(), format = "%d/%m/%Y")
                 , period_from = as.Date("2020-11-02")
                 , period_to = as.Date("2020-11-17")
-                , template = system.file("extdata/clino_annual_safety_report_bm.docx", package = "SwissASR")
+                , template = system.file("extdata/clino_annual_safety_report_fm.docx", package = "SwissASR")
                 , international = FALSE
                 , trial_type = "imp"
                 # dataframe variables
@@ -394,49 +395,72 @@ asr <- function(data,
 
 
   # ..general info, details of trial ----
-  period <- glue("{period_from} to {period_to}")
-
-  for(i in c("trial_title",
-             "protocol_number",
-             "basec_number",
-             "snctp_number",
-             "swissmedic_number",
-             "ec_name",
-             "product_name",
-             "sponsor_contact",
-             "inst_name_address",
-             "report_date",
-             "period",
-             "n_centers_t",
-             "n_centers_p",
-             "n_centers_c",
-             "n_centers_o",
-             "n_pat_t",
-             "n_pat_e",
-             "n_pat_c",
-             "n_pat_p")){
-    x <- get(i)
-    doc <- doc %>%
-      cursor_bookmark(i) %>%
-      body_add_par(x, pos = "after")
-  }
-
-
-
+  #
+  # for(i in c("trial_title",
+  #            "protocol_number",
+  #            "basec_number",
+  #            "snctp_number",
+  #            "swissmedic_number",
+  #            "ec_name",
+  #            "product_name",
+  #            "sponsor_contact",
+  #            "inst_name_address",
+  #            "report_date",
+  #            "period",
+  #            "n_centers_t",
+  #            "n_centers_p",
+  #            "n_centers_c",
+  #            "n_centers_o",
+  #            "n_pat_t",
+  #            "n_pat_e",
+  #            "n_pat_c",
+  #            "n_pat_p")){
+  #   x <- get(i)
+  #   doc <- doc %>%
+  #     cursor_bookmark(i) %>%
+  #     body_add_par(x, pos = "after")
+  # }
 
 
-  ## participant safety ----
+  period <- glue("{period_from} to {period_to}")
+## New code to insert the fields instead of bookmarks
+    doc <- doc %>%
+      set_doc_properties(trial_title = get("trial_title"),
+                                  protocol_number = get("protocol_number"),
+                                  basec_number = get("basec_number"),
+                                  snctp_number = get("snctp_number"),
+                                  swissmedic_number = get("swissmedic_number"),
+                                  ec_name = get("ec_name"),
+                                  product_name = get("product_name"),
+                                  sponsor_contact = get("sponsor_contact"),
+                                  inst_name_address = get("inst_name_address"),
+                                  report_date = get("report_date"),
+                                  period = get("period"),
+                                  n_centers_t = get("n_centers_t"),
+                                  n_centers_p = get("n_centers_p"),
+                                  n_centers_c = get("n_centers_c"),
+                                  n_centers_o = get("n_centers_o"),
+                                  n_pat_t = as.character(n_pat_t),
+                                  n_pat_e = as.character(n_pat_e),
+                                  n_pat_c = as.character(n_pat_c),
+                                  n_pat_p = as.character(n_pat_p) )
+
+
+  #}  ## participant safety ----
   summ <- asr_safety_summary(data = data,
                              period_data = period_data,
                              trial_type = trial_type,
                              n_pat_e = n_pat_e)
 
+  # doc <- doc %>%
+  #   cursor_bookmark("partsafety_text")
+  # for(i in 1:length(summ$txt)){
+  #   txt <- summ$txt[i]
+  #   doc <- doc %>% body_add_par(txt, style = "Text")
+  # }
+
   doc <- doc %>%
-    cursor_bookmark("partsafety_text")
-  for(i in 1:length(summ$txt)){
-    txt <- summ$txt[i]
-    doc <- doc %>% body_add_par(txt, style = "Text")
-  }
+    officer::set_doc_properties(partsafety_text = paste0(summ$txt, collapse = " ") )
 
   # map <- data.frame(
   #   col_key = c("x1", "x2", "x3", "x4", "x5"),
@@ -613,6 +637,11 @@ asr <- function(data,
   print(doc, target = target)
 
 
+   doc <- doc %>%
+     doc_properties()
+
+  docx_update(input = target)
+
 }
 
 

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 Participant safety is a big issue in clinical trials and reporting safety related events to the authorities is mandatory for certain trial types. One aspect of this is the annual safety report (ASR) which contains both summary information and listings of safety events. The `SwissASR` R package helps in compiling this report.
 
-Provide a dataframe with the given variables and the function will return a filled out (as far as possible - some things require PI input) ASR in MS Word format. This could then be forwarded to the PI for supplimental details, signing and submission to the relevant governing bodies.
+Provide a dataframe with the given variables and the function will return a filled out (as far as possible - some things require PI input) ASR in MS Word format. This could then be forwarded to the PI for supplemental details, signing and submission to the relevant governing bodies.
 
 ## Example usage