Merge branch 'main' of https://github.com/inbo/protocolsource into spp-001-nl

Author: hansvancalster

.github/workflows/generate-artifact-pr.yml

@@ -30,7 +30,7 @@ jobs:
 
       - name: Query dependencies
         run: |
-          install.packages('remotes')
+          install.packages('remotes', type = "source")
           saveRDS(remotes::dev_package_deps(dependencies = NA), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
@@ -49,8 +49,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = NA) #fails to install protocolhelper
-          remotes::install_github("inbo/protocolhelper")
+          remotes::install_deps(dependencies = NA, type = "source") #fails to install protocolhelper
+          remotes::install_github("inbo/protocolhelper", type = "source")
         shell: Rscript {0}
 
       - name: Session info

.gitignore

@@ -42,5 +42,6 @@ vignettes/*.pdf
 
 # Other
 docs/
+from_docx/
 css/
 _bookdown_files/

.zenodo.json

@@ -66,6 +66,12 @@
       "affiliation": "Research Institute for Nature and Forest",
       "type": "Researcher",
       "orcid": "0000-0001-7679-743X"
+    },
+    {
+      "name": "Scheers, Kevin",
+      "affiliation": "Research Institute for Nature and Forest",
+      "type": "Researcher",
+      "orcid": "0000-0002-4756-4247"
     }
   ]
 }

CONTRIBUTING.md

@@ -46,9 +46,11 @@ Note also that any dependency packages needed by the packages listed in the [DES
 
 Apart from the above R packages, you will also need a working installation of TinyTeX, which is an external open-source software package that is needed to render protocols to PDF format (i.e. when you run `protocolhelper::render_protocol()` see [Workflow](#workflow)).
 
-To install this, we recommend to follow the [installation instructions](https://github.com/inbo/INBOmd/#installation) provided by the `INBOmd` R package.
-Please make sure to install this from an R session that runs outside of the RStudio `protocolsource.Rproj`.
-So, close the RStudio project and any other R sessions and start the most recent version of R that is installed on your system and copy-paste the installation instructions in the R console.
+To install this:
+
+-   close the RStudio project and any other R sessions and start the most recent version of R that is installed on your system
+
+-   follow the [installation instructions](https://github.com/inbo/INBOmd/#installation) provided by the `INBOmd` R package and copy-paste the installation instructions in the R console.
 
 ## `(R)markdown` syntax and learning `Rmarkdown`
 
@@ -276,13 +278,16 @@ This will allow you to check the resulting output locally.
 
 ### From an existing docx protocol
 
+Even if you are converting an older published protocol, we recommend leaving the date field to it's default value (current date) and instead mention in the `NEWS.md` file that this is a conversion from protocol so-and-so published first on date such-and-such.
+
+
 ```r
 library(protocolhelper)
 create_sfp(title = "Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen van bedekking van soorten in (semi-)terrestrische vegetatie",
            short_title = "vegopname terrest",
            authors = "De Bie, Els",
            orcids = "0000-0000-1234-5678",
-           date = "2016-07-19", 
+           date = "`r Sys.Date()`", 
            reviewers = "Hans Van Calster, Lieve Vriens, Jan Wouters, Wouter Van Gompel, Els Lommelen", 
            file_manager = "Hans Van Calster", 
            theme = "vegetation",
@@ -296,6 +301,8 @@ create_sfp(title = "Klassieke vegetatieopname in een proefvlak aan de hand van v
 
 ### From a new template
 
+For a field protocol (sfp) (you need to specify a theme):
+
 ```r
 library(protocolhelper)
 create_sfp(title = "titel van het protocol",
@@ -313,7 +320,7 @@ create_sfp(title = "titel van het protocol",
            render = FALSE)
 ```
 
-Alternatively, for a project-specific protocol:
+Alternatively, for a project-specific protocol (you need to specify a project_name):
 
 ```r
 library(protocolhelper)
@@ -329,6 +336,25 @@ create_spp(title = "Bodemstalen nemen",
            render = FALSE)
 ```
 
+Or for a standard operating procedure (similarly for sip or sap; no need to specify theme or project_name):
+
+```r
+library(protocolhelper)
+create_sop(title = "titel van het protocol",
+           subtitle = "optionele subtitel", 
+           short_title = "korte titel",
+           authors = c("Achternaam1, Voornaam1", "Achternaam2, voornaam2"),
+           orcids = c("0000-0000-1234-5678", "0000-0000-1234-8765"),
+           date = "`r Sys.Date()`", 
+           reviewers = "Voornaam Naam, ...", 
+           file_manager = "Voornaam Naam", 
+           language = "nl",
+           from_docx = NULL,
+           protocol_number = NULL, 
+           render = FALSE)
+```
+
+
 ## <a name="parameterized"></a>What to do in case of parameterized protocols?
 
 See [the bookdown manual](https://bookdown.org/yihui/rmarkdown/parameterized-reports.html) for a general explanation about parameterized reports.

DESCRIPTION

@@ -21,7 +21,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Remotes:
     github::inbo/protocolhelper,
-    github::inbo/checklist
+    github::inbo/checklist,
+    github::inbo/inbodb
 Imports: 
     checklist,
     dplyr,

NEWS.md

@@ -1,3 +1,24 @@
+### First version of protocol: sfp-406-nl
+
+- Title: Vegetatieopname en LSVI-bepaling *Luronium natans*
+- Published on: 2023-06-21
+- Version number: 2023.06
+- Link to this version: [sfp-406-nl version 2023.06](2023.06/index.html)
+
+### Update of protocol: sfp-403-nl
+
+- Title: Vegetatieopname en LSVI-bepaling habitat 3260
+- Published on: 2023-06-20
+- Version number: 2023.05
+- Link to this version: [sfp-403-nl version 2023.05](2023.05/index.html)
+
+### First version of protocol: sfp-113-nl
+
+- Title: Bepaling doorzicht waterkolom oppervlaktewater op basis van de Secchi-diepte
+- Published on: 2023-06-20
+- Version number: 2023.04
+- Link to this version: [sfp-113-nl version 2023.04](2023.04/index.html)
+
 ### First version of protocol: sfp-401-nl
 
 - Title: Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen van bedekking van soorten in (semi-)terrestrische vegetatie