tidying up documentation and changelog prior to 3.2-0 release

CONTRIBUTING.md

@@ -68,7 +68,8 @@ functions are not intended for direct interaction with the user, as such, the
 documentation of most arguments is centralized in the details section of man/GGIR.Rd. 
 If you for example want to add an extra parameter to `params_247` then this should
 be documented there. Further, you should not forget to include the new argument in
-functions \link{load_params} and \link{check_params}.
+functions \link{load_params} and \link{check_params}. The pull request template has a
+form that will help you check all these points.
 
 #### Package vignettes
 
@@ -113,12 +114,20 @@ For updating or adding information to the github.io website, we need to use
 [the pkgdown configuration file](_pkgdown.yml) that can be found in the repositories 
 root directory, as well as with the chapter vignettes discussed above.
 
+
+General comment: As contributor please NEVER run the command `pkgdown::build_site()`.
+I (Vincent van Hees) will run this command in the master branch prior to each new
+GGIR release. If multiple contributors would be running this command in their own 
+development branches we risk complex merge conflicts between the many html files 
+that are auto-generated by this function.
+
 **To edit information in an existing chapter**
 
 1. Open the vignette corresponding to the chapter you wish to edit (see the _pkgdown.yml) 
 file for the chapter and its vignette path (href).
 2. Make your changes in the vignette.
-3. Run the `pkgdown::build_site()` function.
+
+As stated above do NOT run `pkgdown::build_site()`.
 
 **To add a new chapter**
 
@@ -132,15 +141,17 @@ usethis::use_vignette(name = "chapterSleep",
 
 2. Open the [_pkgdown.yml](_pkgdown.yml) file and fill up the name and reference of the
 new chapter under menu. Make sure to follow the coding and structure of the rest of chapters.
-3. Run the `pkgdown::build_site()` function.
+
+As stated above do NOT run `pkgdown::build_site()`.
 
 **To remove a chapter**
 
 1. Remove the lines corresponding to the chapter in the [_pkgdown.yml](_pkgdown.yml) file
 in line 42 onwards.
 2. Optionally you may remove the Rmd file corresponding to the chapter, but only by doing the
 step 1, the chapter will not appear in the github.io website.
-3. Run the `pkgdown::build_site()` function.
+
+As stated above do NOT run `pkgdown::build_site()`.
 
 **To edit the name of a chapter**
 
@@ -152,12 +163,7 @@ page for the chapter.
 #### Adding the changes to the master branch
 
 The last step would be committing and pushing your changes to github and making a
-pull request as with any other contribution to the package. Note that, running the 
-`pkgdown::build_site()` function will edit the files within the docs folder, and 
-probably add some new files. This only applies when editing information from the 
-github.io website. It is important that these changes to the files in the
-docs folder are also part of the pull requests, as otherwise the website would not 
-be updated.
+pull request as with any other contribution to the package. 
 
 ## New release
 

NEWS.md

@@ -1,7 +1,5 @@
 # CHANGES IN GGIR VERSION 3.2-0
 
-- New visual report: Bug fixed in handling recordings that start at midnight #1257
-
 - Part 2:
 
   - Bug fixed in handling part 1 output with the uncommon scenario of having only 1 metric (in object metashort) #1265
@@ -16,6 +14,8 @@
 
 - Visualisations:
 
+  - Bug fixed in handling recordings that start at midnight #1257
+
   - The new and old general pdf report have been renamed to clarify which one is old (eventually to be deprecated) and which one is new.
 
   - Report_...pdf has been renamed to old_report_...pdf.
@@ -30,13 +30,14 @@
 
   - Fix bug related to determining the files to be included in the part 2 csv report, 
   causing some files to be unnecessarily excluded from the part 2 csv report if the number
-  of files in the part 2 milestone data is larger than than number of milestone files
-  in the part 1 milestone data. #1252
+  of files in the part 2 milestone data is smaller than than number of milestone files
+  in the part 1 milestone data, because internally it uses the part 1 milestone data
+  file list as reference. #1252
 
   - Speed up activity diary extraction. #1250
 
   - Make sure part 2 event report, e.g. based on step detection, is saved to csv format 
-  with intended sep and dec arguments rather than default.
+  with intended sep_reports and dec_reports parameter values rather than default.
 
   - Simplify MVPA parameter specification in part 2 (mvpathreshold, boutcriter). When not 
   specified, GGIR copies the values from the corresponding part 5 parameter values (threshold.mod and