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Update indicators #122

Merged
merged 52 commits into from
Nov 22, 2023
Merged

Update indicators #122

merged 52 commits into from
Nov 22, 2023

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damianooldoni
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This PR updates all indicators, both checklist and occurrence based ones. The indicators are now using as inputs the most updated versions of:

  • unified checklist (GRIIS checklist for Belgium)
  • occurrence cubes of alien taxa in Belgium
  • occurrence species cubes for Belgium
    @timadriaens: one thing still to be done is checking the taxa in reference/species_of_infraspecific_alien_taxa.tsv. This has a relatively small impact on the 10-12th pipelines.
    I will mention this in an issue with more details.

@damianooldoni
Rerun preprocessing checklist indicators
5025056
@damianooldoni
Add pkg:: to avoid pkg conflict error
dd22b69
@damianooldoni
Run/knit checklist indicators
b85f2e7
@damianooldoni
Add input cubes to gitignore
34b7a91 
Ignoring on interim was wrong.
@damianooldoni
Restyle automatically code in chunks
de7a8f3
@damianooldoni
Get cubes from zenodo
084e356
@damianooldoni
Remove data with no cell codes
f91adac
@damianooldoni
Remove progress bars
cce51e4
@damianooldoni
Avoid using deprecated path arg in readr
f5a6465
@damianooldoni
Use pkgname::functionname for no conflicts errors
a07d70d
@damianooldoni
Allow negative lat/lon values
91d7ff8
@damianooldoni
Add dot to end of sentence
6400f57
@damianooldoni
Remove suspected data with no eea cell code
d82bb29
@damianooldoni
Remove data with no classKey from baseline
693692f
@damianooldoni
No specify path in extra variable
184c908
@damianooldoni
Remove progress bar
a540dc8
@damianooldoni
Remove progress bar
7728fd5
@damianooldoni
Use pkgname::funcname
3061cd1
@damianooldoni
Run all chunks
55c79e3
@damianooldoni
Remove duplicate chunk label
1121d3a
@damianooldoni
Knit preprocessing occ indicators
01813c0
@damianooldoni
Use pkgname::funcname in 6th pipeline
2cca9a2
@damianooldoni
Run all chunks of 6th pipeline
6ca32de
@damianooldoni
Add styler to setup opts
51abb28
@damianooldoni
Knit 6th pipeline
79ef961
@damianooldoni
Use styler on chunks code
030c272
@damianooldoni
Use file instead of path arg and use pkg::func everywhere
26a2414
@damianooldoni
knit 8th pipeline - generate figures and tsv files
085d231
@damianooldoni
Use tidy styler option for chunk codes
1100397
@damianooldoni
Use file arg in readr funcs and use pkg::func
5c5429f
@damianooldoni
Knit and produce outputs 8th pipeline
8761217
@damianooldoni
Update infraspecific alien taxa reference file
5e2c4a6 
Outdated keys checked. Some taxa are removed.
Some new infraspecific taxa are added.
@damianooldoni
Specify why we need these two packages
4f805b1
@damianooldoni
Update zenodo DOIs
c19d06f
@damianooldoni
Use pkgname::funcname everywhere in 10th pipeline
8577e53
@damianooldoni
Use file arg instead of deprecated path
3b0a43c
@damianooldoni
Improve text
a2c706a
@damianooldoni
Apply pkg::func to some chunks where forgotten
ebd4079
@damianooldoni
Run chunks updating data output
65956f5
@damianooldoni
Knit 10th pipeline
cce1ecb
@damianooldoni
Use pkg::fun everywhere in 11th pipeline
4136302
@damianooldoni
Add tidy styler opt to chunks options
99d2604
@damianooldoni
Fold code chunk in 11th pipeline
70f4e1f
@damianooldoni
Use walk instead of map to avoid messages
ab93f22
@damianooldoni
Improve text
007ae70
@damianooldoni
Knit 11th pipeline and produce outputs
f463fb1
@damianooldoni
Add tidy styler to chunk opts in 10th pipeline
486b831
@damianooldoni
Download and read cubes at data/input
42489b0 
Some of these cubes were already downloaded for occupancy indicators in /data/input which is actually the best place.
@damianooldoni
Use styler opt for code chunks
7f1c905
@damianooldoni
Use pkg::fun and split too long lines of code
f155f77
@damianooldoni
Knit 10th pipeline again
f7cbe35
@damianooldoni
Knit and produce outputs 12th pipeline
62c8f91
@damianooldoni damianooldoni merged commit 2749a4c into main Nov 22, 2023
@damianooldoni damianooldoni deleted the update-indicators branch November 22, 2023 16:21
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