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Merge 2025 data call changes#226

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rix133 merged 152 commits intomainfrom
dev
Apr 16, 2025
Merged

Merge 2025 data call changes#226
rix133 merged 152 commits intomainfrom
dev

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@rix133 rix133 commented Apr 11, 2025

I guess there will be no more updates and while as the dev works and we have all import functions implemented i think pulling the whole dev into main. Or if you think we should only pull those parts that are essential we shoud pick some commits to merge with main into a new branch?

nicholascarey and others added 30 commits October 14, 2024 14:09
@nicholascarey
Typo in Rbuildignore - docs not doc
dee9562
@rix133
init ratio estimation example
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@rix133
Merge branch 'dev' of github.com:ices-tools-dev/RDBEScore into dev
6ce2af9
@rix133
getting the hang of ratio calcuation from the est Object
a38b679
@davidcurrie2001
Added verbose parameter (issue #200)
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@davidcurrie2001
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
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…o dev
@rix133
Merge pull request #206 from ices-tools-dev/main
48937c2 
Merge pull request #192 from ices-tools-dev/dev
@davidcurrie2001
createRDBESDataObject now works with list of data.tables. Closes #196
c0ac5f9
@davidcurrie2001
Don't export createTableOfRDBESIds() (Closes #205)
3ac1405
@davidcurrie2001
Deleted removePrefixFromVarNames() function (closes #204)
0e6d88b
@rix133
mapping how to do ratio estimation by lenght class
6ad4885
@rix133
mapping how to do ratio estimation by lenght class
40e40cb
@rix133
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
9c60579 
…o dev

# Conflicts:
#	vignettes/ratio-estimating-rdbesdataobjects.Rmd
@davidcurrie2001
Moved renameSpeciesSA() function to R folder
3351d83
@davidcurrie2001
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
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…o dev
@karolinamg
doEstimationRatio
6fba67e
@davidcurrie2001
Update renameSpeciesSA() and write tests (#199)
649a56a
@davidcurrie2001
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
365c013 
…o dev
@davidcurrie2001
Renamed renameSpeciesSA() to updateSAwithTaxonFromSL() (#199)
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@davidcurrie2001
Vignette for updateSAwithTaxonFromSL (#199)
1096cd0
@davidcurrie2001
Fix missing bracket
045d906
@davidcurrie2001
CHanged default value for killOrphans to True, and added a call to re…
7a20788 
…moveBrokenSpeciesListLinks() function
@anacfernandes
Update createRDBESDataObject.R
605aad4 
Add text to close Issue #194
@davidcurrie2001
filterRDBESEstObject() function and tests created (closes #208)
57f4599
@davidcurrie2001
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
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…o dev
@karolinamg
Upd doEstimationRatio structure
9f9862d
@rix133
getting subsets of lower table data by upper table fields
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@davidcurrie2001
Remove restrictions on lower hierarchy (closes #7)
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@davidcurrie2001
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore int…
525afcb 
…o dev
@rix133
subsetting list of data tables by fields
caca253
@rix133 rix133 requested a review from davidcurrie2001 April 11, 2025 11:17
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davidcurrie2001 commented Apr 11, 2025

I guess there will be no more updates and while as the dev works and we have all import functions implemented i think pulling the whole dev into main. Or if you think we should only pull those parts that are essential we shoud pick some commits to merge with main into a new branch?

My feeling would be to merge it all in, but will that then include some functions related to ratio estimation that are unfinished?

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rix133 commented Apr 11, 2025

apparently there is still some work to do as vignettes are outdated

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rix133 commented Apr 11, 2025 •
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My feeling would be to merge it all in, but will that then include some functions related to ratio estimation that are unfinished?

Yes true, my idea is that we remove the @export tag from the unfinshed stuff and add to its description that it is unfinished I think that not having an @export tag on stuff that is not finished also in dev is a good practice.

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davidcurrie2001 commented Apr 11, 2025

My feeling would be to merge it all in, but will that then include some functions related to ratio estimation that are unfinished?

Yes true, my idea is that we remove the @export tag from the unfinshed stuff and add to its description that it is unfinished I think that not having an @export tag on stuff that is not finished also in dev is a good practice.

Yes, that's a good way to deal with it. If a user is poking about and using un-exported functions then it is at their own risk.

rix133 and others added 16 commits April 11, 2025 17:05
@rix133
fix vignette data
3a3ad9d
@rix133
fix agrstat data
bf8b78a
@rix133
fix unknown macros for formulas
36ac2cd
@davidcurrie2001
ProjectID added
9006fdb
@davidcurrie2001
Update ProjectID to same as Github
6a07f3e 
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore into dev

# Conflicts:
#	RDBEScore.Rproj
@davidcurrie2001
Updated data source and fixed error with parameter name (#227)
9aadb40
@davidcurrie2001
Updated data source and made changes for the new IS table (#227)
017485d
@davidcurrie2001
Account for addition of IS table. Don't validate data types for the t…
35e8876 
…est data (not best solution). (#227)
@davidcurrie2001
Take account of new IS table. Change validation to ignore datatypes (…
7d5719e 
…not best solution) (#227)
@davidcurrie2001
Minor change (#227)
1d3e588
@davidcurrie2001
Make index entry same as title (#227)
8cf371a
@rix133
fix title #227
b92a310
@davidcurrie2001
Minor change
56b09dd 
Merge branch 'dev' of https://github.com/ices-tools-dev/RDBEScore into dev

# Conflicts:
#	vignettes/ratio-estimating-rdbesdataobjects.Rmd
@davidcurrie2001
Removed some rogue slashes
23a531b
@rix133
fix documentation #220
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@rix133
fix roxygen notes #220
92ee0d3 
Merge branch 'dev' of github.com:ices-tools-dev/RDBEScore into dev

# Conflicts:
#	R/listPackageFunctions.R
#	man/getRdTitle.Rd
#	man/listPackageFunctions.Rd
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davidcurrie2001 commented Apr 16, 2025

@rix133 are you happy to merge this in? It looks ok to me. I can see 2 of the checks are failing. The test-coverage check errors looks like its a problem with the Github action ("Missing download info for actions/upload-artifact@v3"). The tests pass on my laptop. The mac-os-latest check is failing with "ERROR: compilation failed for package ‘data.table’" - since we're not on CRAN yet can we live with that?

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rix133 commented Apr 16, 2025

I think it is OK

@rix133 rix133 closed this Apr 16, 2025
@rix133 rix133 reopened this Apr 16, 2025
@rix133 rix133 merged commit fe5d301 into main Apr 16, 2025
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@rix133 rix133 mentioned this pull request Apr 16, 2025
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@rix133 @davidcurrie2001 @Kasia-MIR @nicholascarey @karolinamg @anacfernandes @KirstenBirchHaakansson