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Catch lottery stox4 #155

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merged 24 commits into from
Jan 5, 2025
Merged

Catch lottery stox4 #155

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8a06f54
Updated README wrp R-versions tested
Dec 27, 2024
1adcb10
changed system for test-coverage-runner, as Reca is not tested on mac…
Dec 27, 2024
afd3ffe
Fixed issue with not being able to run Reca with temporal resolution …
Dec 27, 2024
83bad00
Fixed issue with plotting with other column variables than 'Area' in …
Dec 27, 2024
e7600c8
Fixed issue with reporting IndividualAge as SamplingVariable in Repor…
Dec 28, 2024
af84d1b
Changed test-coverage analysis to linux
Dec 28, 2024
4b962fd
Hid arguments to ComputeIndividualSamplingParameters, depending on th…
Dec 28, 2024
2d2dc19
rebuilt
Dec 28, 2024
5a3d093
Cleaned up possible values for domain def in PSU-estimate
Dec 28, 2024
b10dbb5
Implemented strict sampling frame expansion method
Dec 29, 2024
bdca0d9
some minor cleanup
Dec 29, 2024
a8ecf27
Removed codecov stuff not working
Dec 30, 2024
aa77c69
Added some documentaition and test for strict option for frame epansion
Dec 30, 2024
0465bbb
devloped some "imputation" options. Will probably revert to simpler a…
Dec 31, 2024
f8cd44e
Simplified frame extension
Dec 31, 2024
3637530
Designed extension functions for 0-abundance domains.
Dec 31, 2024
9614f4c
Redesigned domain interpolation
Jan 3, 2025
f0ac9cf
Fixed domain interpolation so that it treats all maringal zero-domain…
Jan 3, 2025
02821a8
Added documentation
Jan 3, 2025
58e800e
Note about testing needs
Jan 3, 2025
70ee68e
Refined mean estimates for domain interpolation.
Jan 5, 2025
56c3482
exposed ExtendAnalyticalSamplingFrameCoverage to StoX
Jan 5, 2025
c3f6546
Exposed InterpolateAnalyticalDomainEstimates to StoX
Jan 5, 2025
777dc5b
rewrote test that did not work on mac
Jan 5, 2025
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97 changes: 0 additions & 97 deletions .github/workflows/test-coverage.yaml
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: RstoxFDA
Version: 1.5.0-9003
Date: 2024-12-27
Date: 2024-12-28
Title: Fisheries Dependent Analysis with RstoX
Authors@R: c(
person(given = "Edvin",
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -24,8 +24,10 @@ export(DefinePeriod)
export(DefineSamplingHierarchy)
export(DefineStockSplittingParameters)
export(DefineWeightConversionFactor)
export(ExtendAnalyticalSamplingFrameCoverage)
export(FilterAgeLengthOutliersStoxBiotic)
export(FilterWeightLengthOutliersStoxBiotic)
export(InterpolateAnalyticalDomainEstimates)
export(LiftStrata)
export(ListBioticDifference)
export(LoadFdaStratumPolygon)
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4 changes: 4 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
# 1.5.0-9003
* Added functions for sampling frame expansion (ExtendAnalyticalSamplingFrameCoverage), and domain interpolation (InterpolateAnalyticalDomainEstimates) (#154)
* Changed how Stratification variables and Domain variables are matched to landings with AnalyticalRatioEstimate (# 125)
* Replaced DefinePSUSamplingParameters (processdata) with ComputePSUSamplingParameters (no processdata) and ReadPSUSamplingParameters (no processdata). This change breaks some pre-release projects (v. v1.3-9006). (#127)
* Replaced DefineIndividualSamplingParameters (processdata) with ComputeIndividualSamplingParameters (no processdata). This change breaks some pre-release projects (v. v1.3-9006).
* Added documentation for ECA convergence analsysis (#153)
* Fixed issue with reporting IndividualAge as SamplingVariable in ReportFdaSampling (#146)
* Fixed issue with running RunRecaModels with temporal resolution 'month' (#144)
* Fixed issue with plotting with other column variables than 'Area' in PlotFisheriesOverviewSpatial (#147)
* Fixed naming of age groups in reports from analytical estimates (#145)
* Fixed documentation for handling NA age groups (#151)
* Fixed issue with using integer columns in landings as stratification column in ratio estimates (#133)
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2 changes: 1 addition & 1 deletion R/StoxAnalysisFunctions.R
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Expand Up @@ -702,7 +702,7 @@ getLandingsFromStoxLandings <- function(RecaParameterData, StoxLandingData, Temp
quarter <- data.table::quarter(StoxLandingData$Landing$CatchDate)
}
else if (TemporalResolution == "Month"){
month <- month(StoxLandingData$Landing$CatchDate)
month <- data.table::month(StoxLandingData$Landing$CatchDate)
}
else if (TemporalResolution == "Day"){
date <- StoxLandingData$Landing$CatchDate
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