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Catch lottery stox4 #169

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Feb 4, 2025
Merged

Catch lottery stox4 #169

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8ccbfb9
Added new report functions to overview.
Feb 2, 2025
05a5120
Added example file with more detailed sampling frame annotation
Feb 2, 2025
48ad4cd
updated R version requirements in documentation
Feb 3, 2025
be0422c
fixed error in error message
Feb 3, 2025
27a8204
bugfix error message AssignPSUSamplingParameters
Feb 4, 2025
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: RstoxFDA
Version: 1.5.0-9003
Date: 2025-01-24
Version: 1.5.0-9004
Date: 2025-02-04
Title: Fisheries Dependent Analysis with RstoX
Authors@R: c(
person(given = "Edvin",
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3 changes: 3 additions & 0 deletions NEWS.md
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# 1.5.0-9004
* Fixed a bug which caused AssignPSUSamplingParameters to report the wrong records as missing, when data is not provided for all sampled records

# 1.5.0-9003
* Added function to annotate length groups: AddLengthGroupStoxBiotic (#163), and report total catch by age group: ReportAnalyticalCatchAtLength (#150)
* Added function to report mean of weight and length by age: ReportAnalyticalLengthAtAge, and ReportAnalyticalWeightAtAge (#150).
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2 changes: 1 addition & 1 deletion R/StoxAnalyticalBaselineFunctions.R
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Expand Up @@ -717,7 +717,7 @@ AssignPSUSamplingParameters <- function(PSUSamplingParametersData, StoxBioticDat

records <- PSUSamplingParametersData$SelectionTable$SamplingUnitId[!is.na(PSUSamplingParametersData$SelectionTable$SamplingUnitId)]
if (!all(records %in% StoxBioticData[[level]][[SamplingUnitId]])){
missing <- records[!(records %in% StoxBioticData[[l]][[SamplingUnitId]])]
missing <- records[!(records %in% StoxBioticData[[level]][[SamplingUnitId]])]
stop(paste("Records are not found for all sampled PSUs. Missing for the following SamplingUnitIds (", SamplingUnitId,"): ", truncateStringVector(missing), sep=""))
}

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72 changes: 72 additions & 0 deletions inst/testresources/lotteryParameters/lotteryDesignNSHdetailed.txt
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Stratum N n SelectionMethod FrameDescription Order SamplingUnitId InclusionProbability HTsamplingWeight SelectionProbability HHsamplingWeight SelectionDescription CountryVessel VesselLengthGroup TargetSpecies TargetStock
Sild2022 Nordsjo 811 71 Poisson "" 3 38401 0.213196915139625 0.0080680146704093 0.00217741935483873 0.00766305544800977 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 46 38433 0.247412405326388 0.00695226189957357 0.00258064516129031 0.00646570303425833 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 5 38440 0.1700984890555 0.0101122346740615 0.00169354838709679 0.00985249986172684 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 71 38445 0.108975250145035 0.0157840962672098 0.00104838709677424 0.015915576699712 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 44 38438 0.641175307024414 0.00268269195676777 0.0092741935483871 0.00179915214866318 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 36 38441 0.233906828422691 0.00735367945703649 0.0024193548387097 0.00689674990320879 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 39 38448 0.267229615158194 0.00643669616488522 0.00282258064516128 0.00591149991703619 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 7 38403 0.0767615148687669 0.0224080496844438 0.000725806451612909 0.0229891663440293 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 66 38435 0.143125007547176 0.0120179964948861 0.00140322580645158 0.0118909481089811 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 67 38436 0.147680162555427 0.0116473046160613 0.00145161290322582 0.0114945831720147 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 70 38443 0.0182839435244132 0.0940757576031566 0.000167741935483856 0.0994723543732134 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 9 38446 0.267229615158194 0.00643669616488522 0.00282258064516128 0.00591149991703619 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 43 38447 0.247412405326388 0.00695226189957357 0.00258064516129031 0.00646570303425833 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 10 38402 0.108975250145035 0.0157840962672098 0.00104838709677424 0.015915576699712 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 48 38434 0.220161129326957 0.00781280439599331 0.00225806451612898 0.00738937489629538 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 27 38442 0.068529393639208 0.0250998257490547 0.000645161290322549 0.0258628121370345 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 32 38444 0.147680162555427 0.0116473046160613 0.00145161290322582 0.0114945831720147 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 68 38437 0.147680162555427 0.0116473046160613 0.00145161290322582 0.0114945831720147 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 61 38439 0.311481476435603 0.00552224118980031 0.00338709677419358 0.00492624993086342 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 31 38431 0.0889747087440887 0.019332188475939 0.000846774193548394 0.0197049997234537 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 55 38415 0.136247006433322 0.0126246872064253 0.00133064516129033 0.0125395452785614 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 33 38406 0.097027756531011 0.0177276678399005 0.000927419354838754 0.0179915214866309 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 13 38417 0.101027788104015 0.0170257695562093 0.000967741935483879 0.017241874758022 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 18 38419 0.0849215381190344 0.0202548832384721 0.00080645161290327 0.0206902497096254 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 29 38408 0.184718409696934 0.00931188094275289 0.0018548387096774 0.00899576074331599 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 37 38412 0.216686691440281 0.00793807791147411 0.00221774193548385 0.00752372716713699 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 40 38422 0.0518463272604551 0.0331764259865801 0.00048387096774194 0.034483749516044 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 51 38432 0.162691408611336 0.0105726285961522 0.00161290322580643 0.0103451248548134 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 60 38429 0.338519898362406 0.00508116612155855 0.00375000000000003 0.00444951606658632 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 11 38404 0.162691408611336 0.0105726285961522 0.00161290322580643 0.0103451248548134 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 28 38413 0.097027756531011 0.0177276678399005 0.000927419354838754 0.0179915214866309 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 2 38414 0.240689370659604 0.00714645534332767 0.00249999999999995 0.00667427409987967 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 17 38405 0.267229615158194 0.00643669616488522 0.00282258064516128 0.00591149991703619 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 1 38411 0.458713264018625 0.00374978439464236 0.0055645161290323 0.00299858691443861 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 24 38416 0.116853084910627 0.014719986557035 0.00112903225806449 0.0147787497925908 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 25 38427 0.589628784636336 0.00291721822925146 0.00806451612903225 0.00206902497096266 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 38 38409 0.162691408611336 0.0105726285961522 0.00161290322580643 0.0103451248548134 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 23 38424 0.347296770955766 0.00495275505815625 0.00387096774193552 0.00431046868950549 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 30 38421 0.116853084910627 0.014719986557035 0.00112903225806449 0.0147787497925908 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 35 38430 0.116853084910627 0.014719986557035 0.00112903225806449 0.0147787497925908 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 56 38426 0.233906828422691 0.00735367945703649 0.0024193548387097 0.00689674990320879 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 54 38407 0.068529393639208 0.0250998257490547 0.000645161290322549 0.0258628121370345 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 21 38418 0.229685923270579 0.00748881696596698 0.00236952419354841 0.00704178724789118 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 42 38428 0.143125007547176 0.0120179964948861 0.00140322580645158 0.0118909481089811 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 50 38420 0.0425447856855458 0.040429768567782 0.000395161290322577 0.0422249994074016 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 20 38423 0.463520590962966 0.0037108941276137 0.00564516129032255 0.00295574995851809 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 16 38410 0.267034025829916 0.00644141072916334 0.00282016129032259 0.00591657126383371 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 34 38425 0.0930100890906527 0.0184934328721696 0.000887096774193519 0.0188093179178429 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 45 0.254076449772695 0.00676991449058477 0.00266129032258067 0.00626977263928072 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 8 0.0849215381190344 0.0202548832384721 0.00080645161290327 0.0206902497096254 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 15 0.260682016891707 0.00659836784885341 0.00274193548387092 0.00608536756165498 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 12 0.0602245433032077 0.0285610441306723 0.0005645161290323 0.0295574995851786 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 47 0.068529393639208 0.0250998257490547 0.000645161290322549 0.0258628121370345 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 53 0.216686691440281 0.00793807791147411 0.00221774193548385 0.00752372716713699 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 59 0.570866304669027 0.00301309750630624 0.00766129032258067 0.00217792102206594 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 26 0.199083079634323 0.00863999010961628 0.00201612903225812 0.0082760998838504 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 63 0.1700984890555 0.0101122346740615 0.00169354838709679 0.00985249986172684 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 65 0.1700984890555 0.0101122346740615 0.00169354838709679 0.00985249986172684 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 52 0.174511532419619 0.00985651673092022 0.00174193548387092 0.00957881931001258 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 22 0.202634883401628 0.00848854753020615 0.00205645161290324 0.00811382341553975 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 4 0.068529393639208 0.0250998257490547 0.000645161290322549 0.0258628121370345 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 6 0.132402285228299 0.0129912851282484 0.00129032258064521 0.0129314060685161 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 64 0.101027788104015 0.0170257695562093 0.000967741935483879 0.017241874758022 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 58 0.0808504995083754 0.0212747707125089 0.000766129032258034 0.0217792102206604 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 69 0.140074844132902 0.0122796912584854 0.00137096774193546 0.01217073512331 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 62 0.0552064585338686 0.0311571487234098 0.000516129032258061 0.0323285151712917 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 49 0.112922833036567 0.0152323121265962 0.00108870967741936 0.0153261108960195 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 19 0.386753608156008 0.00444747198929469 0.0044354838709677 0.00376186358356849 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 14 0.413480846839946 0.00415998915591446 0.0048387096774194 0.0034483749516044 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 41 0.247412405326388 0.00695226189957357 0.00258064516129031 0.00646570303425833 "" NOR >15m HER Nordsjo
Sild2022 Nordsjo 811 71 Poisson "" 57 0.0518463272604551 0.0331764259865801 0.00048387096774194 0.034483749516044 "" NOR >15m HER Nordsjo
8 changes: 7 additions & 1 deletion vignettes/Stox-Analytical.Rmd
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Expand Up @@ -46,7 +46,7 @@ For testing pre-releases of StoX, obtain the stox packages from the testing repo
install.packages(c("RstoxData", "RstoxBase", "RstoxFramework", "RstoxFDA"), repos = c("https://stoxproject.github.io/testingRepo/"))
```

This will install latest pre-release available for your version of R and operating system. Make sure you have R 4.2 or 4.3 if testing on Mac or Windows.
This will install latest pre-release available for your version of R and operating system. Make sure you have R 4.4 or 4.4 if testing on Mac or Windows.

After you have finished testing, you may want to revert to the production packages. This may require explicitly uninstalling the packages first, as they have higher version numbers than production packages:

Expand All @@ -67,6 +67,7 @@ A minimal StoX project implementing analytical catch at age estimates with catch
| ReadSamples | ReadBiotic | Reads sample data |
| StoxBiotic | StoxBiotic | Convert sample data to StoxBiotic |
| AddSamplingId | AddToStoxBiotic | Add serialnumber to StoxBiotic |
| AddLengthGroups | AddLengthGroupStoxBiotic | If catch-at-length is desired. Adds a column to StoxBiotic, grouping individuals by length. |
| ReadPSUsamplingParameters | ReadPSUSamplingParameters | Read sampling parameters for each haul. These ar provided from the catch lottery. |
| ComputeINDsamplingParameters | ComputeIndividualSamplingParameters | Defines sampling parameters for each individual, within haul. Parameters are inferred from data with configurable assumptions. |
| AssignPSUSamplingParameters | AssignPSUSamplingParameters | Matches selections to data records, handles non-response corrections |
Expand All @@ -83,6 +84,11 @@ The following functions provides reporting from analytical estimates:
|:------|:-----|
| ReportAnalyticalCatchAtAge | Tabulate total catch of each age group |
| PlotCatchAtAgeTotals | Plot total catch of each age group |
| ReportAnalyticalCatchAtLength | Tabulate total catch of each length group |
| ReportAnalyticalLengthAtAge | Tabulate mean length of each age group |
| PlotMeanLengthAtAge | Plot mean length of each age group |
| ReportAnalyticalWeightAtAge | Tabulate mean weight of each age group |
| PlotMeanWeightAtAge | Plot mean weight of each age group |

In addition some functions are relevant in this context, that may also be used with other estimation approaches, such as Reca:

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