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CRAN status:
icesSAG provides R functions that access the web services of the ICES Stock Assessment Graphs database.
icesSAG is implemented as an R package and is currently hosted on r-universe and available on CRAN.
The stable version of icesSAG can be installed from CRAN using the
install.packages command:
install.packages("icesSAG", repos = "https://cloud.r-project.org")or a potentially more recent, but less stable version installed from r-universe:
install.packages("icesSAG", repos = "https://ices-tools-prod.r-universe.dev")For a summary of the package:
library(icesSAG)
?icesSAGTo download the summary data for all sandeel stocks published in 2018 use:
summary_data <- getSAG(stock = "sandeel", year = 2023)
head(summary_data)## Year recruitment high_recruitment low_recruitment low_SSB SSB high_SSB low_F F high_F catches landings
## 1 1983 285000075 404690458 200709063 307520 452254 665108 0.478 0.596 0.744 382629 NA
## 2 1984 75526942 108094090 52771793 136696 194269 276092 0.540 0.674 0.840 498671 NA
## 3 1985 518266424 723794791 371099778 307364 431059 604534 0.577 0.720 0.898 460057 NA
## 4 1986 75376039 107979318 52616996 202400 265402 348014 0.389 0.484 0.602 382844 NA
## 5 1987 49081856 72043445 33438554 708828 977741 1348673 0.302 0.377 0.471 373021 NA
## 6 1988 201037095 284748295 141935577 420971 577810 793081 0.421 0.523 0.651 422805 NA
## discards IBC Unallocated_Removals LandingsBMS TBiomass LogbookRegisteredDiscards StockPublishNote Purpose Fage
## 1 NA NA NA NA NA NA Stock published Advice 1-2
## 2 NA NA NA NA NA NA Stock published Advice 1-2
## 3 NA NA NA NA NA NA Stock published Advice 1-2
## 4 NA NA NA NA NA NA Stock published Advice 1-2
## 5 NA NA NA NA NA NA Stock published Advice 1-2
## 6 NA NA NA NA NA NA Stock published Advice 1-2
## fishstock recruitment_age AssessmentYear units stockSizeDescription stockSizeUnits fishingPressureDescription
## 1 san.sa.1r 0 2023 tonnes SSB tonnes F
## 2 san.sa.1r 0 2023 tonnes SSB tonnes F
## 3 san.sa.1r 0 2023 tonnes SSB tonnes F
## 4 san.sa.1r 0 2023 tonnes SSB tonnes F
## 5 san.sa.1r 0 2023 tonnes SSB tonnes F
## 6 san.sa.1r 0 2023 tonnes SSB tonnes F
## fishingPressureUnits AssessmentKey AssessmentComponent
## 1 NA 17718 NA
## 2 NA 17718 NA
## 3 NA 17718 NA
## 4 NA 17718 NA
## 5 NA 17718 NA
## 6 NA 17718 NA
ggplot(summary_data[complete.cases(summary_data[c("Year", "recruitment")]),],
aes(x=Year, y=recruitment, group = fishstock, colour = fishstock)) +
geom_line()
If you want to see all the web service calls being made set this option
sag_messages(TRUE)The result will be
codKeys <- findAssessmentKey("cod", year = 2017)which allows you to investigate the actual web service data if you are interested: https://sag.ices.dk/SAG_API/api/StockList?year=2017
ICES provides public access to the results of published stock assessments. If you are an ICES stock assessor and wish to access unpublished results, or to upload your results, this can be done using token authentication.
This is easy to set up, simply run the following line and all future requests to the SAG database will be authenticated.
sag_use_token(TRUE)To upload the results of a stock assessment to SAG you must provide two pieces of information, Stock information, such as stock code, assessment year and reference points, and yearly results, such as landings and estimated fishing mortality. There are two helper functions to create the required objects.
stockInfo()returns a list (it requires a stock code, assessment year and contact
email as a minimum), with the correctly named elements. And,
stockFishdata()returns a data.frame (it requires year as default) with the correctly
named columns
A simple (almost) minimal example is:
info <-
stockInfo(
StockCode = "whg.27.7a",
AssessmentYear = 2021,
ContactPerson = "[email protected]",
StockCategory = 3,
Purpose = "Unofficial",
ModelType = "A",
ModelName = "XSA"
)
fishdata <- stockFishdata(1950:2020)
# simulate some landings for something a bit intesting
set.seed(1232)
fishdata$Landings <- 10^6 * exp(cumsum(cumsum(rnorm(nrow(fishdata), 0, 0.1))))
# you can create an XML file to upload yourself
xml <- createSAGxml(info, fishdata)
# here we use a temporary file to store the XML, but you can safe this to your output or report folder
tempfile <- tempfile(fileext = ".xml")
cat(xml, file = tempfile)
# this file can then be uploaded using the SAG webservices
key <- uploadStock(tempfile, upload = TRUE)
# if you want to just check the file and not upload:
uploadStock(tempfile, upload = FALSE)You can check that the data was uploaded by searching for our stock. Note you will need to make sure the icesSAG.use_token option is set to TRUE
sag_use_token(TRUE)
findAssessmentKey('whg.27.7a', 2020, full = TRUE)## [1] AssessmentKey StockKeyLabel Purpose StockDatabaseID StockKey
## [6] StockDescription Status AssessmentYear SpeciesName ModifiedDate
## [11] SAGStamp LinkToAdvice AssessmentComponent
## <0 rows> (or 0-length row.names)
We can also look at the landings graph created from the data that were uploaded, NOTE you may need to modify the settings at sag.ices.dk.
plot(getLandingsGraph(key))or download all four summary graphs and display them in a 2x2 grid.
graphs <- getSAGGraphs(key)
plot(graphs)ICES Stock Assessment Graphs database: https://sg.ices.dk
ICES Stock Assessment Graphs web services: https://sg.ices.dk/webservices.aspx
icesSAG is developed openly on GitHub.
Feel free to open an issue there if you encounter problems or have suggestions for future versions.
The current development version can be installed using:
library(devtools)
install_github("ices-tools-prod/icesSAG@development")