git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@114690 82a268e6-3cf1-43bd-a215-b396298e98cf
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##--------------------------------------------------------
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## CMSY analysis with estimation of total biomass, including Bayesian Schaefer
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## written by Rainer Froese with support from Gianpaolo Coro in 2013-2014
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## This version adjusts biomass to average biomass over the year
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## It also contains the FutureCrash option to improve prediction of final biomass
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## Version 21 adds the purple point to indicate the 25th percentile of final biomass
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## Version 22 accepts that no biomass or CPUE area available
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##--------------------------------------------------------
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library(R2jags) # Interface with JAGS
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library(coda)
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#-----------------------------------------
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# Some general settings
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#-----------------------------------------
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# set.seed(999) # use for comparing results between runs
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rm(list=ls(all=TRUE)) # clear previous variables etc
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options(digits=3) # displays all numbers with three significant digits as default
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graphics.off() # close graphics windows from previous sessions
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#-----------------------------------------
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# General settings for the analysis
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#-----------------------------------------
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sigR <- 0.02 # overall process error; 0.05 works reasonable for simulations, 0.02 for real data; 0 if deterministic model
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n <- 10000 # initial number of r-k pairs
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batch.mode <- T # set to TRUE to suppress graphs
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write.output <- T # set to true if table of output is wanted
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FutureCrash <- "No"
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#-----------------------------------------
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# Start output to screen
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#-----------------------------------------
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cat("-------------------------------------------\n")
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cat("Catch-MSY Analysis,", date(),"\n")
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cat("-------------------------------------------\n")
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#------------------------------------------
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# Read data and assign to vectors
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#------------------------------------------
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# filename_1 <- "AllStocks_Catch4.csv"
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# filename_2 <- "AllStocks_ID4.csv"
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# filename_1 <- "SimCatch.csv"
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# filename_2 <- "SimSpec.csv"
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# filename_2 <- "SimSpecWrongS.csv"
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# filename_2 <- "SimSpecWrongI.csv"
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# filename_2 <- "SimSpecWrongF.csv"
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# filename_2 <- "SimSpecWrongH.csv"
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# filename_2 <- "SimSpecWrongL.csv"
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# filename_1 <- "FishDataLim.csv"
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# filename_2 <- "FishDataLimSpec.csv"
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filename_1 <- "WKLIFE4Stocks.csv"
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filename_2 <- "WKLIFE4ID.csv"
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outfile<-"outfile"
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outfile.txt <- "outputfile.txt"
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cdat <- read.csv(filename_1, header=T, dec=".", stringsAsFactors = FALSE)
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cinfo <- read.csv(filename_2, header=T, dec=".", stringsAsFactors = FALSE)
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cat("Files", filename_1, ",", filename_2, "read successfully","\n")
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# Stocks with total biomass data and catch data from StartYear to EndYear
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# stocks <- sort(as.character(cinfo$stock)) # All stocks
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stocks<-"HLH_M07"
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# select one stock after the other
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for(stock in stocks) {
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# assign data from cinfo to vectors
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res <- as.character(cinfo$Resilience[cinfo$stock==stock])
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StartYear <- as.numeric(cinfo$StartYear[cinfo$stock==stock])
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EndYear <- as.numeric(cinfo$EndYear[cinfo$stock==stock])
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r_low <- as.numeric(cinfo$r_low[cinfo$stock==stock])
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r_hi <- as.numeric(cinfo$r_hi[cinfo$stock==stock])
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stb_low <- as.numeric(cinfo$stb_low[cinfo$stock==stock])
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stb_hi <- as.numeric(cinfo$stb_hi[cinfo$stock==stock])
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intyr <- as.numeric(cinfo$intyr[cinfo$stock==stock])
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intbio_low <- as.numeric(cinfo$intbio_low[cinfo$stock==stock])
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intbio_hi <- as.numeric(cinfo$intbio_hi[cinfo$stock==stock])
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endbio_low <- as.numeric(cinfo$endbio_low[cinfo$stock==stock])
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endbio_hi <- as.numeric(cinfo$endbio_hi[cinfo$stock==stock])
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Btype <- as.character(cinfo$Btype[cinfo$stock==stock])
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FutureCrash <- as.character(cinfo$FutureCrash[cinfo$stock==stock])
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comment <- as.character(cinfo$comment[cinfo$stock==stock])
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# extract data on stock
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yr <- as.numeric(cdat$yr[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])
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ct <- as.numeric(cdat$ct[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that catch is given in tonnes, transforms to '000 tonnes
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if(Btype=="observed" | Btype=="CPUE" | Btype=="simulated") {
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bt <- as.numeric(cdat$TB[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that biomass is in tonnes, transforms to '000 tonnes
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} else {bt <- NA}
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nyr <- length(yr) # number of years in the time series
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cat("->---------------------------------------
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Species: NA
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Name and region: NA , NA
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Stock: HLH_M07
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Catch data used from years 1 - 50
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Prior initial relative biomass = 0.5 - 0.9
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Prior intermediate rel. biomass= 0.01 - 0.4 in year 25
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Prior final relative biomass = 0.4 - 0.8
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If current catches continue, is the stock likely to crash within 3 years? No
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Prior range for r = 0.2 - 0.8 , prior range for k = 125 - 9965
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Results from Bayesian Schaefer model using catch & biomass ( simulated )
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MSY = 91.7 , 95% CL = 83.9 - 100
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Mean catch / MSY = 0.882
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r = 0.425 , 95% CL = 0.374 - 0.483
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k = 863 , 95% CL = 783 - 951
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Results of CMSY analysis
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Altogether 2055 unique viable r-k pairs were found
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1142 r-k pairs above the initial geometric mean of r = 0.343 were analysed
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r = 0.522 , 95% CL = 0.349 - 0.782
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k = 683 , 95% CL = 438 - 1067
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MSY = 89.2 , 95% CL = 82.2 - 96.7
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Predicted biomass in last year = 0.676 2.5th perc = 0.435 97.5th perc = 0.768
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Predicted biomass in next year = 0.673 2.5th perc = 0.433 97.5th perc = 0.758
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----------------------------------------------------------
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",file=outfile.txt,append=T)
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}
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@ -56,10 +56,11 @@ public static AlgorithmConfiguration getConfig() {
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D4ScienceDistributedProcessing.maxMessagesAllowedPerJob=2;
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D4ScienceDistributedProcessing.maxMessagesAllowedPerJob=2;
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// config.setParam("StocksFile","http://goo.gl/g6YtVx");
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// config.setParam("StocksFile","http://goo.gl/g6YtVx");
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config.setParam("StocksFile","http://goo.gl/X79e9E");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short1.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short1.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short2.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short2.csv");
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//config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Longtest.csv");
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//config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Longtest.csv");
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config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_1000sptest.csv");
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// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_1000sptest.csv");
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// config.setParam("StocksFile","http://goo.gl/B09ZL0"); //50species
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// config.setParam("StocksFile","http://goo.gl/B09ZL0"); //50species
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//config.setParam("IDsFile","http://goo.gl/9rg3qK");
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//config.setParam("IDsFile","http://goo.gl/9rg3qK");
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// config.setParam("StocksFile","http://goo.gl/Mp2ZLY");
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// config.setParam("StocksFile","http://goo.gl/Mp2ZLY");
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#Generated by Maven
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#Thu Apr 16 18:26:30 CEST 2015
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version=1.0.0-SNAPSHOT
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groupId=org.gcube.dataanalysis
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artifactId=ecological-engine-smart-executor
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<?xml version="1.0" encoding="UTF-8"?>
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<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<ID></ID>
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<Type>Library</Type>
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<Profile>
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<Description>Ecological Engine Executor Library</Description>
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<Class>EcologicalEngineExecutor</Class>
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<Name>ecological-engine-smart-executor</Name>
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<Version>1.0.0</Version>
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<Packages>
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<Software>
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<Name>ecological-engine-smart-executor</Name>
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<Version>1.0.0-SNAPSHOT</Version>
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<MavenCoordinates>
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>ecological-engine-smart-executor</artifactId>
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<version>1.0.0-SNAPSHOT</version>
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</MavenCoordinates>
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<Files>
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<File>ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar</File>
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</Files>
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</Software>
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</Packages>
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</Profile>
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</Resource>
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