diff --git a/PARALLEL_PROCESSING/CMSY_22_noplot.R.test b/PARALLEL_PROCESSING/CMSY_22_noplot.R.test deleted file mode 100644 index b77ea9e..0000000 --- a/PARALLEL_PROCESSING/CMSY_22_noplot.R.test +++ /dev/null @@ -1,119 +0,0 @@ -##-------------------------------------------------------- -## CMSY analysis with estimation of total biomass, including Bayesian Schaefer -## written by Rainer Froese with support from Gianpaolo Coro in 2013-2014 -## This version adjusts biomass to average biomass over the year -## It also contains the FutureCrash option to improve prediction of final biomass -## Version 21 adds the purple point to indicate the 25th percentile of final biomass -## Version 22 accepts that no biomass or CPUE area available -##-------------------------------------------------------- -library(R2jags) # Interface with JAGS -library(coda) - -#----------------------------------------- -# Some general settings -#----------------------------------------- -# set.seed(999) # use for comparing results between runs -rm(list=ls(all=TRUE)) # clear previous variables etc -options(digits=3) # displays all numbers with three significant digits as default -graphics.off() # close graphics windows from previous sessions - -#----------------------------------------- -# General settings for the analysis -#----------------------------------------- -sigR <- 0.02 # overall process error; 0.05 works reasonable for simulations, 0.02 for real data; 0 if deterministic model -n <- 10000 # initial number of r-k pairs -batch.mode <- T # set to TRUE to suppress graphs -write.output <- T # set to true if table of output is wanted -FutureCrash <- "No" - -#----------------------------------------- -# Start output to screen -#----------------------------------------- -cat("-------------------------------------------\n") -cat("Catch-MSY Analysis,", date(),"\n") -cat("-------------------------------------------\n") - -#------------------------------------------ -# Read data and assign to vectors -#------------------------------------------ -# filename_1 <- "AllStocks_Catch4.csv" -# filename_2 <- "AllStocks_ID4.csv" -# filename_1 <- "SimCatch.csv" -# filename_2 <- "SimSpec.csv" -# filename_2 <- "SimSpecWrongS.csv" -# filename_2 <- "SimSpecWrongI.csv" -# filename_2 <- "SimSpecWrongF.csv" -# filename_2 <- "SimSpecWrongH.csv" -# filename_2 <- "SimSpecWrongL.csv" -# filename_1 <- "FishDataLim.csv" -# filename_2 <- "FishDataLimSpec.csv" -filename_1 <- "WKLIFE4Stocks.csv" -filename_2 <- "WKLIFE4ID.csv" - -outfile<-"outfile" -outfile.txt <- "outputfile.txt" - -cdat <- read.csv(filename_1, header=T, dec=".", stringsAsFactors = FALSE) -cinfo <- read.csv(filename_2, header=T, dec=".", stringsAsFactors = FALSE) -cat("Files", filename_1, ",", filename_2, "read successfully","\n") - -# Stocks with total biomass data and catch data from StartYear to EndYear -# stocks <- sort(as.character(cinfo$stock)) # All stocks -stocks<-"HLH_M07" - -# select one stock after the other -for(stock in stocks) { - # assign data from cinfo to vectors - res <- as.character(cinfo$Resilience[cinfo$stock==stock]) - StartYear <- as.numeric(cinfo$StartYear[cinfo$stock==stock]) - EndYear <- as.numeric(cinfo$EndYear[cinfo$stock==stock]) - r_low <- as.numeric(cinfo$r_low[cinfo$stock==stock]) - r_hi <- as.numeric(cinfo$r_hi[cinfo$stock==stock]) - stb_low <- as.numeric(cinfo$stb_low[cinfo$stock==stock]) - stb_hi <- as.numeric(cinfo$stb_hi[cinfo$stock==stock]) - intyr <- as.numeric(cinfo$intyr[cinfo$stock==stock]) - intbio_low <- as.numeric(cinfo$intbio_low[cinfo$stock==stock]) - intbio_hi <- as.numeric(cinfo$intbio_hi[cinfo$stock==stock]) - endbio_low <- as.numeric(cinfo$endbio_low[cinfo$stock==stock]) - endbio_hi <- as.numeric(cinfo$endbio_hi[cinfo$stock==stock]) - Btype <- as.character(cinfo$Btype[cinfo$stock==stock]) - FutureCrash <- as.character(cinfo$FutureCrash[cinfo$stock==stock]) - comment <- as.character(cinfo$comment[cinfo$stock==stock]) - - - # extract data on stock - yr <- as.numeric(cdat$yr[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear]) - ct <- as.numeric(cdat$ct[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that catch is given in tonnes, transforms to '000 tonnes - if(Btype=="observed" | Btype=="CPUE" | Btype=="simulated") { - bt <- as.numeric(cdat$TB[cdat$stock==stock & cdat$yr >= StartYear & cdat$yr <= EndYear])/1000 ## assumes that biomass is in tonnes, transforms to '000 tonnes - } else {bt <- NA} - nyr <- length(yr) # number of years in the time series - - cat("->--------------------------------------- -Species: NA -Name and region: NA , NA -Stock: HLH_M07 -Catch data used from years 1 - 50 -Prior initial relative biomass = 0.5 - 0.9 -Prior intermediate rel. biomass= 0.01 - 0.4 in year 25 -Prior final relative biomass = 0.4 - 0.8 -If current catches continue, is the stock likely to crash within 3 years? No -Prior range for r = 0.2 - 0.8 , prior range for k = 125 - 9965 -Results from Bayesian Schaefer model using catch & biomass ( simulated ) -MSY = 91.7 , 95% CL = 83.9 - 100 -Mean catch / MSY = 0.882 -r = 0.425 , 95% CL = 0.374 - 0.483 -k = 863 , 95% CL = 783 - 951 -Results of CMSY analysis -Altogether 2055 unique viable r-k pairs were found -1142 r-k pairs above the initial geometric mean of r = 0.343 were analysed -r = 0.522 , 95% CL = 0.349 - 0.782 -k = 683 , 95% CL = 438 - 1067 -MSY = 89.2 , 95% CL = 82.2 - 96.7 -Predicted biomass in last year = 0.676 2.5th perc = 0.435 97.5th perc = 0.768 -Predicted biomass in next year = 0.673 2.5th perc = 0.433 97.5th perc = 0.758 ----------------------------------------------------------- -",file=outfile.txt,append=T) - -} - \ No newline at end of file diff --git a/neuralnetwork_Fis-30189_staticsuitable_neuralname b/neuralnetwork_Fis-30189_staticsuitable_neuralname deleted file mode 100644 index 3456fee..0000000 Binary files a/neuralnetwork_Fis-30189_staticsuitable_neuralname and /dev/null differ diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java b/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java index 8c099bf..46e4c6d 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java +++ b/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java @@ -56,10 +56,11 @@ public static AlgorithmConfiguration getConfig() { D4ScienceDistributedProcessing.maxMessagesAllowedPerJob=2; // config.setParam("StocksFile","http://goo.gl/g6YtVx"); + config.setParam("StocksFile","http://goo.gl/X79e9E"); // config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short1.csv"); // config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short2.csv"); //config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Longtest.csv"); - config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_1000sptest.csv"); +// config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_1000sptest.csv"); // config.setParam("StocksFile","http://goo.gl/B09ZL0"); //50species //config.setParam("IDsFile","http://goo.gl/9rg3qK"); // config.setParam("StocksFile","http://goo.gl/Mp2ZLY"); diff --git a/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar b/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar new file mode 100644 index 0000000..a54b5be Binary files /dev/null and b/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar differ diff --git a/target/maven-archiver/pom.properties b/target/maven-archiver/pom.properties new file mode 100644 index 0000000..4d03d39 --- /dev/null +++ b/target/maven-archiver/pom.properties @@ -0,0 +1,5 @@ +#Generated by Maven +#Thu Apr 16 18:26:30 CEST 2015 +version=1.0.0-SNAPSHOT +groupId=org.gcube.dataanalysis +artifactId=ecological-engine-smart-executor diff --git a/target/profile.xml b/target/profile.xml new file mode 100644 index 0000000..495f836 --- /dev/null +++ b/target/profile.xml @@ -0,0 +1,25 @@ + + + + Library + + Ecological Engine Executor Library + EcologicalEngineExecutor + ecological-engine-smart-executor + 1.0.0 + + + ecological-engine-smart-executor + 1.0.0-SNAPSHOT + + org.gcube.dataanalysis + ecological-engine-smart-executor + 1.0.0-SNAPSHOT + + + ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar + + + + + \ No newline at end of file