tests/testthat/test-sr-para-cor-steepness.R
In ichimomo/frasyr: Fisheries Research Agency (FRA) provides the method for calculating sustainable yield (SY) with R
library(frasyr)
context("check the correlation between parameters and the steepness")
# vpaとget.SRdataの結果を読み込み
load(system.file("extdata","res_vpa_pma.rda",package = "frasyr"))
load(system.file("extdata","SRdata_pma.rda",package = "frasyr"))
SRmodel.list <- expand.grid(SR.rel = c("HS","BH","RI"), AR.type = c(0, 1), out.AR=c(TRUE,FALSE), L.type = c("L1", "L2"))
res.SRfit <- list()
# fit.SR計算
for (i in 1:nrow(SRmodel.list)){
res.SRfit[[i]] <- fit.SR(SRdata = SRdata_pma,SR=SRmodel.list$SR.rel[i],method=SRmodel.list$L.type[i],AR=SRmodel.list$AR.type[i],out.AR=SRmodel.list$out.AR[i])
}
test_that("output value check",{
year <- as.character(max(res_vpa_pma$input$rec.year))
#各SR推定の設定でテスト
# テスト項目corSR
testcontents.corSR <-c("hessian","cov","cor")
# テスト項目steepness
testcontents.h <-c("SPR0","SB0","R0","h")
SPR0_by_getSPR <- get.SPR(res_vpa_pma)
# test the returens of corSR and calc_steepness for each SR based on the SRmodel.list array
i <- 3 #skip first 3 (AR=0 outAR=T)
# HS L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
# use fit.SR otion
steepness_pma_check2 <- do.call(fit.SR,
list_modify(res.SRfit[[i]]$input, bio_par=derive_biopar(res_vpa_pma,derive_year=year)))
steepness_pma_check2$steepness %>%
expect_equal(steepness_pma_check)
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
i <- i+3 #skip first 3 for L.type=L2 (AR=0 outAR=T)
# HS L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
})
ichimomo/frasyr documentation built on May 3, 2024, 1:30 a.m.
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library(frasyr)
context("check the correlation between parameters and the steepness")
# vpaとget.SRdataの結果を読み込み
load(system.file("extdata","res_vpa_pma.rda",package = "frasyr"))
load(system.file("extdata","SRdata_pma.rda",package = "frasyr"))
SRmodel.list <- expand.grid(SR.rel = c("HS","BH","RI"), AR.type = c(0, 1), out.AR=c(TRUE,FALSE), L.type = c("L1", "L2"))
res.SRfit <- list()
# fit.SR計算
for (i in 1:nrow(SRmodel.list)){
res.SRfit[[i]] <- fit.SR(SRdata = SRdata_pma,SR=SRmodel.list$SR.rel[i],method=SRmodel.list$L.type[i],AR=SRmodel.list$AR.type[i],out.AR=SRmodel.list$out.AR[i])
}
test_that("output value check",{
year <- as.character(max(res_vpa_pma$input$rec.year))
#各SR推定の設定でテスト
# テスト項目corSR
testcontents.corSR <-c("hessian","cov","cor")
# テスト項目steepness
testcontents.h <-c("SPR0","SB0","R0","h")
SPR0_by_getSPR <- get.SPR(res_vpa_pma)
# test the returens of corSR and calc_steepness for each SR based on the SRmodel.list array
i <- 3 #skip first 3 (AR=0 outAR=T)
# HS L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
# use fit.SR otion
steepness_pma_check2 <- do.call(fit.SR,
list_modify(res.SRfit[[i]]$input, bio_par=derive_biopar(res_vpa_pma,derive_year=year)))
steepness_pma_check2$steepness %>%
expect_equal(steepness_pma_check)
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L1 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
i <- i+3 #skip first 3 for L.type=L2 (AR=0 outAR=T)
# HS L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR1 outAR True ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR0 ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# HS L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# BH L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
# RI L2 AR1 outAR False ----
i<-i+1
#再生産関係のパラメータ間相関
corSR_pma_check <- corSR(res.SRfit[[i]])
#スティープネス
steepness_pma_check <- calc_steepness(SR=res.SRfit[[i]]$input$SR,rec_pars=res.SRfit[[i]]$pars,M=res_vpa_pma$input$dat$M[,year],waa=res_vpa_pma$input$dat$waa[,year],maa=res_vpa_pma$input$dat$maa[,year])
#上記結果の読み込み(corSR)
corSR_file <- sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",corSR_file,package = "frasyr"))
#変数名変更
corSR_pma <- eval(parse(text=paste(sprintf("res_corSR_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合corSR
for(j in 1:length(testcontents.corSR)){
expect_equal(corSR_pma$testcontents.corSR[j],corSR_pma_check$testcontents.corSR[j])
}
#上記結果の読み込み(steepness)
steepness_file <- sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d.rda",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i])
load(system.file("extdata",steepness_file,package = "frasyr"))
#変数名変更
steepness_pma <- eval(parse(text=paste(sprintf("res_steepness_pma_%s_%s_AR%d_outAR%d",SRmodel.list$SR.rel[i],SRmodel.list$L.type[i], SRmodel.list$AR.type[i],SRmodel.list$out.AR[i]))))
#読み込んだ結果と照合h
for(j in 1:length(testcontents.h)){
expect_equal(steepness_pma$testcontents[j],steepness_pma_check$testcontents[j])
}
# get.SPRからのSPR0と照合h
expect_equal(steepness_pma_check$SPR0, SPR0_by_getSPR$ysdata[1,4])
})
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