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afsc-assessments · Oct 25, 2024 · e156b26 · e156b26
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diff --git a/2023_ASSESSMENT/EBS_Pacific_cod2023_10_25.docx b/2023_ASSESSMENT/EBS_Pacific_cod2023_10_25.docx
diff --git a/2023_ASSESSMENT/EBS_Pacific_cod2023_10_25_LB_JT_JN.docx b/2023_ASSESSMENT/EBS_Pacific_cod2023_10_25_LB_JT_JN.docx
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/PCod all ages 2000 to 2023 Barbeaux AGE3.csv b/2024_ASSESSMENT/AGING_ERROR_BIAS/PCod all ages 2000 to 2023 Barbeaux AGE3.csv
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/Results3_Both10.zip b/2024_ASSESSMENT/AGING_ERROR_BIAS/Results3_Both10.zip
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/ResultsBoth10_Linear2.zip b/2024_ASSESSMENT/AGING_ERROR_BIAS/ResultsBoth10_Linear2.zip
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/ResultsREREADS.zip b/2024_ASSESSMENT/AGING_ERROR_BIAS/ResultsREREADS.zip
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/Running_agingerror.r b/2024_ASSESSMENT/AGING_ERROR_BIAS/Running_agingerror.r
@@ -0,0 +1,114 @@
+
+
+## splined aging error
+data<-AgeingError:::CreateData("dataBoth10.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data_echo.out")
+PCOD_spline <- AgeingError:::CreateSpecs("spline5.spc", DataSpecs = data,verbose = TRUE)
+
+PCOD_spline <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data,
+  ModelSpecsInp = PCOD_spline,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results_spline",
+  verbose = TRUE
+)
+
+
+PCOD_spline_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results_spline", CalcEff = TRUE, verbose = FALSE)
+
+## linear aging error
+data<-AgeingError:::CreateData("dataBoth10.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data_echo.out")
+PCOD_linear <- AgeingError:::CreateSpecs("linear.spc", DataSpecs = data,verbose = TRUE)
+
+PCOD_linear <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data,
+  ModelSpecsInp = PCOD_linear,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results_linear",
+  verbose = TRUE
+)
+
+
+PCOD_linear_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results_linear", CalcEff = TRUE, verbose = FALSE)
+
+
+## splined aging error w/bias
+data<-AgeingError:::CreateData("dataREREADS.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data_echo.out")
+PCOD_spline_bias <- AgeingError:::CreateSpecs("spline5_bias.spc", DataSpecs = data,verbose = TRUE)
+
+PCOD_spline <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data,
+  ModelSpecsInp = PCOD_spline_bias,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results_spline_bias",
+  verbose = TRUE
+)
+
+
+PCOD_spline_bias_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results_spline_bias", CalcEff = TRUE, verbose = FALSE)
+
+
+
+
+
+
+## splined aging error w/bias
+data<-AgeingError:::CreateData("dataREREADS.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data_echo.out")
+PCOD_linear_bias <- AgeingError:::CreateSpecs("linear_bias.spc", DataSpecs = data,verbose = TRUE)
+
+PCOD_spline <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data,
+  ModelSpecsInp = PCOD_linear_bias,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results_linear_bias",
+  verbose = TRUE
+)
+
+
+PCOD_linear_bias_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results_linear_bias", CalcEff = TRUE, verbose = FALSE)
+
+
+
+
+
+
+
+
+
+
+
+
+age_dat<-data.table(read.csv('paired_age_readings.csv'))
+x=ageing_comparison(xvec=age_dat$read_age, yvec=age_dat$test_age, scale.pts = 0.75,
+                              col.pts = grDevices::heat.colors(100, alpha = .4),
+                              col.hist = grDevices::rgb(0, 0, .5, alpha = .7),
+                              counts = TRUE, maxage = 14,
+                              hist = F, hist.frac = .1,
+                              xlab = "Age reader 1",
+                              ylab = "Age reader 2",
+                              title = NULL,
+                              png = FALSE,
+                              filename = "ageing_comparison.png",
+                              SaveFile = NULL,
+                              verbose = TRUE)
+
+
+x=ageing_comparison(xvec=f3$Second_Age, yvec=f3$Final_Age, scale.pts = 0.75,
+                              col.pts = grDevices::heat.colors(100, alpha = .4),
+                              col.hist = grDevices::rgb(0, 0, .5, alpha = .7),
+                              counts = TRUE, maxage = 14,
+                              hist = F, hist.frac = .1,
+                              xlab = "2018 Read",
+                              ylab = "2004 Read",
+                              title = NULL,
+                              png = FALSE,
+                              filename = "ageing_comparison.png",
+                              SaveFile = NULL,
+                              verbose = TRUE)
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/Stark_rereads.csv b/2024_ASSESSMENT/AGING_ERROR_BIAS/Stark_rereads.csv
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/pcod_age_testing2002-2024.xlsx b/2024_ASSESSMENT/AGING_ERROR_BIAS/pcod_age_testing2002-2024.xlsx
diff --git a/2024_ASSESSMENT/AGING_ERROR_BIAS/processing.r b/2024_ASSESSMENT/AGING_ERROR_BIAS/processing.r
@@ -0,0 +1,97 @@
+
+
+data2<-AgeingError:::CreateData("dataBSAll.dat", NDataSet = 1, verbose = TRUE, EchoFile = "dataAll_echo.out")
+
+PCOD2_spc <- AgeingError:::CreateSpecs("control3.spc", DataSpecs = data2,verbose = TRUE)
+
+
+PCOD2_mod <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data2,
+  ModelSpecsInp = PCOD2_spc,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "ResultsBS10_Spline",
+  verbose = TRUE
+)
+
+
+
+PCOD2_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "ResultsBS10_Spline", CalcEff = TRUE, verbose = FALSE)
+
+
+
+
+
+
+
+
+
+
+
+
+data1<-AgeingError:::CreateData("dataBoth10.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data1_echo.out")
+
+PCOD1_spc <- AgeingError:::CreateSpecs("control3.spc", DataSpecs = data1,verbose = TRUE)
+
+
+PCOD1_mod <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data1,
+  ModelSpecsInp = PCOD1_spc,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "ResultsBoth_Linear",
+  verbose = TRUE
+)
+
+
+
+PCOD1_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "ResultsBoth_Linear", CalcEff = TRUE, verbose = FALSE)
+
+
+## 2000-2007 data aging error
+
+
+data2000<-AgeingError:::CreateData("data2000.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data2000_echo.out")
+
+PCOD2000_spc <- AgeingError:::CreateSpecs("control2.spc", DataSpecs = data2000,verbose = TRUE)
+
+
+PCOD2000_mod <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data2000,
+  ModelSpecsInp = PCOD2000_spc,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results2000",
+  verbose = TRUE
+)
+
+
+PCOD2000_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results2000", CalcEff = TRUE, verbose = FALSE)
+
+
+
+## 2007-2023 data aging error
+
+
+data2007<-AgeingError:::CreateData("data2007.dat", NDataSet = 1, verbose = TRUE, EchoFile = "data2007_echo.out")
+
+PCOD2007_spc <- AgeingError:::CreateSpecs("control2.spc", DataSpecs = data2007,verbose = TRUE)
+
+
+PCOD2007_mod <- AgeingError::DoApplyAgeError(
+  Species = "Pcod",
+  DataSpecs = data2007,
+  ModelSpecsInp = PCOD2007_spc,
+  AprobWght = 1e-06,
+  SlopeWght = 0.01,
+  SaveDir = "Results2007",
+  verbose = TRUE
+)
+
+
+PCOD2007_out <- AgeingError:::ProcessResults(Species = "Pcod", SaveDir = "Results2007", CalcEff = TRUE, verbose = FALSE)
+
+