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Maturation to cdclimate #22

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26283da
v3.09
Mar 11, 2026
66744bd
v3.09
Mar 11, 2026
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22 changes: 22 additions & 0 deletions doc/CDmetaPOPhistory.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,25 @@
Changes v3.09.2026.03.02.2026 ell
0) Added PopVars maturation parameters to cdclimate.
a) add _pass call to mat pars
defaultMature_pass = batchVars['mature_default'][ibatch]
mat_slope_pass = batchVars['mature_eqn_slope'][ibatch]
mat_int_pass = batchVars['mature_eqn_int'][ibatch]
b) Read in defaultMature,mat_slope,mat_int, to Preprocess, moved the tupVal in mainloop calls for sexsplit mat values. Here, just need the first values for _set, _slope and _int for each sex chromo option for initialization. Code updated in PreProcess
FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set=[val for val in process_disp(defaultMature, 0, sexchromo, defaultMature)]

# Logistic equation for maturation as a function of size - slope
FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope = [val for val in process_disp(mat_slope, 0, sexchromo, mat_slope)]

# Logistic equation for maturation as a function of size - intercept
FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int= [val for val in process_disp(mat_int, 0, sexchromo, mat_int)]
c) Next read in the _pass to cdclimate and extract the _set, _slope, and _int pars for each sexchromo option here.
defaultMature_pass,mat_slope_pass,mat_int_pass read into cdclimate, calls added to CDClimate:
FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set=[val for val in process_disp(defaultMature_pass, icdtime, sexchromo, cdclimgentime)]
FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope = [val for val in process_disp(mat_slope_pass, icdtime, sexchromo, cdclimgentime)]
FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int= [val for val in process_disp(mat_int_pass, icdtime, sexchromo, cdclimgentime)]
d) These variables read out of cdclimate and into main loop FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set,FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope,FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int


<<<<<<< Updated upstream
=======
Changes v3.08.2025.07.22 ell / A&M
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4 changes: 2 additions & 2 deletions example_files/popvars/PopVars.csv
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
xyfilename,mate_cdmat,matemoveno,matemoveparA,matemoveparB,matemoveparC,matemovethresh,migrateout_cdmat,migratemoveOutno,migratemoveOutparA,migratemoveOutparB,migratemoveOutparC,migratemoveOutthresh,migrateback_cdmat,migratemoveBackno,migratemoveBackparA,migratemoveBackparB,migratemoveBackparC,migratemoveBackthresh,stray_cdmat,StrayBackno,StrayBackparA,StrayBackparB,StrayBackparC,StrayBackthresh,disperseLocal_cdmat,disperseLocalno,disperseLocalparA,disperseLocalparB,disperseLocalparC,disperseLocalthresh,HomeAttempt,sex_chromo,sexans,selfans,Freplace,Mreplace,AssortativeMate_Model,AssortativeMate_Factor,mature_default,mature_eqn_slope,mature_eqn_int,offno,offans_InheritClassVars,equalClutchSize,Egg_Freq_Mean,Egg_Freq_StDev,Egg_Mean_ans,Egg_Mean_par1,Egg_Mean_par2,Egg_Mortality,Egg_Mortality_StDev,Egg_FemaleProb,startGenes,loci,alleles,muterate,mutationtype,mtdna,cdevolveans,startSelection,implementSelection,betaFile_selection,plasticgeneans,plasticSignalResponse,plasticBehavioralResponse,startPlasticgene,implementPlasticgene,cdinfect,transmissionprob,growth_option,growth_Loo,growth_R0,growth_temp_max,growth_temp_CV,growth_temp_t0,popmodel,popmodel_par1,correlation_matrix,subpopmort_file,egg_delay,egg_add,implement_disease
patchvars/PatchVars.csv,cdmats/Patch7_CdmatrixS1.csv,6,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,1,0.01,0.01,0,max,cdmats/Patch7_Probmatrix_Dispersal.csv,9,0.01,0.01,0,max,mortality,2,Y,N,Y,Y,1,1,age6,0.0539,-6.313,2,random,N,1,1,linear,-445,3.78,N,0,0.5,0,2,2,0.5|0.25|0,random,N,N,0,Out:Back,N,N,0,0,0,Back:0,N,0,temperature,400,0.47,10.5,0.33,-0.075,packing,-0.6821,N,N,0,mating,N
patchvars/PatchVars_anadromy.csv,cdmats/Patch7_CdmatrixS1.csv,6,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,1,0.01,0.01,0,max,cdmats/Patch7_Probmatrix_Dispersal.csv,9,0.01,0.01,0,max,mortality,2,Y,N,Y,Y,1,1,age3,0.0539,-6.313,2,random,N,1,1,linear,-445,3.78,0.62,0,0.5,0,2,2,0.5|0.25|0,random,N,N,0,Out:Back,N,N,0,0,0,Back:0,N,0,temperature,400,0.47,10.5,0.33,-0.075,anadromy,-0.6821,N,N,0,mating,N
patchvars/PatchVars.csv,cdmats/Patch7_CdmatrixS1.csv,6,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,1,0.01,0.01,0,max,cdmats/Patch7_Probmatrix_Dispersal.csv,9,0.01,0.01,0,max,mortality,2,Y,N,Y,Y,1,1,age3|age6|age3,0.13~0.06|0.13~0.06|0.13~0.06,-20.28~-8.09|-20.28~-8.09|-20.28~-8.09,2,random,N,1,1,linear,-445,3.78,N,0,0.5,0,2,2,0,random,N,N,0,Out:Back,N,N,0,0,0,Back:0,N,0,temperature,400,0.47,10.5,0.33,-0.075,packing,-0.6821,N,N,0,mating,N
patchvars/PatchVars_anadromy.csv,cdmats/Patch7_CdmatrixS1.csv,6,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,4,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,1,0.01,0.01,0,max,cdmats/Patch7_Probmatrix_Dispersal.csv,9,0.01,0.01,0,max,mortality,2,Y,N,Y,Y,1,1,age3,0.0539,-6.313,2,random,N,1,1,linear,-445,3.78,0.62,0,0.5,0,2,2,0,random,N,N,0,Out:Back,N,N,0,0,0,Back:0,N,0,temperature,400,0.47,10.5,0.33,-0.075,anadromy,-0.6821,N,N,0,mating,N
patchvars/PatchVars.csv,cdmats/Patch7_CdmatrixS1.csv,4,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,9,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,9,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,4,0.01,0.01,0,max,cdmats/Patch7_CdmatrixS1.csv,2,0.01,0.01,0,max,mortality,2,Y,N,Y,Y,1,1,size300,0.13~0.06,-20.28~-8.09,2,random,N,1,0,exp,126.07,0.0061,0.62,0.18,0.5,0,2,2,0,random,N,N,0,Eggs,N,N,0,0,0,Back,N,1.5,temperature,250,0.57,12,0.25,-0.196,logistic_back,-0.6821,N,N,0,mating,N
patchvars/PatchVars.csv,cdmats/Patch7_CdmatrixS1.csv,6,1.346,202.4846,6,6000,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,9,0,0,0,max~max,cdmats/Patch7_Probmatrix_onewayBarriersXRiverineS1.csv,9,0,0,0,max~max,cdmats/Patch7_CdmatrixS1.csv,2,0.01,0.01,0,max,cdmats/Patch7_CdmatrixS1.csv,2,0.01,0.01,0,max,mortality,2,H,0.5,Y,Y,1,1,N,0.13~0.06,-20.28~-8.09,2,random,N,0.5,0.1,exp,126.07,0.0061,0,0,0.5,0,2,2,0,random,N,N,0,Back,N,N,0,0,0,Back,N,1.5,temperature,250,0.57,12,0.25,-0.196,N,-0.6821,N,N,0,mating,N
26 changes: 20 additions & 6 deletions src/CDmetaPOP_PreProcess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1099,12 +1099,12 @@ def ReadXY(xyfilename):
#End::ReadXY()

# ---------------------------------------------------------------------------------------------------
def DoCDClimate(datadir,icdtime,cdclimgentime,matecdmatfile,dispOutcdmatfile,dispBackcdmatfile,straycdmatfile,matemoveno_pass,dispmoveOutno,dispmoveBackno,StrBackno,matemovethresh,dispmoveOutthresh,dispmoveBackthresh,StrBackthresh,matemoveparA,matemoveparB,matemoveparC,dispmoveOutparA,dispmoveOutparB,dispmoveOutparC,dispmoveBackparA,dispmoveBackparB,dispmoveBackparC,StrBackparA,StrBackparB,StrBackparC,MgOut_patch_prob,Str_patch_prob,K,outsizevals,backsizevals,outgrowdays,backgrowdays,fitvals,popmort_back,popmort_out,eggmort,Kstd,popmort_back_sd,popmort_out_sd,eggmort_sd,outsizevals_sd,backsizevals_sd,outgrowdays_sd,backgrowdays_sd,pop_capture_back,pop_capture_out,cdevolveans,N0_pass,allefreqfiles_pass,classvarsfiles_pass,assortmateModel_pass,assortmateC_pass,subpopmort_pass,PopTag,dispLocalcdmatfile,dispLocalno,dispLocalparA,dispLocalparB,dispLocalparC,dispLocalthresh,comp_coef_pass,betaFile_selection,xvars_betas_pass,outhabvals_pass,backhabvals_pass,plastic_signalresp_pass,plastic_behaviorresp_pass,plasticans,muterate_pass,sexchromo,MgBack_patch_prob,Disperse_patch_prob,alldiseaseVars_files,implementdisease,pathogen_load,disease_fitvals_pass):
def DoCDClimate(datadir,icdtime,cdclimgentime,matecdmatfile,dispOutcdmatfile,dispBackcdmatfile,straycdmatfile,matemoveno_pass,dispmoveOutno,dispmoveBackno,StrBackno,matemovethresh,dispmoveOutthresh,dispmoveBackthresh,StrBackthresh,matemoveparA,matemoveparB,matemoveparC,dispmoveOutparA,dispmoveOutparB,dispmoveOutparC,dispmoveBackparA,dispmoveBackparB,dispmoveBackparC,StrBackparA,StrBackparB,StrBackparC,MgOut_patch_prob,Str_patch_prob,K,outsizevals,backsizevals,outgrowdays,backgrowdays,fitvals,popmort_back,popmort_out,eggmort,Kstd,popmort_back_sd,popmort_out_sd,eggmort_sd,outsizevals_sd,backsizevals_sd,outgrowdays_sd,backgrowdays_sd,pop_capture_back,pop_capture_out,cdevolveans,N0_pass,allefreqfiles_pass,classvarsfiles_pass,assortmateModel_pass,assortmateC_pass,subpopmort_pass,PopTag,dispLocalcdmatfile,dispLocalno,dispLocalparA,dispLocalparB,dispLocalparC,dispLocalthresh,comp_coef_pass,betaFile_selection,xvars_betas_pass,outhabvals_pass,backhabvals_pass,plastic_signalresp_pass,plastic_behaviorresp_pass,plasticans,muterate_pass,sexchromo,MgBack_patch_prob,Disperse_patch_prob,alldiseaseVars_files,implementdisease,pathogen_load,disease_fitvals_pass,defaultMature_pass,mat_slope_pass,mat_int_pass):
'''
DoCDCliamte()
Reads in cost distance matrices and converts to probabilities.
'''

# -------------------------------
# Extract cdclimate values here
# -------------------------------
Expand Down Expand Up @@ -1351,6 +1351,11 @@ def DoCDClimate(datadir,icdtime,cdclimgentime,matecdmatfile,dispOutcdmatfile,dis
# Add Beta0
tempbetas_selection.append(0.0 if not betavals[0][0] else float(betavals[0][0]))

# Maturation values - split by sexchromo possible - _set, _slope, _int
FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set=[val for val in process_disp(defaultMature_pass, icdtime, sexchromo, cdclimgentime)]
FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope = [val for val in process_disp(mat_slope_pass, icdtime, sexchromo, cdclimgentime)]
FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int= [val for val in process_disp(mat_int_pass, icdtime, sexchromo, cdclimgentime)]

# ----------------------
# Patch based parameters
# ----------------------
Expand Down Expand Up @@ -1489,7 +1494,7 @@ def DoCDClimate(datadir,icdtime,cdclimgentime,matecdmatfile,dispOutcdmatfile,dis
FXXdispmoveBackno,MXYdispmoveBackno,MYYdispmoveBackno,FYYdispmoveBackno,\
FXXStrno,MXYStrno,MYYStrno,FYYStrno,\
FXXdispLocalno,MXYdispLocalno,MYYdispLocalno,FYYdispLocalno,\
tempMgOut_patch_prob,tempStr_patch_prob,tempoutsize,tempbacksize,tempoutgrow,tempbackgrow,tempfitvals,tempK,temppopmort_back,temppopmort_out,tempeggmort,tempKstd,temppopmort_back_sd,temppopmort_out_sd,tempeggmort_sd,tempoutsize_sd,tempbacksize_sd,tempoutgrow_sd,tempbackgrow_sd,temppopCapBack,temppopCapOut,tempN0,tempAllelefile,tempClassVarsfile,assortmateModel, assortmateC,subpopmort_mat,tempcompcoef,tempbetas_selection,tempxvars_betas,tempouthabvals,tempbackhabvals,plastic_signalresp,plastic_behaviorresp,muterate,age_percmort_out,age_percmort_out_sd,age_percmort_back,age_percmort_back_sd,size_percmort_out,size_percmort_out_sd,size_percmort_back,size_percmort_back_sd,age_MgOUT,age_MgBACK,age_S,age_DispProb,age_mature,age_mu,age_sigma,f_leslie,f_leslie_std,age_cap_out,age_cap_back,tempMgBack_patch_prob,tempDisperse_patch_prob,tupDisease_Vars
tempMgOut_patch_prob,tempStr_patch_prob,tempoutsize,tempbacksize,tempoutgrow,tempbackgrow,tempfitvals,tempK,temppopmort_back,temppopmort_out,tempeggmort,tempKstd,temppopmort_back_sd,temppopmort_out_sd,tempeggmort_sd,tempoutsize_sd,tempbacksize_sd,tempoutgrow_sd,tempbackgrow_sd,temppopCapBack,temppopCapOut,tempN0,tempAllelefile,tempClassVarsfile,assortmateModel, assortmateC,subpopmort_mat,tempcompcoef,tempbetas_selection,tempxvars_betas,tempouthabvals,tempbackhabvals,plastic_signalresp,plastic_behaviorresp,muterate,age_percmort_out,age_percmort_out_sd,age_percmort_back,age_percmort_back_sd,size_percmort_out,size_percmort_out_sd,size_percmort_back,size_percmort_back_sd,age_MgOUT,age_MgBACK,age_S,age_DispProb,age_mature,age_mu,age_sigma,f_leslie,f_leslie_std,age_cap_out,age_cap_back,tempMgBack_patch_prob,tempDisperse_patch_prob,tupDisease_Vars,FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set,FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope,FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int

return tupClimate
# End::DoCDClimate()
Expand Down Expand Up @@ -1800,7 +1805,7 @@ def DoStochasticUpdate(K_mu,K_std,popmort_back_mu,popmort_back_sd,popmort_out_mu
#End::DoStochasticUpdate()

# ---------------------------------------------------------------------------------------------------
def DoPreProcess(outdir,datadir,irun,ithmcrun,xyfilename,loci,alleles,gen,logfHndl,cdevolveans,subpopemigration,subpopimmigration,sizeans,burningen_cdevolve,cor_mat_ans,inheritans_classfiles,sexans,spcNO,ibatch,betaFile_selection,FXXmat_set,FXXmat_int,FXXmat_slope,MXYmat_set,MXYmat_int,MXYmat_slope,MYYmat_set,MYYmat_int,MYYmat_slope,FYYmat_set,FYYmat_int,FYYmat_slope,sexchromo,eggFreq_mu,eggFreq_sd,implementdisease):
def DoPreProcess(outdir,datadir,irun,ithmcrun,xyfilename,loci,alleles,gen,logfHndl,cdevolveans,subpopemigration,subpopimmigration,sizeans,burningen_cdevolve,cor_mat_ans,inheritans_classfiles,sexans,spcNO,ibatch,betaFile_selection,defaultMature,mat_slope,mat_int,sexchromo,eggFreq_mu,eggFreq_sd,implementdisease):

'''
DoPreProcess()
Expand Down Expand Up @@ -1915,9 +1920,18 @@ def DoPreProcess(outdir,datadir,irun,ithmcrun,xyfilename,loci,alleles,gen,logfHn
cor_mat = np.asarray(np.asarray(cor_mat)[1:,1:],dtype='float')

# -----------------------------------------------------------------------------
# Extract variables needed for initialization that vary with cdclimategen (bar)
# Extract variables needed for initialization that vary with cdclimategen (bar)
# -----------------------------------------------------------------------------
#pdb.set_trace()

# Check Deterministic mature set value either age or size - split by bar and sex options, icdtime = 0 and length of cdclimate just needs to match the split par length
FXXmat_set, MXYmat_set, MYYmat_set, FYYmat_set=[val for val in process_disp(defaultMature, 0, sexchromo, defaultMature)]

# Logistic equation for maturation as a function of size - slope
FXXmat_slope,MXYmat_slope,MYYmat_slope,FYYmat_slope = [val for val in process_disp(mat_slope, 0, sexchromo, mat_slope)]

# Logistic equation for maturation as a function of size - intercept
FXXmat_int,MXYmat_int,MYYmat_int,FYYmat_int= [val for val in process_disp(mat_int, 0, sexchromo, mat_int)]

K, Kstd, pop_capture_back, N0, allefreqfiles, classvarsfiles, tempdiseaseVarsfile = [],[],[],[],[],[],[]
for isub in range(len(K_temp)):
mu = int(K_temp[isub].split('|')[0])
Expand Down
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