import sys
sys.path.append('..\pyfunctions')
from numpy.random import seed
seed(756)
sys.path.append('..\\')
from GetAgeFreq import GetAgeFreq
from numpy import log
from scipy.stats import linregress
csvfile = '..\\TreeNobXdate.csv'
col = 0 #Use first column from file
SurveyYear = 2005
MaxYear = 1980
MinYear = 1875
data = GetAgeFreq(csvfile,
col=col,
SurveyYear=SurveyYear,
MaxYear=MaxYear,
MinYear=MinYear)
nyear = len(data)
fudge = [.0001, .001, .01, .1, 1]
year = [t for t in range(nyear)]
for t in fudge:
lFA = [log(t + s) for s in data]
print(t, linregress(year, lFA)[0], linregress(year, lFA)[-1])
'''
20180513 Create Model and generate MCMC
'''
import sys
sys.path.append('../')
from GetAgeFreq import GetAgeFreq
from ConstRecruitConstM import ConstRecruitConstM
from ExecuteModel import ExecuteModel
#Get the YearBornFrequency as a list
col=0
SurveyYear=2005
MaxYear=1980
MinYear=1875
csvfile='../TreeNobXdate.csv'
yearbornfrequency=GetAgeFreq(csvfile,col=col,SurveyYear=SurveyYear,MaxYear=MaxYear,MinYear=MinYear)
#Create the model
Model=ConstRecruitConstM(yearbornfrequency,MinYear=MinYear)
#Generate the MCMC
ExecuteModel(Model,Niter=1100000,burn=100000,thin=100,basename='MCMC',db='hdf5',verbose=2,maxSimplex=0,maxPowell=0,rseed=20180513)
#The values of yearborn
self.YearBorn = [MinYear + i for i in range(self.nyear)]
self.MidYear = MinYear + .5 * self.nyear
#Inherited from Mortality-class
#Generate array of ProbSurv-nodes to represent probability of survival until the survey for each of year-class
self.Mortality()
#Inherited from Recruitment-class
#Generate array of LogRecruit-nodes to represent log of recruitment for each year-class
self.Recruitment()
#Inherited from SurveySampling-class
#Generate array of LogProb-nodes to represent the log of the probability of appearing in the sample for each year-class
self.CalcProbYearClass()
#Inherited from SurveySampling-class
#Assess data against the LogProb-nodes
self.SampleAnimals()
#Test the function
if __name__ == "__main__":
from GetAgeFreq import GetAgeFreq
csvfile = 'TreeNobXdate.csv'
yearbornfrequency = GetAgeFreq(csvfile,
col=0,
SurveyYear=2005,
MaxYear=1980,
MinYear=1875)
test = LogNormRecruitConstM(yearbornfrequency)