convergeIPM: Iterates until obtaining the number of bins required so that...

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

Increases bin number by a specified binIncrease until the difference in the chosen measure falls below a tolerance level

Usage

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convergeIPM(growObj, survObj, fecObj, nBigMatrix, minSize, maxSize, 
				discreteTrans = 1, integrateType = "midpoint", 
				correction = "none",  preCensus = TRUE, tol=1e-4,
				binIncrease=5, chosenBin=1, response="lambda")

Arguments

growObj

a growth object.

survObj

a survival object.

fecObj

a fecundity object.

nBigMatrix

numeric, initial number of bins of size used in the matrix - will be increased for the assessment

minSize

numeric, minimum size used for meshpoints

maxSize

numeric, maximum size used for meshpoints of the P matrix.

discreteTrans

matrix of discrete transitions; or 1 if there is none

integrateType

integration type.

correction

correction (see makeIPMPmatrix)

preCensus

boolean defining whether fecundity is pre or post census; defaults to pre

tol

desired tolerance level

binIncrease

increments in increase in the number of bins (should be an integer)

chosenBin

desired bin for which life expectancy should be assessed; default is 1st.

response

what variable is convergence to be tested for; options are "lambda", "R0", "lifeExpect"; for the latter, the desired bin should be considered

Details

Different choices for responses will yield different values. The pattern of change in lambda (or other response variables) can be complex, so it is advisable to start with large binIncrease and small tolerance, and then once one knows a general idea of how big the matrix needs to be, run the function again with a smaller binIncrease but start it closer to the goal.

For the life expectancy option, if discrete stages are included via discreteTrans then if chosenBin=1, this function will use the first discrete bin.

Value

binIncrease

the number of bins used to increase matrix size in assessing tolerance

Pmatrix

the final Pmatrix if only LE is being considered

IPM

the final IPM

R0

the final R0

lambda

the final lambda

LE

the final vector of life expectancies

Note

This code was modified from original code by Melissa Eitzel.

Author(s)

C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.

See Also

diagnosticsPmatrix

Examples

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dff<-generateData()
gr1<-makeGrowthObj(dff)
sv1<-makeSurvObj(dff)
fv1<-makeFecObj(dff,Transform="log")

res <- convergeIPM(growObj=gr1, 
 survObj=sv1, fecObj=fv1, 
 nBigMatrix=10, minSize=-2,
 maxSize=15,discreteTrans = 1, 
 integrateType = "midpoint", 
 correction = "none", 
 preCensus = TRUE, tol=1e-3,binIncrease=10)

res <- convergeIPM(growObj=gr1, 
survObj=sv1, fecObj=fv1, 
 nBigMatrix=10, minSize=-2,
 maxSize=15,discreteTrans = 1, 
 integrateType = "midpoint", 
 correction = "none", 
 preCensus = TRUE, tol=1e-3,
 binIncrease=10, response="R0")

res <- convergeIPM(growObj=gr1, survObj=sv1, fecObj=fv1, 
 nBigMatrix=10, minSize=-2,
 maxSize=15,discreteTrans = 1, 
 integrateType = "midpoint", 
 correction = "none", 
 preCensus = TRUE, tol=1e-3,binIncrease=10, 
 response="lifeExpect")


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