convergeIPM: Iteratively find best number of bins for a given tolerance...

In levisc8/IPMpack: Builds and analyses Integral Projection Models (IPMs)

Description

Iteratively increases the number of bins specified in binIncrease until the difference in the chosen measure falls below the selected tolerance level.

Usage

convergeIPM(growObj, survObj, fecObj, nBigMatrix, minSize, maxSize,
  discreteTrans = 1, integrateType = "midpoint", correction = "none",
  preCensus = TRUE, tol = 1e-04, binIncrease = 5, chosenBin = 1,
  response = "lambda")

Arguments

growObj	An object of class growObj
survObj	An object of class survObj
fecObj	An object of class fecObj
nBigMatrix	A numeric specifying the initial number of bins used in the matrix. This number will be increased in the function
minSize	A numeric specifying the lower size bound for the big matrix's meshpoints
maxSize	A numeric specifying the upper size bound for the big matrix's meshpoints
discreteTrans	A matrix of discrete transitions. If there are none, specify as 1
integrateType	The type of function to integrate over. The default is midpoint. This uses the probability density function. cumul is the other option. This uses the cumulative density function.
correction	The type of correction to use for eviction. The first option is constant which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for survival at that size. The second option is discretizeExtremes which will place all transitions to sizes smaller than minSize into the smallest bin, and transitions to sizes larger than maxSize into the largest bin.
preCensus	A logical defining whether the fecObj is pre or post-census. The default is pre-census.
tol	The desired tolerance level for response.
binIncrease	The number of bins to add in each successive iteration.
chosenBin	The desired bin for which life expectancy should be assessed. The default is the first.
response	The variable to test for convergence. The options are lambda, R0, and lifeExpect. The latter will calculate the life expectancy for individuals in chosenBin.

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

A list with the following elements:

• binIncrease - The number of bins used to increase the matrix size

• Pmatrix - The final Pmatrix if only life expectancy is being considered

• IPM - The final IPM reached at convergence

• 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

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")

levisc8/IPMpack documentation built on May 7, 2019, 3:20 p.m.