sampleIPMOutput | R Documentation |
Gets synthetic values including life expectancy, passage time, and, if a fecundity matrix is available, population growth rate (lambda), stable stage distribution, reproductive output, etc. It is helpful when building multiple IPMs for study of parameter uncertainty or stochastic dynamics.
sampleIPMOutput(IPMList=NULL,PMatrixList=NULL,passageTimeTargetSize=c(), sizeToAgeStartSize=c(),sizeToAgeTargetSize=c(),warn=TRUE)
IPMList |
List of survival-size IPM matrices for which summary statistics desired. When this information is included, population growth rate (lambda), and stable stage distribution will be provided. |
PMatrixList |
List of survival-growth (P) matrices for which summary statistics desired. When this information is included, only passage time and sizeToAge calculations will be provided |
passageTimeTargetSize |
Target size for passage time. If none is provided defaults to the median of the IPM meshpoints. |
sizeToAgeStartSize |
Starting size to determine the expected age which sizeToAgeTargetSize will be reached. If none is provided defaults to the minimum of the IPM meshpoints. |
sizeToAgeTargetSize |
Target size to determine the expected age which sizeToAgeTargetSize will be reached. If none is provided defaults to the IPM meshpoints. |
warn |
turn warning messages on/off. |
LE |
matrix of life expectancies, columns correspond to meshpoints, rows corresponding to each element of the list of P matrices |
pTime |
matrix of passage times to the targetSize from each of the meshpoints (columns) and for each element in the P matrix list (columns). |
lambda |
vector of population growth rates corresponding to value obtained combining each element of the list of P matrices with the corresponding element in the list of F matrices; if no F matrix list is provided, it returns a vector of NAs. |
stableStage |
matrix of stable stage distributions rows corresponding to values obtained. combining each element of the list of Pmatrices with the corresponding element in the list of Fmatrices; if no Fmatrix list is provided, this is a matrix of NAs. |
meshpoints |
matrix meshpoints. |
resSize |
matrix providing target sizes for size to age estimate (assuming age=1 at sizeStart), of length nsizeToAge space equally between the smallest and largest meshpoints. |
resAge |
matrix providing time in time-steps to get to resSize, rows corresponding sequential elements in the list of P matrices. |
This function has replaced the functionality of getIPMoutput and getIPMoutputDirect. Those functions are no longer supported but have been hidden (.getIPMoutput and .getIPMoutputDirect) and can be accessed for backward compatibility.
Cory Merow, C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans.
Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.
sampleIPM
, sampleVitalRateObj
, sampleSequentialIPMs
# =========================================================================== # Sample Vital Rate Objects # Parametric bootstrap sample for a growth object dff <- generateData(type='discrete') gr1 <- makeGrowthObj(dff) gr1List=sampleVitalRateObj(gr1,nSamp=9) # Parametric bootstrap sample for a survival object sv1 <- makeSurvObj(dff) sv1List=sampleVitalRateObj(sv1,nSamp=9) # Parametric bootstrap sample for a fecundity object fv1 <- makeFecObj(dff) fv1List=sampleVitalRateObj( fv1,nSamp=9, nDiscreteOffspringTransitions =100, nOffspring=100) # Parametric bootstrap sample for a discrete transition object dt1 <- makeDiscreteTrans(dff) dt1List=sampleVitalRateObj( dt1,nSamp=9, nDiscreteGrowthTransitions=100) # =========================================================================== # Make a list of growth/survival (P) matrices (omitting fecundity) Pmatrixlist=sampleIPM( growObjList=gr1List, survObjList=sv1List, fecObjList =NULL, nBigMatrix = 20, minSize = -5, maxSize = 20) # plot results par(mfrow=c(3,3)) lapply(Pmatrixlist,image) # Combine the list of fecundity objects with a single survival # and growth object in a list of IPMs to look at just the impact # of uncertainty in fecundity parameter estimates on population growth rate IPMlist2=sampleIPM( growObjList=list(gr1), survObjList=list(sv1), fecObjList =fv1List, discreteTransList=list(dt1), nBigMatrix = 20, minSize = -5, maxSize = 20) # plot results lapply(IPMlist2,image) # Combine the lists of all vital rate objects in a list of IPMs # to look at the impact of uncertainty in all parameters on population # growth rate IPMlist3=sampleIPM( growObjList=gr1List, survObjList=sv1List, fecObjList =fv1List, discreteTransList=list(dt1), nBigMatrix = 20, minSize = -5, maxSize = 20) # plot results lapply(IPMlist3,image) # =========================================================================== # Summarize the outputs # Get uncertainty in passage time from the list of growth/survival matrices IPMout1=sampleIPMOutput(PMatrixList=Pmatrixlist) qLE=apply(IPMout1[['LE']],2,quantile,probs=c(.025,.5,.975)) plot(IPMout1$meshpoints,qLE[2,],type='l',ylim=c(0,max(qLE))) lines(IPMout1$meshpoints,qLE[1,],type='l',lty=3) lines(IPMout1$meshpoints,qLE[3,],type='l',lty=3) # Get uncertainty in lambda from the list of IPMs where only # fecundity varied IPMout2=sampleIPMOutput(IPMList=IPMlist2) qlambda=quantile(IPMout2[['lambda']],probs=c(.025,.5,.975)) boxplot(IPMout2[['lambda']]) # Get uncertainty in lambda and passage time from size 5 to a # series of size from the list of IPMs where all vital rates varied IPMout3=sampleIPMOutput( IPMList=IPMlist3, passageTimeTargetSize=c(10), sizeToAgeStartSize=c(5), sizeToAgeTargetSize=c(6,7,8,9,10)) qlambda=quantile(IPMout3[['lambda']],probs=c(.025,.5,.975)) boxplot(IPMout3[['resAge']])
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