IPMpack (version 1.6)

survivorship: Estimates survivorship between two time censuses.

Description

Calculates the fraction of the cohort surviving across age for a chosen starting continuous stage value.

Usage

survivorship(IPMmatrix, loc, maxAge)

Arguments

IPMmatrix

an IPMmatrix object describing growth and survival transitions across stage (e.g. size) and environment.

loc

a starting size location in the IPM matrix for age 1 (i.e., either the index of the desired size in the meshpoints, or, if there are discrete stages, the index + the number of discrete stages; if this is not an integer, then it will be assumed th

maxAge

the maximum age up to which survivorship is desired for or possible.

Value

• surv.curv
  vector of length maxAge providing survivorship at each age from 1 to maxAge.
• stageAgeSurv
  matrix of dimensions nBigMatrix*maxAge providing the population structure at every age for a cohort starting with an individual of size size1.
• mortality
  vector of length maxAge providing mortality at each age from 1 to maxAge.

References

Tuljapurkar & Horvitz. 2006. From stage to age in variable environments. Life expectancy and survivorship. Ecology 87, p1497-1509.

Examples

# For only continuous stages (e.g. size)
dff <- generateData()
Pmatrix <- createIPMPmatrix(minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff), 
survObj = makeSurvObj(dff))
su <- survivorship(Pmatrix, 1, 300)
plot(su$surv.curv, type = "l", col = "dark gray", ylab = "survivorship", 
xlab= "Continuous (e.g. size) stage", ylim = c(0,1))

# For continuous (e.g. size) and discrete (e.g. seedbank) stages
Pmatrix <- createCompoundPmatrix(minSize = min(dff$size,na.rm = TRUE),
maxSize = max(dff$size,na.rm = TRUE), envMatrix = makeEnvObj(dff),
growObj = makeGrowthObj(dff, Formula = sizeNext~size+size2+covariate),
survObj = makeSurvObj(dff, Formula = surv~size+size2+covariate), 
discreteTrans = 1)
su <- survivorship(Pmatrix,1,300)