Generates random data in the form used by IPMpack based on the population dynamics of Carlina vulgaris

Description

Simulates growth, survival and fecundity and density dependent seedling establishment to create a dataframe of the form required by the functions and methods used in IPMpack. Demographic stage data is only continuous. Note that the number or rows corresponding to each year of the data-frame does not inform about population size, since rows exist that correspond to offspring appearing in the subsequent year.

Usage

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simulateCarlina(nSamp=200,nYrs=1000,nSampleYrs=15,
		m0=-1.37,ms=0.59,
		b0=-12.05,bs=3.64,
		A=-1,B=2,
		ag=1.14,bg=0.74,sig=0.29,
		mean.kids=3.16,sd.kids=0.5,
		meanYear=c(0,0,0),
		matVarYear=matrix(c(1.03,0,0,0,0.037,0.041,0,0.041,0.075),3,3),
		varA=0,varB=0,densDep=TRUE,
		maxPerYr=1000,maxStoreSeedlingsPerYr=200,
		sizes = c())

Arguments

nSamp

number of samples desired in the base population, defaults to 2000

nYrs

number of years in the simulation, defaults to 1000

nSampleYrs

number of years sampled, defaults to 15

m0

intercept survival

ms

slope survival

b0

intercept flowering

bs

slope flowering

A

intercept reproductive allometry seed production

B

slope reproductive allometry seed production

ag

intercept growth

bg

slope growth

sig

variance growth

mean.kids

mean kid size

sd.kids

variance kid size

meanYear

mean year effects

matVarYear

var-covariance in year effects for survival, growth and offspring size

varA

variance in seed intercept year effects - defaults to zero

varB

variance in seed slope year effects - defaults to zero

densDep

density dependence in seedling establishment or not?

maxPerYr

total number of individuals for which measurements will be transferred to the subsequent year (population will be resampled with replacement to obtain a population of this size)

maxStoreSeedlingsPerYr

max number of seedling recruits for which data will be stored in every year

sizes

starting sizes in the population (optional)

Value

A list including: dataf: A dataframe with headings: - "size": continuous variable, indicating current size. - "sizeNext" continuous variable, indicating size in the next time step. - "surv": boolean, indicating whether individual survived or not to the next time step. - "covariate": discrete covariate. - "covariateNext": discrete covariate in the next time step. - "fec": continuous variable, indicating fecundity. - nSeedlings: number seedlings corresponding to that year - m.year: intercept of mortality for that year - cg.year: intercept of growth for that year - b.year: intercept of offspring size for that year - offspringNext: where the row corresponds to offspring, this takes the value offspringNexxt - year: year of the sample

list.par: - a list of all the other parameters matVarYear - variance covariance matrix for demographic functions trueGrow - stochastic growth rate, log lambda s meantrueGrow - mean of lambda t vartrueGrow - variance of log lambda t

Author(s)

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

See Also

generateData

Examples

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#Uncomment to run
#dff <- simulateCarlina(nSamp=1000)
#head(dff$dataf)

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