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Last data update: 2014.03.03

R: Makes a list of IPMs where there is a discrete covariate.

sampleSequentialIPMs

R Documentation

Makes a list of IPMs where there is a discrete covariate.

Description

Wrapper function to build the IPM corresponding to every level of the discrete covariate, and return a list of these.

Usage

sampleSequentialIPMs(dataf, nBigMatrix = 10, minSize = -2, 
    maxSize = 10,	
	integrateType = "midpoint", correction = "none", 
	explSurv = surv ~ size + size2 + covariate, 
	explGrow = sizeNext ~ size + size2 + covariate,
	regType = "constantVar", 
	explFec = fec ~size,  Family="gaussian", 
	Transform = "none", 
	fecConstants = data.frame(NA))

Arguments

`dataf`	a dataframe with columns ‘size’, ‘sizeNext’, 'surv', 'fec', 'covariate', 'covariatel'; and 'age' indicating which individuals are seedlings for identifying the mean and variance in seedling size.
`nBigMatrix`	number of bins in size.
`minSize`	minimum size.
`maxSize`	maximum size.
`integrateType`	integration type.
`correction`	correction for unintentional eviction (individuals move outside the size range of the IPM). This correction redistributes individuals so that column sums of the IPM match expected survival for that column.
`explSurv`	Formula and explanatory variables used in the survival model.
`explGrow`	explanatory variables used in the growth model.
`regType`	Formula and regression Type for growth (normal density function, truncated, etc).
`explFec`	explanatory variables used in the fecundity.
`Family`	a character vector containing the names of the families to be used for the glms, e.g., binomial, poisson, etc. Again, these must appear in the order defined by the list of formula
`Transform`	a character vector containing the names of the transforms to be used for the response variables, e.g., log, sqrt, -1, etc. Again, these must appear in the order defined by the list of formula
`fecConstants`	data.frame of constant multipliers for the fecundity model.

Value

list of matrices corresponding to covariates, in order.

Note

Formerly makeListIPMs(). makeListIPMs() is no longer supported but has been hidden (.makeListIPMs()) and can be accessed for backward compatibility.

Author(s)

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

Examples

dff <- generateData()
IPMlist <- sampleSequentialIPMs(dff, Transform="log")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/sampleSequentialIPMs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sampleSequentialIPMs
> ### Title: Makes a list of IPMs where there is a discrete covariate.
> ### Aliases: sampleSequentialIPMs .makeListIPMs
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> dff <- generateData()
> IPMlist <- sampleSequentialIPMs(dff, Transform="log")
surv ~ size + size2 + covariate
<environment: 0x705fdf8>
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>