miniMod: Minimize lefkoMod Object by Conversion to vrm_input Object

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Minimize lefkoMod Object by Conversion to vrm_input Object

Description

This function takes a lefkoMod object, which consists of vital rate models, their associated dredge model tables, and related metadata, and converts them to minimal data frame lists useable in MPM creation and projection. The main advantage to using this approach is in memory savings.

Usage

miniMod(
  lMod,
  hfv_data = NULL,
  stageframe = NULL,
  all_years = NULL,
  all_patches = NULL,
  all_groups = NULL,
  all_indcova = NULL,
  all_indcovb = NULL,
  all_indcovc = NULL
)

Arguments

lMod	A lefkoMod object.
hfv_data	The hfv_data formatted data frame used to develop object lMod.
stageframe	The stageframe used to develop object lMod.
all_years	A vector giving the times / years used to develop object lMod, exactly as used in the latter. Only needed if object hfv_data not provided.
all_patches	A vector giving the patch names used to develop object lMod, exactly as used in the latter. Only needed if object hfv_data not provided.
all_groups	A vector giving the stage groups used to develop object lMod, exactly as used in the latter. Only needed if object stageframe not provided.
all_indcova	The name of individual covariate a if quantitative and non-categorical, or of the categories used if the covariate is a factor variable. Only needed if object hfv_data not provided but individual covariates used in vital rate models.
all_indcovb	The name of individual covariate a if quantitative and non-categorical, or of the categories used if the cvoariate is a factor variable. Only needed if object hfv_data not provided but individual covariates used in vital rate models.
all_indcovc	The name of individual covariate a if quantitative and non-categorical, or of the categories used if the covariate is a factor variable. Only needed if object hfv_data not provided but individual covariates used in vital rate models.

Value

An object of class vrm_input. See function vrm_import() for details.

Examples

data(lathyrus)

sizevector <- c(0, 4.6, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 1, 2, 3, 4, 5, 6, 7, 8,
  9)
stagevector <- c("Sd", "Sdl", "Dorm", "Sz1nr", "Sz2nr", "Sz3nr", "Sz4nr",
  "Sz5nr", "Sz6nr", "Sz7nr", "Sz8nr", "Sz9nr", "Sz1r", "Sz2r", "Sz3r", 
  "Sz4r", "Sz5r", "Sz6r", "Sz7r", "Sz8r", "Sz9r")
repvector <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1)
obsvector <- c(0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
immvector <- c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
  0)
indataset <- c(0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 4.6, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 
  0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5)

lathframeln <- sf_create(sizes = sizevector, stagenames = stagevector, 
  repstatus = repvector, obsstatus = obsvector, matstatus = matvector, 
  immstatus = immvector, indataset = indataset, binhalfwidth = binvec, 
  propstatus = propvector)

lathvertln <- verticalize3(lathyrus, noyears = 4, firstyear = 1988,
  patchidcol = "SUBPLOT", individcol = "GENET", blocksize = 9, 
  juvcol = "Seedling1988", sizeacol = "lnVol88", repstracol = "Intactseed88",
  fecacol = "Intactseed88", deadacol = "Dead1988", 
  nonobsacol = "Dormant1988", stageassign = lathframeln, stagesize = "sizea",
  censorcol = "Missing1988", censorkeep = NA, NAas0 = TRUE, censor = TRUE)

lathvertln$feca2 <- round(lathvertln$feca2)
lathvertln$feca1 <- round(lathvertln$feca1)
lathvertln$feca3 <- round(lathvertln$feca3)

lathmodelsln3 <- modelsearch(lathvertln, historical = TRUE, 
  approach = "mixed", suite = "main", 
  vitalrates = c("surv", "obs", "size", "repst", "fec"), juvestimate = "Sdl",
  bestfit = "AICc&k", sizedist = "gaussian", fecdist = "poisson", 
  indiv = "individ", patch = "patchid", year = "year2",
  year.as.random = TRUE, patch.as.random = TRUE, show.model.tables = TRUE,
  quiet = "partial")

lathmodels_mini <- miniMod(lathmodelsln3, hfv_data = lathvertln,
  stageframe = lathframeln)
lathmodels_mini

lefko3 documentation built on Sept. 11, 2024, 9:35 p.m.