hist_null: Create Historical MPMs Assuming No Influence of Individual History

Description

Function hist_null() uses ahistorical MPMs to create the equivalent MPMs in the structure of historical MPMs. These MPMs have the same dimensions and stage structure of hMPMs but assume no influence of individual history, and so can be compared to actual hMPMs.

Usage

hist_null(mpm, format = 1L, err_check = FALSE)

Value

An object of class lefkoMat, with the same list structure as the input object, but with A, U, and F elements replaced with lists of historically-structured matrices, and with element hstages changed from NA to an index of stage pairs corresponding to the rows and columns of the new matrices. If err_check = TRUE, then a list of three data frames showing the values used to determine matrix element index values is also exported.

Arguments

mpm: An ahistorical MPM of class lefkoMat.
format: An integer stipulating whether historical matrices should be produced in Ehrlen format (1) or deVries format (2).
err_check: A logical value indicating whether to output the main index data frames used to sort elements in the matrices.

Notes

This function does not currently identify biologically impossible transitions. Ahistorical transition values are placed in all theoretically possible historical transitions.

Examples

Run this code

sizevector <- c(1, 1, 2, 3)
stagevector <- c("Sdl", "Veg", "SmFlo", "LFlo")
repvector <- c(0, 0, 1, 1)
obsvector <- c(1, 1, 1, 1)
matvector <- c(0, 1, 1, 1)
immvector <- c(1, 0, 0, 0)
propvector <- c(0, 0, 0, 0)
indataset <- c(1, 1, 1, 1)
binvec <- c(0.5, 0.5, 0.5, 0.5)

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

# POPN C 2003-2004
XC3 <- matrix(c(0, 0, 1.74, 1.74,
0.208333333, 0, 0, 0.057142857,
0.041666667, 0.076923077, 0, 0,
0.083333333, 0.076923077, 0.066666667, 0.028571429), 4, 4, byrow = TRUE)

# 2004-2005
XC4 <- matrix(c(0, 0, 0.3, 0.6,
0.32183908, 0.142857143, 0, 0,
0.16091954, 0.285714286, 0, 0,
0.252873563, 0.285714286, 0.5, 0.6), 4, 4, byrow = TRUE)

mats_list <- list(XC3, XC4)
yr_ord <- c(1, 2)
pch_ord <- c(1, 1)

anth_lefkoMat <- create_lM(mats_list, anthframe, hstages = NA, historical = FALSE,
  poporder = 1, patchorder = pch_ord, yearorder = yr_ord)
  
nullmodel1 <- hist_null(anth_lefkoMat, 1) # Ehrlen format
nullmodel2 <- hist_null(anth_lefkoMat, 2) # deVries format