subset_lM: Create New lefkoMat Object as Subset of Another lefkoMat...

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Create New lefkoMat Object as Subset of Another lefkoMat Object

Description

Function subset_lM() creates a new lefkoMat object from a subset of matrices in another lefkoMat object.

Usage

subset_lM(lM, mat_num = NA, pop = NA, patch = NA, year = NA)

Arguments

lM	The lefkoMat object to select matrices from.
mat_num	Either a single integer corresponding to the matrix to select within the labels element of lM, or a vector of such integers.
pop	The population designation for matrices to select. Only used if mat_num is not given.
patch	The patch designation for matrices to select. Only used if mat_num is not given.
year	The time t designation for matrices to select. Only used if mat_num is not given.

Value

A lefkoMat object composed of the matrices specified in the options.

Notes

If mat_num is not provided, then at least one of pop, patch, or year must be provided. If at least two of pop, patch, and year are provided, then function subset_lM() will identify matrices as the intersection of provided inputs.

See Also

create_lM()

add_lM()

delete_lM()

Examples

# These matrices are of 9 populations of the plant species Anthyllis
# vulneraria, and were originally published in Davison et al. (2010) Journal
# of Ecology 98:255-267 (doi: 10.1111/j.1365-2745.2009.01611.x).

sizevector <- c(1, 1, 2, 3) # These sizes are not from the original paper
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)

# 2005-2006
XC5 <- matrix(c(0, 0, 0.50625, 0.675,
0, 0, 0, 0.035714286,
0.1, 0.068965517, 0.0625, 0.107142857,
0.3, 0.137931034, 0, 0.071428571), 4, 4, byrow = TRUE)

# POPN E 2003-2004
XE3 <- matrix(c(0, 0, 2.44, 6.569230769,
0.196428571, 0, 0, 0,
0.125, 0.5, 0, 0,
0.160714286, 0.5, 0.133333333, 0.076923077), 4, 4, byrow = TRUE)

XE4 <- matrix(c(0, 0, 0.45, 0.646153846,
0.06557377, 0.090909091, 0.125, 0,
0.032786885, 0, 0.125, 0.076923077,
0.049180328, 0, 0.125, 0.230769231), 4, 4, byrow = TRUE)

XE5 <- matrix(c(0, 0, 2.85, 3.99,
0.083333333, 0, 0, 0,
0, 0, 0, 0,
0.416666667, 0.1, 0, 0.1), 4, 4, byrow = TRUE)

# POPN F 2003-2004
XF3 <- matrix(c(0, 0, 1.815, 7.058333333,
0.075949367, 0, 0.05, 0.083333333,
0.139240506, 0, 0, 0.25,
0.075949367, 0, 0, 0.083333333), 4, 4, byrow = TRUE)

XF4 <- matrix(c(0, 0, 1.233333333, 7.4,
0.223880597, 0, 0.111111111, 0.142857143,
0.134328358, 0.272727273, 0.166666667, 0.142857143,
0.119402985, 0.363636364, 0.055555556, 0.142857143), 4, 4, byrow = TRUE)

XF5 <- matrix(c(0, 0, 1.06, 3.372727273,
0.073170732, 0.025, 0.033333333, 0,
0.036585366, 0.15, 0.1, 0.136363636,
0.06097561, 0.225, 0.166666667, 0.272727273), 4, 4, byrow = TRUE)

# POPN G 2003-2004
XG3 <- matrix(c(0, 0, 0.245454545, 2.1,
0, 0, 0.045454545, 0,
0.125, 0, 0.090909091, 0,
0.125, 0, 0.090909091, 0.333333333), 4, 4, byrow = TRUE)

XG4 <- matrix(c(0, 0, 1.1, 1.54,
0.111111111, 0, 0, 0,
0, 0, 0, 0,
0.111111111, 0, 0, 0), 4, 4, byrow = TRUE)

XG5 <- matrix(c(0, 0, 0, 1.5,
0, 0, 0, 0,
0.090909091, 0, 0, 0,
0.545454545, 0.5, 0, 0.5), 4, 4, byrow = TRUE)

# POPN L 2003-2004
XL3 <- matrix(c(0, 0, 1.785365854, 1.856521739,
0.128571429, 0, 0, 0.010869565,
0.028571429, 0, 0, 0,
0.014285714, 0, 0, 0.02173913), 4, 4, byrow = TRUE)

XL4 <- matrix(c(0, 0, 14.25, 16.625,
0.131443299, 0.057142857, 0, 0.25,
0.144329897, 0, 0, 0,
0.092783505, 0.2, 0, 0.25), 4, 4, byrow = TRUE)

XL5 <- matrix(c(0, 0, 0.594642857, 1.765909091,
0, 0, 0.017857143, 0,
0.021052632, 0.018518519, 0.035714286, 0.045454545,
0.021052632, 0.018518519, 0.035714286, 0.068181818), 4, 4, byrow = TRUE)

# POPN O 2003-2004
XO3 <- matrix(c(0, 0, 11.5, 2.775862069,
0.6, 0.285714286, 0.333333333, 0.24137931,
0.04, 0.142857143, 0, 0,
0.16, 0.285714286, 0, 0.172413793), 4, 4, byrow = TRUE)

XO4 <- matrix(c(0, 0, 3.78, 1.225,
0.28358209, 0.171052632, 0, 0.166666667,
0.084577114, 0.026315789, 0, 0.055555556,
0.139303483, 0.447368421, 0, 0.305555556), 4, 4, byrow = TRUE)

XO5 <- matrix(c(0, 0, 1.542857143, 1.035616438,
0.126984127, 0.105263158, 0.047619048, 0.054794521,
0.095238095, 0.157894737, 0.19047619, 0.082191781,
0.111111111, 0.223684211, 0, 0.356164384), 4, 4, byrow = TRUE)

# POPN Q 2003-2004
XQ3 <- matrix(c(0, 0, 0.15, 0.175,
0, 0, 0, 0,
0, 0, 0, 0,
1, 0, 0, 0), 4, 4, byrow = TRUE)

XQ4 <- matrix(c(0, 0, 0, 0.25,
0, 0, 0, 0,
0, 0, 0, 0,
1, 0.666666667, 0, 1), 4, 4, byrow = TRUE)

XQ5 <- matrix(c(0, 0, 0, 1.428571429,
0, 0, 0, 0.142857143,
0.25, 0, 0, 0,
0.25, 0, 0, 0.571428571), 4, 4, byrow = TRUE)

# POPN R 2003-2004
XR3 <- matrix(c(0, 0, 0.7, 0.6125,
0.25, 0, 0, 0.125,
0, 0, 0, 0,
0.25, 0.166666667, 0, 0.25), 4, 4, byrow = TRUE)

XR4 <- matrix(c(0, 0, 0, 0.6,
0.285714286, 0, 0, 0,
0.285714286, 0.333333333, 0, 0,
0.285714286, 0.333333333, 0, 1), 4, 4, byrow = TRUE)

XR5 <- matrix(c(0, 0, 0.7, 0.6125,
0, 0, 0, 0,
0, 0, 0, 0,
0.333333333, 0, 0.333333333, 0.625), 4, 4, byrow = TRUE)

# POPN S 2003-2004
XS3 <- matrix(c(0, 0, 2.1, 0.816666667,
0.166666667, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0.166666667), 4, 4, byrow = TRUE)

XS4 <- matrix(c(0, 0, 0, 7,
0.333333333, 0.5, 0, 0,
0, 0, 0, 0,
0.333333333, 0, 0, 1), 4, 4, byrow = TRUE)

XS5 <- matrix(c(0, 0, 0, 1.4,
0, 0, 0, 0,
0, 0, 0, 0.2,
0.111111111, 0.75, 0, 0.2), 4, 4, byrow = TRUE)

mats_list <- list(XC3, XC4, XC5, XE3, XE4, XE5, XF3, XF4, XF5, XG3, XG4, XG5,
  XL3, XL4, XL5, XO3, XO4, XO5, XQ3, XQ4, XQ5, XR3, XR4, XR5, XS3, XS4, XS5)

yr_ord <- c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1,
  2, 3, 1, 2, 3)

pch_ord <- c(1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7,
  8, 8, 8, 9, 9, 9)

anth_lefkoMat <- create_lM(mats_list, anthframe, hstages = NA, historical = FALSE,
  poporder = 1, patchorder = pch_ord, yearorder = yr_ord)
  
smaller_anth_lM <- subset_lM(anth_lefkoMat, patch = c(1, 2, 3), 
  year = c(1, 2))

lefko3 documentation built on Oct. 14, 2023, 1:07 a.m.