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lefko3 (version 3.7.0)

create_lM: Create lefkoMat Object from Given Input Matrices

Description

Function create_lM() creates lefkoMat objects from supplied matrices and extra information.

Usage

create_lM(
  mats,
  stageframe,
  hstages = NA,
  historical = FALSE,
  agebystage = FALSE,
  UFdecomp = TRUE,
  entrystage = 1,
  poporder = 1,
  patchorder = 1,
  yearorder = NA
)

Arguments

mats

A list of A matrices.

stageframe

A stageframe describing all stages utilized.

hstages

A dataframe outlining the order of historical stages, if matrices provided in mats are historical. Defaults to NA.

historical

A logical value indicating whether input matrices are historical or not. Defaults to FALSE.

agebystage

A logical value indicating whether input matrices are ahistorical age-by-stage matrices. Defaults to FALSE.

UFdecomp

A logical value indicating whether U and F matrices should be inferred. Defaults to TRUE.

entrystage

The stage or stages produced by reproductive individuals. Used to determine which transitions are reproductive for U-F decomposition. Defaults to 1, which corresponds to the first stage in the stageframe.

poporder

The order of populations in the list supplied in object mats. Defaults to 1.

patchorder

The order of patches in the list supplied in object mats. Defaults to 1.

yearorder

The order of monitoring occasions in the list supplied in object mats. Defaults to NA, which leads to each matrix within each population-patch combination being a different monitoring occasion.

Value

A lefkoMat object incorporating the matrices input in object mats as object A, their U and F decompositions in objects U and F (if requested), the provided stageframe as object ahstages, the order of historical stages as object hstages (if historical = TRUE), the order of matrices as object labels, and a short quality control section used by the summary.lefkoMat() function.

Notes

This function does not currently handle age-by-stage matrices.

Examples

Run this code
# NOT RUN {
# These matrices are of 9 populations of the plant species Anthyllis
# vulneraria, and were originally published in Davison et al. (2010) Journal
# of Ecology98:255-267 (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)
mats_list

anth_lefkoMat <- create_lM(mats_list, anthframe, hstages = NA, historical = FALSE,
  poporder = 1, patchorder = 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),
  yearorder = 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))
anth_lefkoMat

# }

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