add_lM: Add Matrices to lefkoMat Object

Description Usage Arguments Value Notes See Also Examples

View source: R/datamanag.R

Description

Function add_lM() adds matrices to lefkoMat objects.

Usage

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add_lM(
  lM,
  Amats = NA,
  Umats = NA,
  Fmats = NA,
  UFdecomp = FALSE,
  entrystage = 1,
  pop = NA,
  patch = NA,
  year = NA
)

Arguments

lM

The lefkoMat object to add matrices to.

Amats

Either a single A matrix, or a list of A matrices. Not necessary if Umats and Fmats are both provided.

Umats

Either a single U matrix, or a list of U matrices. Not necessary if Amats and Fmats are both provided, or if UFdecomp = TRUE and entrystage is provided.

Fmats

Either a single F matrix, or a list of U matrices. Not necessary if Amats and Umats are both provided, or if UFdecomp = TRUE and entrystage is provided.

UFdecomp

A logical value indicating whether U and F matrices should be inferred from A matrices and the given entrystage. 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.

pop

The population designation for each matrix. If object lM includes only a single population, then defaults to that designation. Otherwise requires a designation as input.

patch

The patch designation for each matrix. If object lM includes only a single patch, then defaults to that designation. Otherwise requires a designation as input.

year

The designation for occasion at time *t* corresponding to each matrix. Cannot be left empty.

Value

A lefkoMat object incorporating the new matrices within the object input in lM.

Notes

This function will not allow matrices of different dimension from those input in object lM to be added to that object.

Two of Amats, Umats, and Fmats must be provided for this function to proceed. Also, if Amats, Umats, and Fmats are all provided, then this function will default to replacing Amats with the sum of the respective Umats and Fmats.

See Also

create_lM()

delete_lM()

subset_lM()

Examples

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# 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)
  
# POPN H (EXCLDED FROM ANALYSIS B/C OF UNREALISTIC ELASTICITIES)
XH3 <- matrix(c(0, 0, 0.1125, 1.05,
0.2, 0, 0, 0,
0, 0.5, 0, 0,
0.2, 0.5, 0, 0), 4, 4, byrow = TRUE)

XH3u <- matrix(c(0, 0, 0, 0,
0.2, 0, 0, 0,
0, 0.5, 0, 0,
0.2, 0.5, 0, 0), 4, 4, byrow = TRUE)

XH4 <- matrix(c(0, 0, 0, 0,
0, 0, 0.5, 0,
0.8, 0.5, 0.25, 0.25,
0.2, 0, 0, 0.75), 4, 4, byrow = TRUE)

XH4u <- matrix(c(0, 0, 0, 0,
0, 0, 0.5, 0,
0.8, 0.5, 0.25, 0.25,
0.2, 0, 0, 0.75), 4, 4, byrow = TRUE)

XH5 <- matrix(c(0, 0, 0.2, 1.05,
0, 0, 0, 0,
0.001, 0.001, 0.333333333, 0, #ELEMENTS (3,1),(4,1),(3,2) REPLACED W NONZERO
0.001, 0, 0, 0), 4, 4, byrow = TRUE)

XH5u <- matrix(c(0, 0, 0, 0,
0, 0, 0, 0,
0.001, 0.001, 0.333333333, 0, #ELEMENTS (3,1),(4,1),(3,2) REPLACED W NONZERO
0.001, 0, 0, 0), 4, 4, byrow = TRUE)

anth_lefkoMat <- add_lM(anth_lefkoMat, Amats = list(XH3, XH4, XH5),
  Umats = list(XH3u, XH4u, XH5u), patch = c(10, 10, 10), year = c(1, 2, 3))
  
anth_lefkoMat

lefko3 documentation built on Sept. 8, 2021, 9:07 a.m.