add_lM | R Documentation |
Function add_lM()
adds matrices to lefkoMat objects.
add_lM(
lM,
Amats = NA,
Umats = NA,
Fmats = NA,
UFdecomp = FALSE,
entrystage = 1,
pop = NA,
patch = NA,
year = NA
)
lM |
The lefkoMat object to add matrices to. |
Amats |
Either a single |
Umats |
Either a single |
Fmats |
Either a single |
UFdecomp |
A logical value indicating whether U and F matrices should be
inferred from A matrices and the given |
entrystage |
The stage or stages produced by reproductive individuals.
Used to determine which transitions are reproductive for U-F decomposition.
Defaults to |
pop |
The population designation for each matrix. If object |
patch |
The patch designation for each matrix. If object |
year |
The designation for occasion at time t corresponding to each matrix. Cannot be left empty. |
A lefkoMat
object incorporating the new matrices within the
object input in lM
.
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
.
create_lM()
delete_lM()
subset_lM()
# 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)
mats_list <- list(XC3, XC4, XC5, XE3, XE4, XE5)
yr_ord <- c(1, 2, 3, 1, 2, 3)
pch_ord <- c(1, 1, 1, 2, 2, 2)
anth_lefkoMat <- create_lM(mats_list, anthframe, hstages = NA,
historical = FALSE, poporder = 1, patchorder = pch_ord, yearorder = yr_ord)
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,
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,
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(3, 3, 3), year = c(1, 2, 3))
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