| cond_diff {lefko3} | R Documentation |
Extract Conditional Ahistorical Difference Matrices
Description
Function cond_diff() takes a set of historical difference matrices
resulting from function diff_lM() and decomposes them into
ahistorical difference matrices conditional upon stage in time t-1.
Usage
cond_diff(lDiff, ref = 1L, matchoice = NULL, err_check = NULL)
Arguments
lDiff |
An object of class |
ref |
Choice of mpm to use as reference. Defaults to |
matchoice |
A character denoting whether to use A, U, or F matrices.
Defaults to |
err_check |
A logical value denoting whether to include a data frame
of element equivalence from the conditional matrices to the original
matrices. Used only for debugging purposes. Defaults to |
Value
A lefkoCondDiff object, with the following elements:
Mcond |
A multi-level list holding the conditional matrices derived
from the input |
hstages |
A data frame matrix showing the pairing of ahistorical stages used to create historical stage pairs. |
ahstages |
A data frame detailing the characteristics of associated ahistorical stages. |
labels |
A data frame showing the patch and year of each input full A matrix in order. |
err_check |
An optional data frame showing the order of used element indices to create conditional matrices. |
Examples
sizevector <- c(0, 0, 0, 0, 0, 0, 1, 3, 6, 11, 19.5)
stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm", "Sm", "Md", "Lg",
"XLg")
repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1.5, 1.5, 3.5, 5)
comments <- c("Dormant seed", "1st yr protocorm", "2nd yr protocorm",
"3rd yr protocorm", "Seedling", "Dormant adult",
"Extra small adult (1 shoot)", "Small adult (2-4 shoots)",
"Medium adult (5-7 shoots)", "Large adult (8-14 shoots)",
"Extra large adult (>14 shoots)")
cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
propstatus = propvector, immstatus = immvector, indataset = indataset,
binhalfwidth = binvec, comments = comments)
cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
patchidcol = "patch", individcol = "plantid", blocksize = 4,
sizeacol = "Inf2.04", sizebcol = "Inf.04", sizeccol = "Veg.04",
repstracol = "Inf.04", repstrbcol = "Inf2.04", fecacol = "Pod.04",
stageassign = cypframe_raw, stagesize = "sizeadded", NAas0 = TRUE,
NRasRep = TRUE)
seeds_per_pod <- 5000
cypsupp2_raw <- supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D",
"XSm", "SD", "P1"),
stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "rep", "rep"),
eststage3 = c(NA, NA, NA, NA, NA, NA, "D", "XSm", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, "XSm", "XSm", NA, NA),
givenrate = c(0.03, 0.15, 0.1, 0.1, 0.1, 0.05, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, (0.5 * seeds_per_pod),
(0.5 * seeds_per_pod)),
type =c(1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
stageframe = cypframe_raw, historical = FALSE)
cypsupp3_raw <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
"D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
"SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
"SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
"mat", "mat", "mat", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "D", "XSm", "Sm", NA, NA),
eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, 0.5, 0.5),
type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
stageframe = cypframe_raw, historical = TRUE)
cypmatrix2rp <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", patch = "all", stages = c("stage3", "stage2"),
size = c("size3added", "size2added"), supplement = cypsupp2_raw,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", stages = c("stage3", "stage2"),
size = c("size3added", "size2added"), supplement = cypsupp2_raw,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cypmatrix3rp <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added", "size1added"), supplement = cypsupp3_raw,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added", "size1added"), supplement = cypsupp3_raw,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cypmatrix2r_3 <- hist_null(cypmatrix2r)
cypmatrix2r_3 <- delete_lM(cypmatrix2r_3, year = 2004)
diff_r <- diff_lM(cypmatrix3r, cypmatrix2r_3)
cypmatrix2rp_3 <- hist_null(cypmatrix2rp)
cypmatrix2rp_3 <- delete_lM(cypmatrix2rp_3, year = 2004)
diff_rp <- diff_lM(cypmatrix3rp, cypmatrix2rp_3)
condr1 <- cond_diff(diff_r, ref = 1)
condr2 <- cond_diff(diff_r, ref = 2)
condrp1 <- cond_diff(diff_rp, matchoice = "U", ref = 1)
condrp2 <- cond_diff(diff_rp, matchoice = "F", ref = 2)