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Nullmod 1rowcol #180

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merged 3 commits into from
Jun 10, 2016
Merged

Nullmod 1rowcol #180

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f59a47e
real data in example
psolymos May 24, 2016
96fbde0
handling 1 row/col cases
psolymos May 24, 2016
4617d96
note about 1 row/col cases
psolymos May 24, 2016
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42 changes: 36 additions & 6 deletions R/make.commsim.R
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@ function(method)
"quasiswap" = commsim(method="quasiswap", binary=TRUE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(unlist(r2dtable(n, rs, cs)), c(nr, nc, n))
storage.mode(out) <- "integer"
for (k in seq_len(n))
Expand Down Expand Up @@ -122,6 +124,8 @@ function(method)
"backtrack" = commsim(method="backtrack", binary=TRUE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
btrfun <- function() {
all <- matrix(as.integer(1:(nr * nc)), nrow = nr, ncol = nc)
out <- matrix(0L, nrow = nr, ncol = nc)
Expand Down Expand Up @@ -171,13 +175,17 @@ function(method)
"r2dtable" = commsim(method="r2dtable", binary=FALSE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(unlist(r2dtable(n, rs, cs)), c(nr, nc, n))
storage.mode(out) <- "integer"
out
}),
"swap_count" = commsim(method="swap_count", binary=FALSE, isSeq=TRUE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(0L, c(nr, nc, n))
out[,,1] <- .C("swapcount",
m = x, nr, nc, thin, PACKAGE = "vegan")$m
Expand All @@ -189,6 +197,8 @@ function(method)
"quasiswap_count" = commsim(method="quasiswap_count", binary=FALSE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(unlist(r2dtable(n, rs, cs)), c(nr, nc, n))
storage.mode(out) <- "integer"
for (k in seq_len(n))
Expand All @@ -199,6 +209,8 @@ function(method)
"swsh_samp" = commsim(method="swsh_samp", binary=FALSE, isSeq=FALSE,
mode="double",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
nz <- x[x > 0]
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
storage.mode(out) <- "double"
Expand All @@ -213,6 +225,8 @@ function(method)
"swsh_both" = commsim(method="swsh_both", binary=FALSE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
indshuffle <- function(x) {
drop(rmultinom(1, sum(x), rep(1, length(x))))
}
Expand All @@ -230,6 +244,8 @@ function(method)
"swsh_samp_r" = commsim(method="swsh_samp_r", binary=FALSE, isSeq=FALSE,
mode="double",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
storage.mode(out) <- "double"
I <- seq_len(nr)
Expand All @@ -250,6 +266,8 @@ function(method)
"swsh_samp_c" = commsim(method="swsh_samp_c", binary=FALSE, isSeq=FALSE,
mode="double",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
storage.mode(out) <- "double"
J <- seq_len(nc)
Expand All @@ -270,6 +288,8 @@ function(method)
"swsh_both_r" = commsim(method="swsh_both_r", binary=FALSE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
indshuffle <- function(x) {
drop(rmultinom(1, sum(x), rep(1, length(x))))
}
Expand All @@ -293,6 +313,8 @@ function(method)
"swsh_both_c" = commsim(method="swsh_both_c", binary=FALSE, isSeq=FALSE,
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
if (nr < 2L || nc < 2)
stop("needs at least 2 items")
indshuffle <- function(x) {
drop(rmultinom(1, sum(x), rep(1, length(x))))
}
Expand Down Expand Up @@ -351,7 +373,8 @@ function(method)
J <- seq_len(nc)
for (k in seq_len(n))
for (j in J)
out[, j, k] <- sample(x[,j])
out[, j, k] <- if (nr < 2)
x[,j] else sample(x[,j])
out
}),
"r0_samp" = commsim(method="r0_samp", binary=FALSE, isSeq=FALSE,
Expand All @@ -361,7 +384,8 @@ function(method)
I <- seq_len(nr)
for (k in seq_len(n))
for (i in I)
out[i, , k] <- sample(x[i,])
out[i, , k] <- if (nc < 2)
x[i,] else sample(x[i,])
out
}),
"r00_ind" = commsim(method="r00_ind", binary=FALSE, isSeq=FALSE,
Expand Down Expand Up @@ -426,8 +450,11 @@ function(method)
J <- seq_len(nc)
for (k in seq_len(n))
for (j in J) {
out[,j,k][x[,j] > 0] <- indshuffle(x[,j][x[,j] > 0] - 1L) + 1L
out[,j,k] <- sample(out[,j,k])
if (sum(x[,j]) > 0) {
out[,j,k][x[,j] > 0] <- indshuffle(x[,j][x[,j] > 0] - 1L) + 1L
out[,j,k] <- if (nr < 2)
out[,j,k] else sample(out[,j,k])
}
}
out
}),
Expand All @@ -441,8 +468,11 @@ function(method)
I <- seq_len(nr)
for (k in seq_len(n))
for (i in I) {
out[i,,k][x[i,] > 0] <- indshuffle(x[i,][x[i,] > 0] - 1L) + 1L
out[i,,k] <- sample(out[i,,k])
if (sum(x[i,]) > 0) {
out[i,,k][x[i,] > 0] <- indshuffle(x[i,][x[i,] > 0] - 1L) + 1L
out[i,,k] <- if (nc < 2)
out[i,,k] else sample(out[i,,k])
}
}
out
})
Expand Down
10 changes: 8 additions & 2 deletions man/nullmodel.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -181,9 +181,15 @@ Jari Oksanen and Peter Solymos
\code{\link{commsim}}, \code{\link{make.commsim}},
\code{\link{permatfull}}, \code{\link{permatswap}}
}
\note{
Care must be taken when the input matrix only contains a single
row or column. Such input is invalid for swapping and hypergeometric
distribution (calling \code{\link{r2dtable}}) based algorithms.
This also applies to cases when the input is stratified into subsets.
}
\examples{
set.seed(123)
x <- matrix(rbinom(12*10, 1, 0.5)*rpois(12*10, 3), 12, 10)
data(mite)
x <- as.matrix(mite)[1:12, 21:30]

## non-sequential nullmodel
(nm <- nullmodel(x, "r00"))
Expand Down