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###################################### | |
## Function that organizes the data so that PGLMM can be fit | |
## Created by Matthew Helmus | |
## | |
## attempt at fixing the function for use with larger data sets | |
## diag is replaced with Matrix:::Diagonal | |
###################################### | |
require(Matrix) | |
fixed.pglmm.data <- function (modelflag = 1, sim.dat = NULL, samp = NULL, tree = NULL, | |
traits = NULL, env = NULL, Vcomp = NULL) | |
{ | |
if (!is.null(sim.dat)) { | |
tree <- sim.dat$Vphylo | |
Vcomp <- sim.dat$Vcomp | |
samp <- sim.dat$Y | |
traits <- sim.dat$bspp1 | |
env <- sim.dat$u | |
} | |
is.empty <- function(x) { | |
length(x) == 0 | |
} | |
if (is.empty(samp)) { | |
stop("sample matrix (Y) is empty") | |
} | |
if (is(tree)[1] == "phylo") { | |
if (is.null(tree$edge.length)) { | |
tree <- compute.brlen(tree, 1) | |
} | |
tree <- prune.sample(samp, tree) | |
samp <- samp[, tree$tip.label] | |
V <- vcv.phylo(tree, corr = TRUE) | |
species <- colnames(samp) | |
preval <- colSums(samp)/sum(sum(samp)) | |
species <- species[preval > 0] | |
V <- V[species, species] | |
Vcomp <- Vcomp[species, species] | |
samp <- samp[, colnames(V)] | |
traits <- as.matrix(traits[species, ]) | |
} | |
else { | |
V <- tree | |
species <- colnames(samp) | |
preval <- colSums(samp)/sum(sum(samp)) | |
species <- species[preval > 0] | |
V <- V[species, species] | |
Vcomp <- Vcomp[species, species] | |
samp <- samp[, colnames(V)] | |
traits <- as.matrix(traits[species, ]) | |
} | |
Y <- samp | |
U <- matrix(env, nrow = length(env), ncol = 1) | |
X <- traits | |
nsites <- dim(Y)[1] | |
nspp <- dim(Y)[2] | |
YY <- t(Y) | |
YY <- as.matrix(as.vector(as.matrix(YY))) | |
if (modelflag == 1) { | |
Vfullspp <- kronecker(Diagonal(nsites), V) | |
Vfullsite <- kronecker(Diagonal(nsites), Matrix(1, nspp, | |
nspp)) | |
VV <- list(Vfullspp = Vfullspp, Vfullsite = Vfullsite) | |
XX <- kronecker(matrix(1, nsites, 1), Diagonal(nspp)) | |
return(list(YY = YY, VV = VV, XX = XX)) | |
} | |
if (modelflag == 2) { | |
u <- scale(U) | |
U <- kronecker(u, Matrix(1, nspp, 1)) | |
Vfullspp <- kronecker(matrix(1, nsites, nsites), Diagonal(nspp)) | |
VfullsppV <- kronecker(matrix(1, nsites, nsites), V) | |
VfullUCU <- Diagonal(as.vector(U)) %*% Vfullspp %*% Diagonal(as.vector(U)) | |
VfullUCUV <- Diagonal(as.vector(U)) %*% VfullsppV %*% Diagonal(as.vector(U)) | |
Vfullsite <- kronecker(Diagonal(nsites), Matrix(1, nspp, | |
nspp)) | |
VV <- list(VfullUCU = VfullUCU, VfullUCUV = VfullUCUV, | |
Vfullsite = Vfullsite) | |
XXspp <- kronecker(matrix(1, nsites, 1), Diagonal(nspp)) | |
XX <- cbind(U, XXspp) | |
YY <- as.vector(t(Y)) | |
return(list(YY = YY, VV = VV, XX = XX)) | |
} | |
if (modelflag == 3) { | |
u <- scale(U) | |
U <- kronecker(u, Matrix(1, nspp, 1)) | |
Vfullsite <- kronecker(Diagonal(nsites), Matrix(1, nspp, | |
nspp)) | |
if (is.null(Vcomp)) { | |
compscale <- 1 | |
Vcomp <- solve(V, Diagonal(nspp)) | |
Vcomp <- Vcomp/max(Vcomp) | |
Vcomp <- compscale * Vcomp | |
} | |
Vfullcomp <- kronecker(Diagonal(nsites), Vcomp) | |
VV <- list(Vfullcomp = Vfullcomp, Vfullsite = Vfullsite) | |
XXspp <- kronecker(matrix(1, nsites, 1), Diagonal(nspp)) | |
XX <- cbind(XXspp, ((U %*% matrix(1, 1, nspp)) * XXspp)) | |
YY <- as.vector(t(Y)) | |
return(list(YY = YY, VV = VV, XX = XX)) | |
} | |
if (modelflag == 4) { | |
Vfulltrait <- kronecker(Diagonal(nsites), traits %*% t(traits)) | |
traitscale4 <- 100 | |
Vfulltrait <- traitscale4 * Vfulltrait | |
Vfullsite <- kronecker(Diagonal(nsites), Matrix(1, nspp, | |
nspp)) | |
VV <- list(Vfulltrait = Vfulltrait, Vfullsite = Vfullsite) | |
XXspp <- kronecker(matrix(1, nsites, 1), Diagonal(nspp)) | |
XX <- XXspp | |
YY <- as.vector(t(Y)) | |
return(list(YY = YY, VV = VV, XX = XX)) | |
} | |
if (modelflag == 5) { | |
Vfulltrait <- kronecker(Diagonal(nsites), traits %*% t(traits)) | |
traitscale5 <- 10 | |
Vfulltrait <- traitscale5 * Vfulltrait | |
Vfullspp <- kronecker(Diagonal(nsites), V) | |
Vfullsite <- kronecker(Diagonal(nsites), Matrix(1, nspp, | |
nspp)) | |
VV <- list(Vfulltrait = Vfulltrait, Vfullspp = Vfullspp, | |
Vfullsite = Vfullsite) | |
XXspp <- kronecker(matrix(1, nsites, 1), Diagonal(nspp)) | |
XX <- XXspp | |
YY <- as.vector(t(Y)) | |
return(list(YY = YY, VV = VV, XX = XX)) | |
} | |
} |
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