############### dash_test_3 (Himalyan bird abundance) ###################
library(devtools)
#install_github("kkdey/ecostructure")
library(ecostructure)
data <- get(load(system.file("extdata", "HimalayanBirdsData.rda",
package = "ecostructure")))
taxonomic_counts <- t(exprs(data))
rowSums(taxonomic_counts)
taxonomic_counts_1 <- taxonomic_counts +1
m1 <- colMeans(taxonomic_counts)
system.time(out <- dash(comp_data = taxonomic_counts_1,
optmethod = "mixEM",
mode = m1,
def_positions = list("center" = Inf, "null" = 1, "corner" = 1),
concentration = c(Inf, 100, 50, 20, 10, 5, 2, 1),
weight = list("center" = 10, "null" = 1, "corner" = 1),
bf = TRUE,
verbose=TRUE))
plot(out$posterior_weights[,1], rowSums(taxonomic_counts))
mod_counts <- round((rowSums(taxonomic_counts) %*% t(rep(1, dim(taxonomic_counts)[2])))*out$posmean)
grid_metadata <- pData(phenoData(data))
head(grid_metadata)
elevation_metadata=grid_metadata$Elevation;
east_west_dir = grid_metadata$WorE;
gom_fit <- CountClust::FitGoM(taxonomic_counts, K=2:4, tol=0.1)
elevation_metadata=grid_metadata$Elevation;
east_west_dir = grid_metadata$WorE;
omega <- gom_fit[[2]]$omega
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
rep_counts <- do.call(rbind, replicate(10, taxonomic_counts[c(29, 35),], simplify=FALSE))
zero_counts <- matrix(1, 100, dim(rep_counts)[2])
comb_counts <- rbind(rep_counts, zero_counts)
m1 <- colMeans(comb_counts)
system.time(out <- dash(comp_data = comb_counts,
optmethod = "mixEM",
mode = m1,
def_positions = list("center" = Inf, "null" = 1, "corner" = 1),
concentration = c(Inf, 100, 50, 20, 10, 5, 2, 1),
weight = list("center" = 100, "null" = 1, "corner" = 1),
bf = TRUE,
verbose=TRUE))
mat <- Matrix::rsparsematrix(nrow = 500, ncol = 100, density = 0.3)
mat2 <- as.matrix(mat)
mat2[mat2 != 0] = 1
m1 <- colMeans(as.matrix(mat2))
system.time(out <- dash(comp_data = mat2,
optmethod = "mixEM",
mode = m1,
def_positions = list("center" = Inf, "null" = 1, "corner" = 1),
concentration = c(Inf, 100, 50, 20, 10, 5, 2, 1),
weight = list("center" = 100, "null" = 1, "corner" = 1),
bf = TRUE,
verbose=TRUE))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.