titan boot problems

[ryan1138]

glades_titan_test <- titan(glades.env, glades.taxa, nBoot=1)
# Screening taxa...
#   100% occurrence detected 1 times (0.6% of taxa),
#   use of TITAN less than ideal for this data type.
#   taxa frequency screen complete.
# Partitioning along gradient...
# Calculating observed IndVal maxima and class values...
# Calculating IndVals using mean relative abundance...
# Permuting IndVal scores...
# Summarizing observed results...
# Estimating taxa change points using z-score maxima...
# Bootstrap resampling in sequence...
# 1.. Error in rowMeans(metricArray[, 1, ] == 1, na.rm = T) : 
#   'x' must be an array of at least two dimensions

glades_titan_test <- titan(glades.env, glades.taxa, ncpus = 8, nBoot = 2)
# Screening taxa...
#   100% occurrence detected 1 times (0.6% of taxa),
#   use of TITAN less than ideal for this data type.
#   taxa frequency screen complete.
# Partitioning along gradient...
# Calculating observed IndVal maxima and class values...
# Calculating IndVals using mean relative abundance...
# Permuting IndVal scores...
# Summarizing observed results...
# Estimating taxa change points using z-score maxima...
# Bootstrap resampling in parallel using 8 CPUs... no index will be printed to screen
# Error in ivz.bt.list[[s]][[l]] : 
#   attempt to select less than one element in integerOneIndex

[ryan1138]

Here's another one (after running for several hours, ugh.)

> genus_glimpss_titan<-titan(genus_otu_filter3$GLIMPSS_CHIRO_GENUS, genus_otu_wide_filter3_20[,-1], ncpus=8, nBoot=100)
Screening taxa...
  taxa frequency screen complete.
Partitioning along gradient...
Calculating observed IndVal maxima and class values...
Calculating IndVals using mean relative abundance...
Permuting IndVal scores...
Summarizing observed results...
Estimating taxa change points using z-score maxima...
Bootstrap resampling in parallel using 8 CPUs... no index will be printed to screen
Error in bEnvMatrix[aseq, ] <- unlist(ivz.bt.list[[s]][[l]][[3]]) : 
  number of items to replace is not a multiple of replacement length
> 

[dkahle]

The first line in your first issue is solved. The other issues appear to be the same: the bSeq argument is wrong:

Browse[1]> bSeq
# [[1]]
# [1] 1
# 
# [[2]]
# integer(0)
# 
# [[3]]
# integer(0)
# 
# [[4]]
# integer(0)
# 
# [[5]]
# integer(0)
# 
# [[6]]
# integer(0)
# 
# [[7]]
# integer(0)
# 
# [[8]]
# [1] 2