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chriscesar/Clustsig.woes.R

Last active February 10, 2017 11:22
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Clustsig.woes.R
### Issue of getting 'argument "undef.zero" is missing with no default' error when running simprof with bray curtis distance on species density data
### INFO: I'm running clustsig version 1.1 in R version 3.3.2
### Load package
require(clustsig)
### Import data
df <-
structure(
list(
Abratenu = c(
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Austmode = c(
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Capitell = c(
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Cerstdrm = c(
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Ceraedul = c(
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Copepoda = c(
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Cumogood = c(
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Eteolong = c(
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Hausaren = c(
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Laniconc = c(
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Limebalt = c(
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Littlitt = c(
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Melipalm = c(
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Mcrphthl = c(
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Nematoda = c(
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Nemertea = c(
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Parafult = c(
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Parafulg = c(
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Periulva = c(
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Petrphol = c(
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Phylmuco = c(
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Protchae = c(
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Pygoeleg = c(
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Scolsqua = c(
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Scolarmi = c(
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Tharyx = c(
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Tubipseu = c(
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Turbellr = c(
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Urotpose = c(
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Nephtys = c(
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Pontcrts = c(
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Bathypor = c(
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Corophim = c(
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Eurydice = c(
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),
.Names = c(
"Abratenu",
"Austmode",
"Capitell",
"Cerstdrm",
"Ceraedul",
"Copepoda",
"Cumogood",
"Eteolong",
"Hausaren",
"Laniconc",
"Limebalt",
"Littlitt",
"Melipalm",
"Mcrphthl",
"Nematoda",
"Nemertea",
"Parafult",
"Parafulg",
"Periulva",
"Petrphol",
"Phylmuco",
"Protchae",
"Pygoeleg",
"Scolsqua",
"Scolarmi",
"Tharyx",
"Tubipseu",
"Turbellr",
"Urotpose",
"Nephtys",
"Pontcrts",
"Bathypor",
"Corophim",
"Eurydice"
),
class = "data.frame",
row.names = c(NA,
27L)
)
########################################
## RUN SIMPROF
set.seed(4656) ## no idea if this is even required!
sim <- simprof(df, method.transform = "squareroot",
method.distance = "braycurtis")### ERROR APPEARS HERE & remains even if I define undef.zero=TRUE OR FALSE
### Oddly, I didn't get an error when I accidentally left a numeric variable of the number of replicates taken:
### Including
# df$rep <- 3 ### in the data frame gives me 6 significant clusters.
###Not sure why? Is my data too sparse for braycurtis to play nice with?
### Hoping to produce a dendrogram coloured by cluster
cbPalette <- c(
"#0072B2",
"#e79f00",
"#009E73",
"#9ad0f3",
"#000000",
"#D55E00",
"#CC79A7",
"#F0E442"
)
pl.color <- simprof.plot(sim, leafcolors = cbPalette)
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