Hi all,
I'm trying to ID significant clusters in my species abundance data using the simprof function in the clustsig package (version 1.1) in RStudio (R ver 3.3.2, RStudio version 1.0.136).
My taxa are columns and samples are rows. When I try to run simprof, I get an error telling me:
---------------------------------------------------------------------------------------
Error: argument "undef.zero" is missing, with no default
In addition: Warning messages:
1: This version of the Bray-Curtis index does not use standardization.
2: To use the standardized version, use "actual-braycurtis".
3: See the help documentation for more information.
---------------------------------------------------------------------------------------
From advice skimmed from the archives, I've tried updating clustsig, but still get the same issue. Has anyone seen/overcome this issue? (For what it's worth, the same code runs fine on another, similarly 0-filled data set I have)
Thanks for any help.
Chris
Distressingly aesthetically displeasing (but reproducible) data/code below:
########################################################################
#### IMPORT DATA {Apologies, it's very messy...}
df<-structure(list(Abratenu = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603
), Austmode = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 137.160307989322,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Capitell = c(0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 58.7829891382809, 0, 78.3773188510412,
0, 0, 0, 19.5943297127603, 0, 0, 0, 0, 58.7829891382808), Cerstdrm = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 19.5943297127603), Ceraedul = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 19.5943297127603, 901.339166786972, 0, 58.7829891382808,
0, 0, 0, 0, 0, 7994.4865228062, 0, 0, 0, 0, 5231.68603330699),
Copepoda = c(0, 0, 19.5943297127603, 0, 0, 0, 19.5943297127603,
0, 0, 19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 607.424221095569,
0, 0, 19.5943297127603, 0, 0, 0, 0, 0, 0), Cumogood = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603, 0, 0, 0,
0, 0, 39.1886594255206, 0, 0, 0, 0, 0, 0, 0, 0, 0), Eteolong = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603,
0, 0, 0, 0, 0, 19.5943297127603, 58.7829891382809), Hausaren = c(0,
0, 19.5943297127603, 0, 0, 0, 0, 0, 0, 19.5943297127603,
0, 0, 0, 0, 78.3773188510412, 0, 39.1886594255206, 0, 0,
0, 0, 0, 0, 0, 0, 19.5943297127603, 0), Laniconc = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
195.943297127603, 0, 0, 0, 0, 156.754637702082), Limebalt = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 97.9716485638014, 0, 0, 0, 0, 293.914945691404), Littlitt = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Melipalm = c(0, 0, 19.5943297127603,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0), Mcrphthl = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Nematoda = c(97.9716485638015,
999.310815350775, 19.5943297127603, 39.1886594255206, 0,
78.3773188510411, 1097.28246391458, 97.9716485638014, 39.1886594255206,
313.509275404164, 156.754637702082, 19.5943297127603, 0,
0, 19.5943297127603, 0, 0, 3879.67728312653, 0, 39.1886594255206,
97.9716485638014, 0, 78.3773188510412, 235.131956553124,
372.292264542445, 0, 0), Nemertea = c(0, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0, 0, 0, 19.5943297127603, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603, 0), Parafult = c(0,
19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Parafulg = c(0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603, 0,
19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 0, 0), Periulva = c(0,
0, 19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2664.8288409354,
0, 431.075253680726, 0, 0, 391.886594255207, 39.1886594255206,
19.5943297127603, 0, 0, 58.7829891382809, 0, 19.5943297127603,
0), Petrphol = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Phylmuco = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
39.1886594255206, 0, 0, 0, 0, 0), Protchae = c(313.509275404165,
0, 0, 0, 0, 0, 0, 0, 0, 39.1886594255206, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 39.1886594255206, 0, 0, 0, 0), Pygoeleg = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 97.9716485638015, 0, 0, 0, 0, 470.263913106248), Scolsqua = c(0,
0, 0, 39.1886594255206, 0, 0, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0, 117.565978276562, 39.1886594255206, 19.5943297127603,
0, 176.348967414843, 274.320615978644, 0, 0, 19.5943297127603,
0, 78.3773188510412, 764.178858797652, 0), Scolarmi = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 313.509275404165, 0, 0, 0, 0, 333.103605116925), Tharyx = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 19.5943297127603), Tubipseu = c(0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 176.348967414842), Turbellr = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0), Urotpose = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603
), Nephtys = c(0, 0, 78.3773188510412, 19.5943297127603,
0, 0, 0, 0, 0, 0, 0, 39.1886594255206, 176.348967414843,
0, 0, 0, 0, 58.7829891382808, 0, 0, 117.565978276562, 137.160307989322,
19.5943297127603, 0, 0, 0, 19.5943297127603), Pontcrts = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Bathypor = c(0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 39.1886594255206, 39.1886594255206,
19.5943297127603, 0, 0, 0, 0, 0, 0, 0, 0, 19.5943297127603,
0), Corophim = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 39.1886594255206,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 58.7829891382808), Eurydice = c(19.5943297127603,
0, 0, 19.5943297127603, 19.5943297127603, 0, 0, 0, 0, 39.1886594255206,
19.5943297127603, 0, 0, 0, 39.1886594255206, 19.5943297127603,
333.103605116925, 0, 0, 0, 0, 0, 19.5943297127603, 0, 0,
235.131956553123, 0)), .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))
## Load package
require(clustsig)
set.seed(4656)
sim <- simprof(df, method.transform = "squareroot",
method.distance = "braycurtis"); sim
########################################################################
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