[R-sig-eco] clustsig::simprof returns 'Error: argument "undef.zero" is missing with no default (FIXED DATA)
Roman Luštrik
roman.lustrik at gmail.com
Fri Feb 10 12:14:57 CET 2017
Sorry to be of no help here (restrained for time), but could it be that
because `undef.zero` is not defined explicitly
<https://github.com/cran/clustsig/blob/master/R/simprof.R#L64>, the
argument doesn't get passed on?
Try checking out the repository, explicitly define the argument and run the
analysis. You can use devtools to speed up the development cycle.
Cheers,
Roman
On Fri, Feb 10, 2017 at 9:54 AM, Cesar, Chris P <
chris.cesar at environment-agency.gov.uk> wrote:
> Part 2: Apologies, some copy/paste gremlins took over my previous post.
> Attempt 2 at posting my data/code
>
> Apologies for taking up your screens.
>
> Best regards,
>
> Chris
>
> #####################################################
> #### IMPORT DATA {Apologies, it's very messy...}
>
> df <-
> structure(
> list(
> Abratenu = c(
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
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> 0,
> 19.5943297127603,
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> 0,
> 0,
> 0,
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> 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,
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> 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,
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> 0,
> 0,
> 0
> ),
> Eteolong = c(
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
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> 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,
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> 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,
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> 0,
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> 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,
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> 0,
> 0,
> 0,
> 0,
> 0,
> 0,
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> 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")
> ### if I use Euclidean, I don't get an error, so presumably it's a
> bray-curtis thisg?
> sim
> #####################################################
> #####################################################
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--
In God we trust, all others bring data.
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