[R-sig-eco] Errors with Simprof for cluster significance

[Ansley Silva]

Hello all,

I'm using R version 3.3.1, clustsig package.

I have a community dataset and I originally used hclust in the vegan
package to get dendrograms, however I need significance on the groups that
were formed.  I'd really like to use SIMPROF to look for significance among
the groups, but I am running into errors.


These are the errors I get:

> simprof(apst, num.expected=1000, num.simulated=999,
method.cluster="average", method.distance="braycurtis", alpha=0.05,
sample.orientation = "column", const = 0, silent = TRUE,increment=100)

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.

> simprof(apst, num.expected=1000, num.simulated=999,
method.cluster="average", method.distance="actual-braycurtis", alpha=0.05,
sample.orientation = "column", const = 0, silent = TRUE,increment=100)

Error in if (denom != 0) { : missing value where TRUE/FALSE needed

> simprof(apst, num.expected=1000, num.simulated=999,
method.cluster="average", method.distance="braycurtis", alpha=0.05,
sample.orientation = "column", const = 0, silent = TRUE,increment=100)

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.

> simprof(apst, num.expected=1000, num.simulated=999,
method.cluster="average",
method.transform="log",method.distance="braycurtis", alpha=0.05,
sample.orientation = "column", const = 0, silent = TRUE,increment=100)

Error in if (pval > alpha) { : missing value where TRUE/FALSE needed
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.



I have some samples were the columns added up to zero, so I tried removing
them since I was using method.transform="log".  But that didn't seem to
change anything.
I also tried transposing the data, but no luck there.
I am using braycurtis, but have tried actual-braycurtis and that did not
help.
I have also tried tweeking undef.zero.


​If anyone could help provide some solutions, that would be greatly
appreciated.
Please and thank you,​

-- 
Ansley Silva


*"The clearest way into the Universe is through a forest wilderness." John
Muir*


*Graduate Research Assistant*

*University of Georgia*

*D.B. Warnell School of Forestry and Natural Resources*

*180 East Green Street*

*Athens, GA 30602*
-------------- next part --------------
 packages:  vegan, clustsig
 
 data<- structure(list(necsur = c(1L, 4L, 0L, 8L, 0L, 1L), necame = c(4L, 
5L, 9L, 9L, 4L, 7L), niccar = c(1L, 1L, 1L, 2L, 1L, 4L), nicorb = c(2L, 
20L, 23L, 26L, 3L, 12L), nicpus = c(0L, 0L, 1L, 0L, 0L, 0L), 
    nictor = c(0L, 2L, 1L, 3L, 2L, 1L), delgib = c(10L, 31L, 
    47L, 48L, 15L, 55L), cancha = c(5L, 6L, 4L, 4L, 1L, 6L), 
    melbis = c(3L, 0L, 1L, 3L, 0L, 1L), atelec = c(4L, 6L, 28L, 
    22L, 8L, 52L), copmin = c(0L, 0L, 1L, 1L, 0L, 1L), ontcon = c(3L, 
    3L, 11L, 7L, 1L, 2L), ontdep = c(2L, 0L, 0L, 0L, 0L, 0L), 
    onthec = c(17L, 15L, 9L, 6L, 6L, 2L), ontstr = c(0L, 0L, 
    0L, 1L, 1L, 0L), onttau = c(20L, 13L, 6L, 2L, 0L, 2L), ontpen = c(2L, 
    3L, 5L, 3L, 2L, 4L), onttub = c(2L, 3L, 4L, 1L, 1L, 0L), 
    phavin = c(1L, 0L, 0L, 0L, 0L, 1L), Phyili = c(0L, 0L, 0L, 
    0L, 0L, 1L), canvir = c(0L, 1L, 0L, 0L, 0L, 0L), hybill = c(1L, 
    0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L, 0L, 1L, 1L), 
    galjan = c(0L, 0L, 1L, 1L, 0L, 0L), cyclosig = c(0L, 0L, 
    0L, 0L, 1L, 0L), omomon = c(1L, 2L, 4L, 10L, 1L, 6L), trofov = c(1L, 
    2L, 3L, 1L, 0L, 1L), trouni = c(1L, 0L, 0L, 1L, 0L, 0L), 
    troter = c(0L, 1L, 1L, 0L, 0L, 0L), eusass = c(9L, 8L, 23L, 
    14L, 11L, 28L), hiscoe = c(2L, 1L, 10L, 4L, 2L, 4L), hisabb = c(0L, 
    0L, 0L, 0L, 2L, 0L), cremax = c(4L, 7L, 1L, 2L, 2L, 5L), 
    plamac = c(1L, 0L, 3L, 2L, 2L, 2L), plafem = c(0L, 0L, 0L, 
    0L, 0L, 0L), plafos = c(1L, 1L, 3L, 2L, 1L, 2L), placom = c(6L, 
    3L, 3L, 10L, 13L, 7L), tacfim = c(0L, 0L, 1L, 0L, 0L, 0L)), .Names = c("necsur", 
"necame", "niccar", "nicorb", "nicpus", "nictor", "delgib", "cancha", 
"melbis", "atelec", "copmin", "ontcon", "ontdep", "onthec", "ontstr", 
"onttau", "ontpen", "onttub", "phavin", "Phyili", "canvir", "hybill", 
"cyclev", "galjan", "cyclosig", "omomon", "trofov", "trouni", 
"troter", "eusass", "hiscoe", "hisabb", "cremax", "plamac", "plafem", 
"plafos", "placom", "tacfim"), row.names = c("AP-0", "AP-100", 
"AP-200", "AP-300", "ST-0", "ST-100"), class = "data.frame")

simprof(apst, num.expected=1000, num.simulated=999, method.cluster="average", method.distance="braycurtis", alpha=0.05, sample.orientation = "column", const = 0, silent = TRUE,increment=100)