[R-sig-eco] Rarefied species richness as a diversity index
Hello, I have a question about the rarefy function in the vegan package. I have taken the output values from the rarefy function and used them as a response variable in a regression model. Call I call this a diversity index? Why or why not? Thanks very much, -- 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* [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Errors with Simprof for cluster significance
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*
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&qu
[R-sig-eco] Adonis for significance of clusteredness from hclust (vegan package)
Hello:
I have created a dendrograms using hierarchical cluster analysis with the
vegan package (function: hclust).
By visually observing the dendrogram, I have determined that there are 3
main clusters if I "cut" the tree at the height 0.25 (please see the
dendrogram from the code).
I then created a new dataset, which is essentially the same as the
original, but I have added the categorical variable Group to represent
these 3 main clusters.
ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST
300 is group c.
I want to now if they are significantly different from each other. I
understand, from the output pasted below, that I can accept that there is a
significant effect of Group. Is this the only thing I can say from
Permanova? What would be the code for a follow up test to look at
pair-wise significant differences?
Thanks very much.
Call:
adonis(formula = species ~ Group, data = environ, permutations = 999)
Permutation: free
Number of permutations: 999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Group 2 0.40244 0.201219 4.969 0.66528 0.007 **
Residuals 5 0.20248 0.040495 0.33472
Total 7 0.60492 1.0
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
--
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*
R version 3.3.1 Package:Vegan
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), oicina = c(0L, 0L, 0L,
0L, 0L, 0L), 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), ontsub = c(0L, 0L, 0L, 0L, 0L, 0L),
phaign = c(0L, 0L, 0L, 0L, 0L, 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),
chlema = c(0L, 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L,
0L, 1L, 1L), dicdil = c(0L, 0L, 0L, 0L, 0L, 0L), 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), sappen = c(0L, 0L, 0L, 0L, 0L, 0L), dercan = c(0L,
0L, 0L, 0L, 0L, 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),
cicsex = c(0L, 0L, 0L, 0L, 0L, 0L), spsK = c(0L, 0L, 0L,
0L, 0L, 0L)), .Names = c("necsur", "necame", "niccar", "nicorb",
"nicpus", "nictor", "oicina", "delgib", "cancha", "melbis", "atelec",
"copmin", "ontcon", "ontdep", "onthec", "ontstr", "onttau", "ontpen",
"onttub", "ontsub", "phaign", "phavin", "Phyili", "canvir", "hybill",
"chlema", "cyclev", "dicdil", "galjan", "cyclosig", "omomon",
"trofov", "trouni", "troter", "eusass", "hiscoe", "hisabb", "sappen",
"dercan", "cremax", "plamac", "plafem", "plafos", "placom", "tacfim",
"cicsex", "spsK"), row.names = c("AP-0", "AP-100", "AP-200",
"AP-300", "ST-0", "ST-100"), class = "data.frame")
> apst.log <- decostand(apst, "log")
> apst.bray <- vegdist(apst.log)
> apst.clusters <- hclust(apst.bray, method = "average")
> dev.new()
> plot(apst.clusters, which.plot=2, hang=-1)
#Create dataset with Groups a, b, cco
##Data1 <- read.csv(file="APSTperma.csv", header=TRUE, row.names=NULL, sep=",&quo
[R-sig-eco] Rarefaction: scaling by individual accumulation as samples are pooled one by one
Hello there,
I'm using R Version 3.3.1 and the Vegan package.
I have created rarefaction curves for my invertebrate community dataset. I
have 2 sites: Contaminated (ap) and Uncontaminated (st). Both are centered
around a pond. At the contaminated site the contaminated in concentrated
in the pond. So there is a gradient: distance away from water. At each
site I have transects along a gradient with 4 distances away from the
ponds. There is 0, 100, 200, and 300 meter away from the water's edge. So
in the Rarefaction graph I have 8 curves representing samples collected
from the 4 distances for each of the two site (as can be seen from my
graph).
What I would like to do is created a rarefaction graph with only two
curves, representing contaminated and uncontaminated, where the x-axis is
still scaled by the number of individuals, but there is accumulation by
pooling distances one by one. Similar to the example in Fig.3 (the lower
graph) of old growth vs. second growth in Colwell et al. 2004. I am just
having trouble with coding this and haven't found any examples.
Thanks for any help,
--
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*
> data<- read.csv(file="APSTraref.csv", header=TRUE, row.names=1, sep=",")
> dput(head(data))
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), oicina = c(0L, 0L, 0L,
0L, 0L, 0L), 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), ontsub = c(0L, 0L, 0L, 0L, 0L, 0L),
phaign = c(0L, 0L, 0L, 0L, 0L, 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),
chlema = c(0L, 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L,
0L, 1L, 1L), dicdil = c(0L, 0L, 0L, 0L, 0L, 0L), 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), sappen = c(0L, 0L, 0L, 0L, 0L, 0L), dercan = c(0L,
0L, 0L, 0L, 0L, 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),
cicsex = c(0L, 0L, 0L, 0L, 0L, 0L), spsK = c(0L, 0L, 0L,
0L, 0L, 0L)), .Names = c("necsur", "necame", "niccar", "nicorb",
"nicpus", "nictor", "oicina", "delgib", "cancha", "melbis", "atelec",
"copmin", "ontcon", "ontdep", "onthec", "ontstr", "onttau", "ontpen",
"onttub", "ontsub", "phaign", "phavin", "Phyili", "canvir", "hybill",
"chlema", "cyclev", "dicdil", "galjan", "cyclosig", "omomon",
"trofov", "trouni", "troter", "eusass", "hiscoe", "hisabb", "sappen",
"dercan", "cremax", "plamac", "plafem", "plafos", "placom", "tacfim",
"cicsex", "spsK"), row.names = c("AP-0", "AP-100", "AP-200",
"AP-300", "ST-0", "ST-100"), class = "data.frame")
>
ap<-data[c(1:4), ]
st<-data[c(5:8), ]
s<-specnumber(data)
raremax<-min(rowSums(data))
Srare<-rarefy(data, raremax)
dev.new()
plot(s, Srare, xlab="Average No. of Species", ylab="Rarefied No. of Species")
dev.new()
rarecurve(data, step=5, sample=raremax, col="darkorchid2", cex=1)
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[R-sig-eco] raremax value >2, cannot run rarefy
Hello,
R version 3.2.2, using the vegan package.
I am using the rarefy function to get rarefied values for my rarefaction
curves.
Please see the attached data and code.
Instead of getting an output from rarefy function of values for S and SE, I
am getting the following message:
"There were 20 warnings (use warnings() to see them)"
It seems that the issue might be that my raremax value for this dataset is
equal to 1. When I ran the same code on a dataset with a raremax of 5,
everything is okay. When I ran the same code on a dataset with a raremax
of 0, my output of S and SE were all 0.
I am looking for an explanation for this. Is there a way to get better
values for the output? Would PC-ORD do the same thing?
Thanks much,
--
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*
data<-
structure(list(braalt = c(8L, 0L, 0L, 0L, 0L, 0L), dicfur = c(0L,
0L, 3L, 2L, 0L, 0L), dicpur = c(0L, 0L, 0L, 1L, 0L, 0L), carvin = c(1L,
0L, 0L, 0L, 0L, 0L), carsyl = c(0L, 0L, 1L, 0L, 0L, 0L), cargor = c(1L,
0L, 0L, 0L, 0L, 0L), cyclosig = c(1L, 0L, 0L, 0L, 0L, 0L), helnig = c(0L,
0L, 0L, 0L, 0L, 0L), helcla = c(0L, 0L, 0L, 0L, 0L, 0L), passub = c(0L,
0L, 0L, 0L, 1L, 0L), anirus = c(0L, 0L, 0L, 0L, 0L, 0L), calopa = c(0L,
0L, 0L, 0L, 0L, 0L), eusass = c(0L, 13L, 12L, 14L, 5L, 17L),
hiscoe = c(4L, 2L, 0L, 0L, 2L, 1L), hisfun = c(0L, 0L, 0L,
0L, 0L, 0L), saplug = c(0L, 0L, 0L, 0L, 0L, 0L), ontnod = c(0L,
0L, 0L, 0L, 0L, 0L), cremax = c(2L, 3L, 0L, 7L, 3L, 0L),
plamac = c(0L, 0L, 0L, 0L, 1L, 0L), placom = c(0L, 1L, 0L,
0L, 0L, 0L), plapra = c(0L, 0L, 0L, 2L, 0L, 0L), tacfim = c(0L,
1L, 0L, 2L, 0L, 7L), alesps = c(0L, 0L, 0L, 0L, 0L, 0L),
tetcar = c(0L, 0L, 0L, 0L, 0L, 0L), spsA = c(0L, 0L, 0L,
0L, 0L, 0L), spsB = c(0L, 0L, 0L, 0L, 0L, 0L), spsC = c(0L,
0L, 0L, 0L, 0L, 0L), spsE = c(0L, 0L, 0L, 0L, 0L, 0L), spsF = c(0L,
0L, 0L, 0L, 0L, 0L), spsH = c(0L, 0L, 0L, 0L, 0L, 0L)), .Names =
c("braalt",
"dicfur", "dicpur", "carvin", "carsyl", "cargor", "cyclosig",
"helnig", "helcla", "passub", "anirus", "calopa", "eusass", "hiscoe",
"hisfun", "saplug", "ontnod", "cremax", "plamac", "placom", "plapra",
"tacfim", "alesps", "tetcar", "spsA", "spsB", "spsC", "spsE",
"spsF", "spsH"), row.names = c("PA1-1", "PA1-2", "PA2-1", "PA2-2",
"PA2-3", "PA2-4"), class = "data.frame")
patp<-read.csv(file="PredPATP.csv", header=TRUE, row.names=1, sep=",") #NA
values have to be removed
raremax<-min(rowSums(patp))
patprare<-rarefy(patp, raremax, se=TRUE)
write.csv(patprare, file="ExprtPATPrare.csv")___
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[R-sig-eco] rarefy function in vegan, exporting to spreadsheet
Hi,
I have just joined the list and I hope I am submitting a question in the
correct format.
I have species data that I used to make rarefaction curves. I made my
rarefaction curves based on a dataset where I averaged my traps based on a
predictor variable. This worked fine, however, now I would like to get the
specific rarefied values and SE so I can use it for my diversity index in a
model.
With my uncollapsed dataset, I get the error:
Error in if (any(sample > minsample)) warning(gettextf("Requested 'sample'
was larger than smallest site maximum (%d)", :
missing value where TRUE/FALSE needed
I think I understand the error itself, but I do not know how to correct for
it. Essentially I would like to get rarefied values to use in a linear
model, but I am having difficulty extracting these values. Help is greatly
appreciated.
Thanks,
--
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*
data<-structure(list(necsur = c(3L, 0L, 0L, 2L, 2L, 1L), necame = c(3L,
1L, 12L, 12L, 9L, 20L), niccar = c(0L, 0L, 0L, 1L, 0L, 0L), nicorb = c(0L,
30L, 31L, 3L, 0L, 48L), nicpus = c(0L, 0L, 0L, 0L, 0L, 0L), nictor = c(0L,
0L, 1L, 0L, 0L, 0L), oicina = c(0L, 0L, 0L, 0L, 0L, 0L), delgib = c(5L,
11L, 126L, 16L, 16L, 68L), cancha = c(0L, 0L, 1L, 2L, 2L, 4L),
melbis = c(1L, 0L, 0L, 0L, 0L, 0L), atelec = c(0L, 0L, 0L,
32L, 14L, 1L), copmin = c(0L, 0L, 0L, 0L, 0L, 0L), ontcon = c(0L,
1L, 3L, 0L, 0L, 6L), ontdep = c(0L, 0L, 0L, 0L, 0L, 0L),
onthec = c(1L, 28L, 7L, 14L, 0L, 29L), ontstr = c(0L, 1L,
0L, 2L, 0L, 0L), onttau = c(0L, 0L, 8L, 4L, 0L, 8L), ontpen = c(0L,
0L, 2L, 6L, 0L, 4L), onttub = c(0L, 0L, 3L, 2L, 0L, 6L),
ontsub = c(0L, 0L, 0L, 0L, 0L, 0L), ontorp = c(0L, 0L, 0L,
0L, 0L, 0L), phatri = c(0L, 0L, 0L, 0L, 0L, 1L), phaign = c(0L,
0L, 0L, 0L, 0L, 0L), phavin = c(0L, 0L, 0L, 0L, 0L, 0L),
phival = c(0L, 0L, 0L, 0L, 0L, 0L), diccar = c(0L, 0L, 0L,
0L, 0L, 0L), diggaz = c(0L, 0L, 0L, 0L, 0L, 0L), Phyili = c(0L,
0L, 0L, 0L, 0L, 0L), phyfor = c(0L, 0L, 0L, 0L, 0L, 0L),
physps = c(0L, 0L, 0L, 0L, 0L, 0L), dippun = c(0L, 0L, 0L,
0L, 0L, 0L), diplib = c(0L, 0L, 0L, 0L, 0L, 0L), euehum = c(0L,
0L, 0L, 0L, 0L, 0L), canvir = c(0L, 2L, 2L, 0L, 0L, 1L),
phycle = c(0L, 0L, 0L, 0L, 0L, 0L), pseper = c(0L, 0L, 0L,
0L, 0L, 0L), aphrus = c(0L, 0L, 0L, 0L, 0L, 0L), hybill = c(0L,
0L, 0L, 0L, 0L, 0L), geobla = c(0L, 0L, 0L, 0L, 0L, 0L),
geoege = c(0L, 0L, 0L, 0L, 0L, 0L), boltho = c(0L, 0L, 0L,
0L, 0L, 0L), braalt = c(0L, 0L, 0L, 0L, 0L, 0L), chlery = c(0L,
0L, 0L, 0L, 0L, 0L), chlema = c(0L, 0L, 0L, 0L, 0L, 0L),
cyclae = c(0L, 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L,
0L, 0L, 0L), dicdil = c(0L, 0L, 0L, 0L, 0L, 0L), dicfur = c(0L,
0L, 0L, 0L, 0L, 0L), dicpur = c(0L, 0L, 0L, 0L, 0L, 0L),
galjan = c(0L, 0L, 0L, 0L, 0L, 1L), carvin = c(0L, 0L, 0L,
0L, 0L, 0L), carsyl = c(0L, 0L, 0L, 0L, 0L, 0L), cargor = c(0L,
0L, 0L, 0L, 0L, 0L), cyclosig = c(0L, 0L, 0L, 0L, 0L, 0L),
helnig = c(0L, 0L, 0L, 0L, 0L, 0L), helcla = c(0L, 0L, 0L,
0L, 0L, 0L), scaqua = c(0L, 0L, 0L, 0L, 0L, 1L), scasub = c(0L,
0L, 0L, 0L, 0L, 0L), oodama = c(0L, 0L, 0L, 0L, 0L, 0L),
stemex = c(0L, 0L, 0L, 0L, 0L, 0L), agoalb = c(0L, 0L, 0L,
0L, 0L, 0L), moctet = c(0L, 0L, 0L, 0L, 0L, 0L), pasmar = c(0L,
0L, 0L, 0L, 0L, 0L), passub = c(0L, 0L, 0L, 0L, 0L, 0L),
apesin = c(0L, 0L, 0L, 0L, 0L, 0L), anirus = c(0L, 0L, 0L,
0L, 0L, 0L), calopa = c(0L, 0L, 0L, 0L, 0L, 0L), harsps = c(0L,
0L, 0L, 0L, 0L, 0L), copgly = c(0L, 0L, 0L, 0L, 0L, 0L),
omomon = c(0L, 0L, 4L, 2L, 0L, 2L), omosub = c(0L, 1L, 0L,
0L, 0L, 0L), trofov = c(0L, 0L, 0L, 0L, 0L, 0L), trouni = c(2L,
0L, 0L, 0L, 0L, 0L), trotub = c(0L, 0L, 0L, 0L, 0L, 0L),
troaeq = c(0L, 0L, 0L, 0L, 0L, 0L), troter = c(0L, 1L, 0L,
0L, 0L, 0L), eusass = c(10L, 2L, 9L, 17L, 16L, 9L), hiscoe = c(0L,
1L, 43L, 0L, 0L, 1L), hisabb = c(0L, 0L, 0L, 0L, 0L, 0L),
hisfun = c(0L, 0L, 0L, 0L, 0L, 0L), sappen = c(0L, 0L, 0L,
0L, 0L, 0L), saplug = c(0L, 0L, 0L, 0L, 0L, 0L), ontnod = c(0L,
0L, 0L, 0L, 0L, 0L), dercan = c(0L, 0L, 0L, 0L, 0L, 0L),
cremax = c(8L, 0L, 0L, 0L, 0L, 4L), plamac = c(0L, 1L, 5L,
1L, 0L, 0L), ontcin = c(0L, 0L, 0L, 0L, 0L, 0L), plafem = c(0L,
0L, 0L, 0L, 0L, 0L), plafos = c(0L, 0L, 0L, 1L, 0L, 1L),
placom = c(0L, 10L, 0L, 45L, 33L, 4L), placin = c(0L, 0L,
0L, 0L, 0L, 0L), plapra = c(0L, 0L, 0L, 0L, 0L, 0L), phiumb = c(0L,
0L, 0L, 0L, 0L, 0L), tacfim = c(0L, 0L, 0L, 0L, 0L, 0L),
alesps = c(0L, 0L, 0L, 0L, 0L, 0L), tetcar = c(0L, 0L, 0L,
0L, 0L, 1L), tetvir = c(0L, 0L, 0L, 0L, 0L, 0L), cicsex = c(0L,
0L, 0L, 0L, 0L,
