Running an ANOSIM with specific data in R? - r

Question

I've tried to complete an ANOSIM with data on a study I have carried out but I get multiple errors and i'm not sure how to fix it. Most of the errors are "dissimilarities have 24 observations, but grouping has 23". I'm trying to see the similarity in community structure between multiple samples.
my code so far is
setwd()
#load invertebrate data
Invertebrates<- read.csv(file="Invertebrates.csv",head=TRUE,sep=",")
#install packages
install.packages("vegan")
library(vegan)
#make community matrix
com<-Invertebrates[,2:ncol(Invertebrates)]
m_com<-as.matrix(com)
# group by site
group=Invertebrates[,1]
#ANOSIM
invert.ano<-anosim(m_com,group)
Then I get
Error in anosim(m_com, group) : there should be replicates within groups
Thanks for any help
Invertebrates <- structure(list(Site = structure(c(10L, 14L, 6L, 3L, 24L, 12L, 7L, 18L, 1L, 8L, 15L, 5L, 16L, 23L, 4L, 11L, 21L, 19L, 9L, 13L
), .Label = c("Anax parthenope", "Anisus vortex", "Asellus aquaticus",
"Bathyomphalus contortus", "Bithynia leachii", "Bithynia tentaculata",
"Coenagrion pulchellum", "Corixa punctata", "Dytiscus marginalis",
"Gammarus pulex", "Gyraulus albus", "Haliplus fluviatilis", "Haplotaxis gordioides",
"Ilyocoris cimicoides", "Lymnaea stagnalis", "Lymnaea truncatula",
"Oxygastra curtisii", "Physa fontilnalis", "Piscicola geometra",
"Planorbis cornatus", "Planorbis planorbis", "Radix ovata", "Radix palustris",
"Sialis lutaria"), class = "factor"), Finglesham.Brook.A = c(112L,
1L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Betteshanger.Pond.A = c(0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Betteshanger.Pond.B = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Great.Mongeham.A = c(7L, 0L, 0L, 2L, 2L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Site.7.SS.A = c(6L,
0L, 0L, 0L, 0L, 6L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Great.Mongeham.B = c(32L, 0L, 0L, 0L, 1L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Broad.dike.A = c(0L,
0L, 0L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Broad.dike.B = c(0L, 0L, 0L, 2L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), S3.Broad.dike.SS.B = c(14L,
0L, 7L, 6L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Site.6.NS.B = c(65L, 0L, 0L, 2L, 2L, 0L, 0L, 1L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Fowlmead.Lake.A = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 3L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Site.7.SS.B = c(0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Fowlmead.lake.B = c(0L,
0L, 0L, 0L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), Adelaide.NS.A = c(5L, 0L, 3L, 6L, 2L, 0L, 0L, 0L,
0L, 0L, 2L, 6L, 4L, 1L, 1L, 6L, 4L, 0L, 0L, 0L), Little.Downs.Bridge.B = c(48L,
8L, 0L, 23L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 18L, 0L, 2L, 0L, 1L,
0L, 1L, 0L, 0L), Finglesham.Brook.B = c(78L, 0L, 3L, 15L, 1L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 2L),
Adelaide.SS.A = c(8L, 0L, 0L, 33L, 9L, 0L, 0L, 0L, 0L, 0L,
0L, 12L, 0L, 4L, 19L, 7L, 4L, 0L, 2L, 0L), Adelaide.SS.B = c(4L,
0L, 20L, 9L, 2L, 0L, 0L, 0L, 0L, 0L, 7L, 0L, 0L, 0L, 14L,
0L, 1L, 0L, 0L, 0L), Ham.Fen.SS = c(1L, 0L, 0L, 6L, 3L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
Adelaide.NS.B = c(3L, 0L, 0L, 8L, 0L, 6L, 1L, 0L, 0L, 2L,
0L, 0L, 0L, 0L, 0L, 0L, 12L, 0L, 1L, 0L), Site.6.NS.A = c(58L,
0L, 0L, 2L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L), S3.Broad.dike.SS.A = c(24L, 0L, 0L, 50L,
0L, 0L, 3L, 13L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L), Little.Downs.Bridge.A = c(10L, 16L, 23L, 46L, 0L,
0L, 2L, 0L, 0L, 4L, 0L, 0L, 0L, 0L, 4L, 0L, 5L, 0L, 0L, 0L
)), row.names = c(NA, 20L), class = "data.frame")

Answer 1

If you run
table(Invertebrates$Site)
you will see that there you're grouping variable is not actually grouping anything. That is, there is maximum one observation per group. But ANOSIM requires the data to be grouped.
If I just make up a random grouping variable, like this:
Invertebrates$Group <- sample(c(1,2), nrow(Invertebrates), replace = TRUE)
and rerun your analysis:
Invertebrates$Group <- sample(c(1,2), nrow(Invertebrates), replace = TRUE)
group <- Invertebrates[, "Group"]
invert.ano <- anosim(m_com, group)
It works!