vegan - Error when using R betadisper function -

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the 'betadisper' funtion in vegan [r] calculates multivariate dispersion of group of sites based on distances

i have distance matrix multiple groups of sites:

dis <- vegdist(correct_tree_data)

i created 'groups' using 'factor' function (23 levels 23 groups of sites), , each group has different no. of sites

groups <- factor(c(rep(1,144), rep(2,49), rep(3,121), rep(4,81), rep(5,81), rep(6,81), rep(7,36), rep(8,289), rep(9,324), rep(10,225), rep(11,256), rep(12,225), rep(13,289), rep(14,289), rep(15,144), rep(16,225), rep(17,225), rep(18,225), rep(19,225), rep(20,225), rep(21,225), rep(22,225), rep(23,225)), labels = c("s1_05","s2_05","s3_05","s4_05","s5_05","s6_05","s7_05","s1_10","s2_10","s3_10","s4_10","s5_10","s6_10","s7_10","s8_10","s1_15","s2_15","s3_15","s4_15","s5_15","s6_15","s7_15","s8_15"))

when using 'betadisper' function, however, following error message:

mod <- betadisper(dis, groups)

error in pts[groups == i, , drop = false] : (subscript) logical subscript long

the levels match amount of groups in distance matrix no. of replicates in each group

what else may contributing error?

as long dimensions/lengths match function should work fine:

require(vegan) data(varespec)  dis   <- vegdist(varespec) group <- factor(rep("grazed", nrow(varespec))) mod   <- betadisper(dis, group) mod

homogeneity of multivariate dispersions

call: betadisper(d = dis, group = group)

no. of positive eigenvalues: 15 no. of negative eigenvalues: 8

average distance median: grazed 0.4255

eigenvalues pcoa axes: pcoa1 pcoa2 pcoa3 pcoa4 pcoa5 pcoa6 pcoa7 pcoa8 1.7552 1.1334 0.4429 0.3698 0.2454 0.1961 0.1751 0.1284

however if factor length longer should you'll error:

group <- c(group, "extra data") betadisper(dis, group)

error in pts[groups == i, , drop = false] : (subscript) logical subscript long

i know don't think problem you're having, if provide reproducible example can investigate specific case further.


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