hierarchical clustering - A UPGMA cluster in R with NoData values -

i have matrix of sites. want develop upgma aglomerative cluster. want use r , vegan library that. matrix has sites in not variables measured.

following similar matrix of data:

variable 1;variable 2;variable 3;variable 4;variable 5 0.5849774671338231;0.7962161133598957;0.3478909861199184;0.8027122599553912;0.5596553797833573 0.5904142034898171;0.18185393432022612;0.5503250366728479;na;0.05657408486342197 0.2265148074206368;0.6345513807275411;0.8048128547418062;0.3303602674038131;0.8924461773052935 0.020429460126217602;0.18850489885886157;0.26412619465769416;0.8020472793070729;na 0.006945970735023677;0.8404983401121199;0.058385134042814646;0.5750066564897788;0.737599672122899 0.9909722313946067;0.22356808747617019;0.7290078902086897;0.5621006367587756;0.3387823531518016 0.5932907022602052;0.899773235815933;0.5441346748937264;0.8045695319247985;0.6183003409599681 0.6520679140573288;0.5419713133237936;na;0.7890033752744002;0.8561828607592286 0.31285906479192593;0.3396351688936058;0.5733594373520889;0.03867689654415574;0.1975784885854912 0.5045966366726562;0.6553489439611587;0.029929403932252963;0.42777351534900676;0.8787135401098227 

i planing following code:

library(vegan) # env <- read.csv("matrix_of_sites.csv") env.norm <- decostand(env, method = "normalize") # normalizing data here env.ch <- vegdist(env.nom, method = "euclidean") env.ch.upgma <- hclust(env.ch, method="average") plot(env.ch.upgma) 

after run second line, error:

error in x^2 : non-numeric argument binary operator 

i not familiar r, not sure if due cells no data. how can solve this?

r not think data numeric in matrix, @ least of them interpreted character variables , changed factors. inspect data after reading int r. if data numbers, sum(env) gives numeric result. use str() or summary() functions detailed inspection.

from r's point of view, data file has mixed formatting. r function read.csv assumes items separated comma (,) , decimal separator period (.), , read.csv2 assumes items separated colon (;) , decimal separator comma ,. mix these 2 conventions. can read data formatted that, may have give both sep , dec arguments.

if data correctly in r, decostand stop error: not accept missing values if not add na.rm = true. same next vegdist command: needs na.rm = true analyse data.