[R] Envfit, inconsistant result?

rodrock rodrigo.vargasgaete at gmail.com
Fri Sep 23 14:01:08 CEST 2011

Hi R-experts,

I am using the envfit function over an ordination of floristic data.

The problem is that every time that I run it changes the results. Sometimes
dramatically, selecting variables that the first time were not significant.
I do not get what could be the problem or if is normal given the
permutations are different.

# the NMDS ordination

gap_flor_NMDS_chord <- metaMDS(gaps_flor, distance = "euclid", k = 2, trymax
= 20, autotransform =TRUE,
noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
plot = FALSE, old.wa = FALSE, zerodist = "add")

# the  environmental variables to use with enfit

explain1<- site[c("Tipo", "Gap.size", "Gap diameter (m)", "Size.cat",
"altitud", "Slope (%)", 
"Exp.deg", "form","formcont", "largo_medio_gmak_m", "Dom.Hight",
"d_m_gapmak_cm", "Cat_edad", 
 "uprooted_perc", "Snapped gap maker (%)", "stand_dead_perc",
 "nodet_orig_gmkr_perc",  "Total_borde", "PACL_diff_warm045",
  "rock", "musg_hep", "mantillo", "sm", "tronco_tot", "Time.ctr",
  "fm_gmk", "dc_gmk_perc", "be_gmk_perc", "ach_gmk_perc",
 "Myrceugenia as border tree (%)", "Fm_borde.", "Dc_borde.", "Be_borde.",
 "Aristotelia as border tree (%)")]   

# the  Envfit calculation
exp_flor1 <- envfit(gap_flor_NMDS_chord, explain1, permu = 999, na.rm=T)       

Thanks a lot for your help, comments and input!

Rodrigo Vargas G.
Silviculture Institute
Freiburg University

View this message in context: http://r.789695.n4.nabble.com/Envfit-inconsistant-result-tp3836585p3836585.html
Sent from the R help mailing list archive at Nabble.com.

More information about the R-help mailing list