[R-sig-eco] envfit and adonis restricted permutations
Steve Leonard
s.leonard at latrobe.edu.au
Tue Jun 28 01:39:02 CEST 2011
Hi all,
I am using envfit and adonis to examine patterns in floristic composition
amongst sites that vary with repect to fire history and fire severity
(factors) and a number of environmental variables (mostly continuous).
Within each site vegetation has been sampled in two environments (slope and
gully, one sample in each). I have used the 'strata' argument to restrict
permutations to within sites, as I believe this accounts for the lack of
independence of samples within sites (like including site as a random factor
in a mixed model).
Results of envfit indicate that the variables 'easting' and 'northing' are
not significantly correlated with the ordination of sites, despite having
relatively high R2 values (see 'fit1' below). When I apply envfit with
unrestricted permutations, results are significant for easting and northing
(see 'fit2'). Similarly, easting and northing are significant when I analyse
the same data using adonis (see 'mod1').
Can anyone explain this apparent discrepancy? Is there a problem with the
way I am using 'strata'? Any advice gratefully received.
Thanks
Steve
PS Data files attached if anyone cares to delve into them
> flora<-read.csv("C://r//flora_ord_cd_no_UBG.csv", header=T)
> sv<-read.csv("C://r//flora_sv_no_UBG.csv", header=T)
> attach(sv)
> library(vegan)
This is vegan 1.18-33
Warning message:
package 'vegan' was built under R version 2.13.0
> mds1<-metaMDS(flora, distance="bray", k=3, trace=F, autotransform =F)
> fit1<-envfit(mds1~environment+history+severity+asp_class+easting+northing+ann_rain+Num_fire+TSF+tpi+sr_100_mean+slope,
> choices=c(1:3), strata=site)
> fit1
***VECTORS
NMDS1 NMDS2 NMDS3 r2 Pr(>r)
easting -0.068611 -0.144025 -0.987193 0.2912 0.517
northing -0.015771 0.995731 -0.090943 0.2657 0.366
ann_rain -0.104761 -0.776971 -0.620758 0.3133 0.013 *
Num_fire 0.578255 0.802894 0.144850 0.0213 0.820
TSF -0.450387 -0.325620 -0.831338 0.0476 0.936
tpi -0.889913 0.139690 0.434213 0.0666 0.014 *
sr_100_mean -0.193648 0.585345 -0.787319 0.0390 0.698
slope -0.664790 0.506331 -0.549257 0.0809 0.004 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
P values based on 999 permutations, stratified within strata.
***FACTORS:
Centroids:
NMDS1 NMDS2 NMDS3
environmentg -0.3182 0.0604 0.0177
environments 0.3113 -0.0591 -0.0173
historyNR -0.0686 -0.0104 -0.0526
historyR 0.0702 0.0106 0.0538
severityCB 0.0141 -0.0273 0.3109
severityCS -0.0257 -0.0702 0.2188
severityGB -0.0086 -0.0421 -0.0386
severityRF 0.0199 -0.0132 -0.2918
severityUB 0.0058 0.0891 -0.0738
asp_classE -0.0753 0.0850 0.0162
asp_classN -0.0177 -0.1153 -0.0120
asp_classNE -0.1051 -0.1974 -0.0086
asp_classNW 0.1137 0.0589 -0.0183
asp_classS 0.0738 0.0454 0.0618
asp_classSE 0.0262 0.0909 -0.0408
asp_classSW -0.0778 0.1801 0.0694
asp_classW 0.0502 0.0374 -0.0369
Goodness of fit:
r2 Pr(>r)
environment 0.2354 0.001 ***
history 0.0177 0.001 ***
severity 0.0810 0.001 ***
asp_class 0.0444 0.689
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
P values based on 999 permutations, stratified within strata.
> fit2<-envfit(mds1~environment+history+severity+asp_class+easting+northing+ann_rain+Num_fire+TSF+tpi+sr_100_mean+slope,
> choices=c(1:3))
> fit2
***VECTORS
NMDS1 NMDS2 NMDS3 r2 Pr(>r)
easting -0.068611 -0.144025 -0.987193 0.2912 0.001 ***
northing -0.015771 0.995731 -0.090943 0.2657 0.001 ***
ann_rain -0.104761 -0.776971 -0.620758 0.3133 0.001 ***
Num_fire 0.578255 0.802894 0.144850 0.0213 0.267
TSF -0.450387 -0.325620 -0.831338 0.0476 0.041 *
tpi -0.889913 0.139690 0.434213 0.0666 0.010 **
sr_100_mean -0.193648 0.585345 -0.787319 0.0390 0.070 .
slope -0.664790 0.506331 -0.549257 0.0809 0.003 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
P values based on 999 permutations.
***FACTORS:
Centroids:
NMDS1 NMDS2 NMDS3
environmentg -0.3182 0.0604 0.0177
environments 0.3113 -0.0591 -0.0173
historyNR -0.0686 -0.0104 -0.0526
historyR 0.0702 0.0106 0.0538
severityCB 0.0141 -0.0273 0.3109
severityCS -0.0257 -0.0702 0.2188
severityGB -0.0086 -0.0421 -0.0386
severityRF 0.0199 -0.0132 -0.2918
severityUB 0.0058 0.0891 -0.0738
asp_classE -0.0753 0.0850 0.0162
asp_classN -0.0177 -0.1153 -0.0120
asp_classNE -0.1051 -0.1974 -0.0086
asp_classNW 0.1137 0.0589 -0.0183
asp_classS 0.0738 0.0454 0.0618
asp_classSE 0.0262 0.0909 -0.0408
asp_classSW -0.0778 0.1801 0.0694
asp_classW 0.0502 0.0374 -0.0369
Goodness of fit:
r2 Pr(>r)
environment 0.2354 0.001 ***
history 0.0177 0.029 *
severity 0.0810 0.001 ***
asp_class 0.0444 0.291
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
P values based on 999 permutations.
> mod1<-adonis(flora~environment+history+severity+asp_class+easting+northing+ann_rain+Num_fire+TSF+tpi+sr_100_mean+slope,
> method="bray", strata=site)
> mod1
Call:
adonis(formula = flora ~ environment + history + severity + asp_class +
easting + northing + ann_rain + Num_fire + TSF + tpi + sr_100_mean + slope,
method = "bray", strata = site)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
environment 1 4.316 4.3155 19.3742 0.08508 0.001 ***
history 1 0.569 0.5687 2.5530 0.01121 0.001 ***
severity 4 2.801 0.7003 3.1440 0.05523 0.001 ***
asp_class 7 2.143 0.3061 1.3744 0.04225 0.295
easting 1 1.115 1.1151 5.0060 0.02198 0.001 ***
northing 1 1.860 1.8598 8.3493 0.03667 0.001 ***
ann_rain 1 0.797 0.7966 3.5762 0.01570 0.007 **
Num_fire 1 0.290 0.2896 1.2999 0.00571 0.158
TSF 1 0.159 0.1591 0.7144 0.00314 0.270
tpi 1 0.454 0.4541 2.0388 0.00895 0.486
sr_100_mean 1 0.369 0.3692 1.6576 0.00728 0.323
slope 1 0.211 0.2111 0.9476 0.00416 0.491
Residuals 160 35.639 0.2227 0.70264
Total 181 50.722 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
http://r-sig-ecology.471788.n2.nabble.com/file/n6522883/flora_ord_cd_no_UBG.csv
flora_ord_cd_no_UBG.csv
http://r-sig-ecology.471788.n2.nabble.com/file/n6522883/flora_sv_no_UBG.csv
flora_sv_no_UBG.csv
-----
Dr Steve Leonard
Research Fellow
Department of Zoology| La Trobe University | Bundoora, 3086 Australia
T: +61 3 9479 2773 | M: +61 429 418 388 | F: +61 3 9479 1551 | W: www.latrobe.edu.au/zoology/
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