lourymigliorelli — Sep 19, 2013, 1:52 PM
install.packages("vegan")
Error: trying to use CRAN without setting a mirror
install.packages("knitr")
Error: trying to use CRAN without setting a mirror
require(vegan)
Loading required package: vegan Loading required package: permute This is
vegan 2.0-8
require(knitr)
env <- read.csv("rs_env_plot.csv")
slope <- read.csv("abun_slope.csv")
head(env)
Study.Site NDVI.mean NDVI.CV Int.NDVI EVI.mean EVI.CV mean.sla.wt
1 Awaawapuhi Trail 0.81 7.23 182.9 0.38 12.41 8.649
2 Nualolo Trail 0.82 3.93 184.4 0.40 11.50 11.729
3 Milolii Ridge 0.79 8.05 179.8 0.40 13.71 12.489
4 Waimea Canyon 0.79 10.92 174.7 0.47 19.44 18.908
5 Honouliuli 0.80 9.62 178.3 0.47 21.05 28.624
6 Kaluakauila Gulch 0.66 17.75 149.2 0.43 28.95 8.825
mean.sla.new sum.sla.wt mean.sla.wt.dom mean.sla.dom sum.sla.wt.dom
1 82.22 95.14 12.085 81.17 48.340
2 76.88 93.83 13.670 77.79 68.352
3 76.68 87.42 22.829 86.98 68.487
4 96.90 132.36 9.428 63.52 18.856
5 99.39 143.12 3.288 63.99 6.576
6 98.76 70.60 20.157 71.95 60.472
mean.sub sum.sub sum.sub.wt Precip Temp Species.Richness Density
1 82.41 741.7 71.49 1823 21 21 245
2 75.57 453.4 71.08 1520 22 13 279
3 74.91 449.5 72.58 1314 20 9 313
4 100.38 501.9 114.15 1452 19 10 166
5 83.70 334.8 129.65 1020 21 12 161
6 85.17 596.2 69.95 1047 22 13 326
Basal.Area Canopy.Height NSR Substrate.Age D common not.singleton
1 4.5 7.11 9.52 4.7 0.8871 98 175
2 6.3 8.37 15.38 4.7 0.8318 189 268
3 2.5 8.88 22.22 4.7 0.6793 227 275
4 3.8 9.82 60.00 4.7 0.7876 1 109
5 3.6 9.44 33.33 3.0 0.7085 4 148
6 2.1 5.98 46.15 3.0 0.4328 249 303
pca.structure indiv comp Evenness H. Abun.Slope
1 1.1009 250 -0.8639 0.8142 2.479 -0.09163
2 2.4268 278 -0.7366 0.7860 2.016 -0.16200
3 0.9945 283 -0.9894 0.6881 1.512 -0.23000
4 0.9118 166 -0.3115 0.7691 1.771 -0.20930
5 0.7024 161 0.4703 0.6928 1.722 -0.14550
6 0.2292 326 0.1177 0.4168 1.069 -0.12439
head(slope)
Abun.Slope
1 -0.09163
2 -0.16200
3 -0.23000
4 -0.20930
5 -0.14550
6 -0.12439
lm(env$Abun.Slope ~ env$Species.Richness)
Call:
lm(formula = env$Abun.Slope ~ env$Species.Richness)
Coefficients:
(Intercept) env$Species.Richness
-0.400 0.018
lm(env$Abun.Slope ~ env$NDVI.mean)
Call:
lm(formula = env$Abun.Slope ~ env$NDVI.mean)
Coefficients:
(Intercept) env$NDVI.mean
-0.411 0.291
lm(env$Abun.Slope ~ env$Substrate.Age)
Call:
lm(formula = env$Abun.Slope ~ env$Substrate.Age)
Coefficients:
(Intercept) env$Substrate.Age
-0.2659 0.0206
lm(env$Abun.Slope ~ env$Precip)
Call:
lm(formula = env$Abun.Slope ~ env$Precip)
Coefficients:
(Intercept) env$Precip
-0.401982 0.000169
lm(env$Abun.Slope ~ env$Temp)
Call:
lm(formula = env$Abun.Slope ~ env$Temp)
Coefficients:
(Intercept) env$Temp
-0.09553 -0.00599
mod = lm(env$Abun.Slope ~ env$Species.Richness+env$NDVI.mean+env$Substrate.Age+env$Precip+env$Temp)
adonis(slope~NDVI.mean+Precip+pca.structure+Species.Richness+Substrate.Age, env, perm = 9999, method="bray")
Warning: results may be meaningless because data have negative entries in
method "bray"
Call:
adonis(formula = slope ~ NDVI.mean + Precip + pca.structure + Species.Richness + Substrate.Age, data = env, permutations = 9999, method = "bray")
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
NDVI.mean 1 0 0
Precip 1 0 0
pca.structure 1 0 0
Species.Richness 1 0 0
Substrate.Age 1 0 0
Residuals 8 0 0
Total 13 0
adonis(slope~Precip+Temp+Species.Richness+Substrate.Age, env, perm = 9999, method="bray")
Warning: results may be meaningless because data have negative entries in
method "bray"
Call:
adonis(formula = slope ~ Precip + Temp + Species.Richness + Substrate.Age, data = env, permutations = 9999, method = "bray")
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Precip 1 0 0
Temp 1 0 0
Species.Richness 1 0 0
Substrate.Age 1 0 0
Residuals 9 0 0
Total 13 0
adonis(slope~Species.Richness+Substrate.Age, env, perm = 9999, method="bray")
Warning: results may be meaningless because data have negative entries in
method "bray"
Call:
adonis(formula = slope ~ Species.Richness + Substrate.Age, data = env, permutations = 9999, method = "bray")
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Species.Richness 1 0 0
Substrate.Age 1 0 0
Residuals 11 0 0
Total 13 0