Análises - Projeto Individual
Arthur Barros
10/09/2022
Vamos usar essas pacotes:
library(tidyverse)
library(readxl)
library(vegan)
library(geodist)
library(ecodist)
library(rmarkdown)
library(hillR)Base de dados
O objetivo do trabalho proposto é investigar a montagem de comunidades em fases iniciais de regeneração da Caatinga. A nossa base de dados é:
geral<-read_excel("data_inext_geral.xlsx")
geral %>%
replace(is.na(.),0) %>%
rowwise() %>%
mutate(Anos_2_4C=sum(c(`4_1`, `4_2`, `4_3`, `4_4`)),
Anos_2_5C=sum(c(`5_1`, `5_2`, `5_3`, `5_4`)),
Anos_2_8C=sum(c(`8_1`, `8_2`, `8_3`, `8_4`)),
Anos_2_9C=sum(c(`9_1`, `9_2`, `9_3`, `9_4`))) %>%
select(especie, `4C`, `5C`, `8C`, `9C`, Anos_2_4C, Anos_2_5C, Anos_2_8C, Anos_2_9C) %>%
pivot_longer(!especie, names_to = "parcelas", values_to = "abund") %>%
pivot_wider(names_from = especie, values_from =abund, values_fn = sum)->Comp_geral_0_a_2_anos
paged_table(Comp_geral_0_a_2_anos)As parcelas com somente “C” no final são referentes ao tempo 0 - antes do CQ, e as demais são após. Para cumprir nosso objetivo, vamos primeiro analisar as parcelas composicionalmente.
Análises Prévias
A título de identificar composionalmente as áreas de estudo para identificar se seria possível realizar esse estudo, fiz algumas análises para explorar a composição dos dados. Além disso, como nosso esforço amostral foi menor do que o de Bezerra et al., (2022). Portanto, utilizei o sample coverage acima de 80% como critério para poder generalizar os dados coletados para a parcela inteira.
dados_nmds <- read_excel("dados_nmds.xltx")
dados_nmds %>%
#colnames()
mutate(`?`=NULL,
`(vazio)`=NULL) %>%
filter(bloco!="6" & bloco!= "7" &
tratamento!="controle") %>%
replace(is.na(.),0)-> dados_nmds_01
NMDS2 <- metaMDS(dados_nmds_01[,c(-1:-3)], k=2, distance = "bray")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0
## Run 1 stress 0
## ... Procrustes: rmse 0.2757989 max resid 0.4603016
## Run 2 stress 0
## ... Procrustes: rmse 0.2918649 max resid 0.4976017
## Run 3 stress 0
## ... Procrustes: rmse 0.2123653 max resid 0.2705756
## Run 4 stress 0
## ... Procrustes: rmse 0.08490994 max resid 0.1201544
## Run 5 stress 0
## ... Procrustes: rmse 0.2417748 max resid 0.3985787
## Run 6 stress 8.670322e-05
## ... Procrustes: rmse 0.3468156 max resid 0.5638679
## Run 7 stress 0
## ... Procrustes: rmse 0.09727989 max resid 0.1425041
## Run 8 stress 0
## ... Procrustes: rmse 0.174533 max resid 0.2771672
## Run 9 stress 0
## ... Procrustes: rmse 0.2373527 max resid 0.3917607
## Run 10 stress 0
## ... Procrustes: rmse 0.1534266 max resid 0.218042
## Run 11 stress 0
## ... Procrustes: rmse 0.3386142 max resid 0.5521031
## Run 12 stress 0
## ... Procrustes: rmse 0.2848592 max resid 0.3916085
## Run 13 stress 0
## ... Procrustes: rmse 0.2336676 max resid 0.3734939
## Run 14 stress 0
## ... Procrustes: rmse 0.2662608 max resid 0.4447605
## Run 15 stress 0
## ... Procrustes: rmse 0.1323121 max resid 0.1847156
## Run 16 stress 0
## ... Procrustes: rmse 0.2356345 max resid 0.3012682
## Run 17 stress 0
## ... Procrustes: rmse 0.2139328 max resid 0.3392743
## Run 18 stress 0
## ... Procrustes: rmse 0.2438955 max resid 0.3974282
## Run 19 stress 0
## ... Procrustes: rmse 0.1768634 max resid 0.2778984
## Run 20 stress 0
## ... Procrustes: rmse 0.1357109 max resid 0.1997182
## *** No convergence -- monoMDS stopping criteria:
## 20: stress < smin
NMDS_data<- data.frame(dados_nmds_01$bloco, dados_nmds_01$parcela, dados_nmds_01$tratamento, NMDS2$points)
#NMDS_data %>%
# colnames()
NMDS_data <- rename(NMDS_data, "bloco"=dados_nmds_01.bloco,
"parcela"=dados_nmds_01.parcela,
"tratamento"=dados_nmds_01.tratamento,
"MDS1"=MDS1, "MDS2"=MDS2)
NMDS_data %>%
filter(parcela=="B") %>%
mutate(bloco=as.factor(bloco)) %>%
ggplot(aes(MDS1, MDS2, color=bloco))+
geom_point(size=3)+
scale_color_discrete(name="Blocos",
labels=c("4", "5", "6", "7", "8", "9")) %>%
labs(caption = NMDS2$stress)
# testar a cobertura das nossas amostraas
library(entropart)
Mc_PI<-MetaCommunity(t(Comp_geral_0_a_2_anos[,-1]))
Mc_PI$SampleCoverage.communities
## P1 P2 P3 P4 P5 P6 P7 P8
## 0.9961240 0.9899363 0.9876114 0.9923077 0.9863908 0.9815756 0.9794368 0.9791130Análises Exploratórias
Calculamos a diversidade taxonômica das nossas áreas usando hills
hill_taxa_parti(Comp_geral_0_a_2_anos[,-1], q = 0)->Div0
paged_table(Div0)
hill_taxa_parti(Comp_geral_0_a_2_anos[,-1], q = 1)->Div1
paged_table(Div1)
hill_taxa_parti(Comp_geral_0_a_2_anos[,-1], q = 2)->Div2
paged_table(Div2)
# Don't run
#hill_taxa(Comp_geral_0_a_2_anos[,-1], q = 0)->xc
#hill_taxa(Comp_geral_0_a_2_anos[,-1], q = 1)->xq1
#hill_taxa(Comp_geral_0_a_2_anos[,-1], q = 2)->xq2
#data.frame(xc, xq1, xq2) %>%
# rename(q0="xc", q1="xq1", q2="xq2") %>%
# mutate(site=Comp_geral_0_a_2_anos$parcelas,
# yr=as.factor(c(rep(0, 4), rep(2, 4))))->testando
library(iNEXT)
Comp_geral_0_a_2_anos %>%
pivot_longer(!parcelas, names_to = "parcelas", values_to = "abund",
names_repair="unique") %>%
rename("parcelas"=parcelas...1, "species"=parcelas...2) %>%
pivot_wider(names_from = parcelas, values_from =abund, values_fn = sum) %>%
rename("Ano0_4C"=`4C`, "Ano0_5C"=`5C`,
"Ano0_8C"=`8C`, "Ano0_9C"=`9C`)->inext_data
Ano0_4C <- c(105, sort(inext_data$Ano0_4C[inext_data$Ano0_4C>0], decreasing = TRUE))
Ano0_5C <- c(105, sort(inext_data$Ano0_5C[inext_data$Ano0_5C>0], decreasing = TRUE))
Ano0_8C <- c(105, sort(inext_data$Ano0_8C[inext_data$Ano0_8C>0], decreasing = TRUE))
Ano0_9C <- c(105, sort(inext_data$Ano0_9C[inext_data$Ano0_9C>0], decreasing = TRUE))
list_inext <- list(
Ano0_4C = Ano0_4C,
Ano0_5C = Ano0_5C,
Ano0_8C = Ano0_8C,
Ano0_9C = Ano0_9C
)
iNEXT(x=list_inext, q=c(0, 1, 2), datatype="abundance")->inext_result
inext_result[["iNextEst"]][["Ano0_4C"]]->com_Ano0_4C
com_Ano0_4C %>%
mutate(site=rep("Ano0_4C", 120),
year=rep("0", 120))->com_Ano0_4C
inext_result[["iNextEst"]][["Ano0_5C"]]->com_Ano0_5C
com_Ano0_5C %>%
mutate(site=rep("Ano0_5C", 120),
year=rep("0", 120))->com_Ano0_5C
inext_result[["iNextEst"]][["Ano0_8C"]]->com_Ano0_8C
com_Ano0_8C %>%
mutate(site=rep("Ano0_8C", 120),
year=rep("0", 120))->com_Ano0_8C
inext_result[["iNextEst"]][["Ano0_9C"]]->com_Ano0_9C
com_Ano0_9C %>%
mutate(site=rep("Ano0_9C", 120),
year=rep("0", 120))->com_Ano0_9C
full_join(com_Ano0_4C, com_Ano0_5C) %>%
full_join(com_Ano0_8C) %>%
full_join(com_Ano0_9C) %>%
filter(method=="interpolated") %>%
select(year, site, order, qD) %>%
mutate(order=as.factor(order)) -> Ano0_diversity
Ano2_4C <- c(105, sort(inext_data$Anos_2_4C[inext_data$Anos_2_4C>0], decreasing = TRUE))
Ano2_5C <- c(105, sort(inext_data$Anos_2_5C[inext_data$Anos_2_5C>0], decreasing = TRUE))
Ano2_8C <- c(105, sort(inext_data$Anos_2_8C[inext_data$Anos_2_8C>0], decreasing = TRUE))
Ano2_9C <- c(105, sort(inext_data$Anos_2_9C[inext_data$Anos_2_9C>0], decreasing = TRUE))
list_inext_ano2 <- list(
Ano2_4C = Ano2_4C,
Ano2_5C = Ano2_5C,
Ano2_8C = Ano2_8C,
Ano2_9C = Ano2_9C
)
iNEXT(x=list_inext_ano2, q=c(0, 1, 2), datatype="abundance")->inext_result_ano2
inext_result_ano2[["iNextEst"]][["Ano2_4C"]]->com_Ano2_4C
com_Ano2_4C %>%
mutate(site=rep("Ano2_4C", 120),
year=rep("2", 120))->com_Ano2_4C
inext_result_ano2[["iNextEst"]][["Ano2_5C"]]->com_Ano2_5C
com_Ano2_5C %>%
mutate(site=rep("Ano2_5C", 120),
year=rep("2", 120))->com_Ano2_5C
inext_result_ano2[["iNextEst"]][["Ano2_8C"]]->com_Ano2_8C
com_Ano2_8C %>%
mutate(site=rep("Ano2_8C", 120),
year=rep("2", 120))->com_Ano2_8C
inext_result_ano2[["iNextEst"]][["Ano2_9C"]]->com_Ano2_9C
com_Ano2_9C %>%
mutate(site=rep("Ano2_9C", 120),
year=rep("2", 120))->com_Ano2_9C
full_join(com_Ano2_4C, com_Ano2_5C) %>%
full_join(com_Ano2_8C) %>%
full_join(com_Ano2_9C) %>%
filter(method=="interpolated") %>%
select(year, site, order, qD) %>%
mutate(order=as.factor(order)) ->Ano2_diversity
full_join(Ano0_diversity, Ano2_diversity)->div_interp
div_interp %>%
#str()
mutate(year=as.factor(year),
site=as.factor(site)) %>%
#glimpse()
#head()
pivot_wider(names_from = order, values_from =qD) %>%
rename("div0"=`0`,"div1"=`1`,"div2"=`2`) %>%
unnest()->data_modelos
library(see)
library(performance)
glm(div0~year, data = data_modelos, family = "gaussian")->glm0
summary(glm0)
##
## Call:
## glm(formula = div0 ~ year, family = "gaussian", data = data_modelos)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -22.240 -3.017 1.150 4.406 14.749
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 23.2401 0.8405 27.650 < 2e-16 ***
## year2 -3.2341 1.1886 -2.721 0.00728 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 53.68951)
##
## Null deviance: 8450.9 on 151 degrees of freedom
## Residual deviance: 8053.4 on 150 degrees of freedom
## AIC: 1040.8
##
## Number of Fisher Scoring iterations: 2
check_model(glm0)
glm(div1~year, data = data_modelos, family = "gaussian")->glm1
summary(glm1)
##
## Call:
## glm(formula = div1 ~ year, family = "gaussian", data = data_modelos)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -8.6201 -0.8809 -0.0306 2.0284 2.9389
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 8.2011 0.2758 29.737 < 2e-16 ***
## year2 1.4190 0.3900 3.638 0.000377 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 5.780288)
##
## Null deviance: 943.56 on 151 degrees of freedom
## Residual deviance: 867.04 on 150 degrees of freedom
## AIC: 702.02
##
## Number of Fisher Scoring iterations: 2
check_model(glm1)
glm(div2~year, data = data_modelos, family = "gaussian")->glm2
summary(glm2)
##
## Call:
## glm(formula = div2 ~ year, family = "gaussian", data = data_modelos)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -5.5452 -0.8135 -0.2119 1.0168 2.1338
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4.9499 0.1872 26.445 < 2e-16 ***
## year2 1.5953 0.2647 6.027 1.24e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 2.6627)
##
## Null deviance: 496.12 on 151 degrees of freedom
## Residual deviance: 399.40 on 150 degrees of freedom
## AIC: 584.2
##
## Number of Fisher Scoring iterations: 2
check_model(glm2)
Análises Estatísticas
Reinventariamos as parcelas de CQ de Bezerra et al., (2022) - 4, 5, 8 e 9 após dois anos do distúrbio. Ou seja, em regeneração. E comparamos a composição entre ambas.
dist_geral_0_a_2_anos<-vegdist(Comp_geral_0_a_2_anos[,-1], method = "bray", binary = F)
group<- c(rep('Controle', 4), rep('Após 2 anos', 4))
permanova<-adonis(dist_geral_0_a_2_anos~group, permutations = 10000, pairwise=T)
permanova
##
## Call:
## adonis(formula = dist_geral_0_a_2_anos ~ group, permutations = 10000, pairwise = T)
##
## Permutation: free
## Number of permutations: 10000
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## group 1 0.69552 0.69552 3.0348 0.3359 0.0302 *
## Residuals 6 1.37509 0.22918 0.6641
## Total 7 2.07061 1.0000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
beta_disp_data <- betadisper(dist_geral_0_a_2_anos, group, type = "centroid")
beta_disp_data
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist_geral_0_a_2_anos, group = group, type =
## "centroid")
##
## No. of Positive Eigenvalues: 7
## No. of Negative Eigenvalues: 0
##
## Average distance to centroid:
## Após 2 anos Controle
## 0.4085 0.3892
##
## Eigenvalues for PCoA axes:
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7
## 0.782681 0.463281 0.329519 0.263944 0.160562 0.064754 0.005865
permutest(beta_disp_data, permutations = 999, pairwise = TRUE)
##
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
##
## Response: Distances
## Df Sum Sq Mean Sq F N.Perm Pr(>F)
## Groups 1 0.00074 0.000740 0.0437 999 0.857
## Residuals 6 0.10159 0.016932
##
## Pairwise comparisons:
## (Observed p-value below diagonal, permuted p-value above diagonal)
## Após 2 anos Controle
## Após 2 anos 0.865
## Controle 0.84132
plot(beta_disp_data, hull = TRUE, ellipse = F,
xlab="PCoA1", ylab="PCoA2", main = " ")
#points(beta_disp_data$centroids[,1:2], pch=20, cex=2, col=1:2)
boxplot(beta_disp_data, ylab = "Distância para o centroide", xlab="Parcelas")
beta_disp_data$distances
## [1] 0.3213738 0.2595527 0.3650654 0.6110029 0.3812003 0.2782095 0.4755027
## [8] 0.4990239Com o intuito de entender em qual direção a compoisção das comunidades estão indo considerando sua (dis)similaridade inicial, utilizei a análise procruste e fiz um teste de permutação
Comp_geral_0_a_2_anos %>%
filter(parcelas==c("4C", "5C", "8C", "9C"))->ano_0
dist_ano_0<-vegdist(ano_0[,-1], method = "bray", binary = F)
Comp_geral_0_a_2_anos %>%
filter(parcelas==c("Anos_2_4C", "Anos_2_5C", "Anos_2_8C", "Anos_2_9C"))->ano_2
dist_ano_2<-vegdist(ano_2[,-1], method = "bray", binary = F)
nmds_0<- metaMDS(dist_ano_0, trymax = 1000)
## Run 0 stress 0
## Run 1 stress 0
## ... Procrustes: rmse 0.1074605 max resid 0.1794326
## Run 2 stress 0
## ... Procrustes: rmse 0.1185455 max resid 0.1625193
## Run 3 stress 7.62023e-05
## ... Procrustes: rmse 0.1958867 max resid 0.3238776
## Run 4 stress 0
## ... Procrustes: rmse 0.05228468 max resid 0.08066166
## Run 5 stress 0
## ... Procrustes: rmse 0.109296 max resid 0.1503559
## Run 6 stress 0
## ... Procrustes: rmse 0.1684064 max resid 0.2873286
## Run 7 stress 0
## ... Procrustes: rmse 0.1624985 max resid 0.2209921
## Run 8 stress 0
## ... Procrustes: rmse 0.05173622 max resid 0.0785351
## Run 9 stress 0
## ... Procrustes: rmse 0.1246087 max resid 0.1559198
## Run 10 stress 0
## ... Procrustes: rmse 0.1140922 max resid 0.1806846
## Run 11 stress 0
## ... Procrustes: rmse 0.0931171 max resid 0.1118254
## Run 12 stress 0
## ... Procrustes: rmse 0.1068038 max resid 0.1544107
## Run 13 stress 0
## ... Procrustes: rmse 0.2321341 max resid 0.2772565
## Run 14 stress 0
## ... Procrustes: rmse 0.1814704 max resid 0.3129956
## Run 15 stress 0
## ... Procrustes: rmse 0.1827635 max resid 0.3140131
## Run 16 stress 0
## ... Procrustes: rmse 0.08501908 max resid 0.1272748
## Run 17 stress 8.969486e-05
## ... Procrustes: rmse 0.178856 max resid 0.2942988
## Run 18 stress 0
## ... Procrustes: rmse 0.03625508 max resid 0.04819846
## Run 19 stress 0
## ... Procrustes: rmse 0.1652893 max resid 0.261917
## Run 20 stress 9.82764e-05
## ... Procrustes: rmse 0.1964437 max resid 0.3337713
## Run 21 stress 0
## ... Procrustes: rmse 0.09249173 max resid 0.1264143
## Run 22 stress 0
## ... Procrustes: rmse 0.09551039 max resid 0.1411489
## Run 23 stress 0
## ... Procrustes: rmse 0.1773257 max resid 0.2086973
## Run 24 stress 0
## ... Procrustes: rmse 0.1186636 max resid 0.1934278
## Run 25 stress 0
## ... Procrustes: rmse 0.1379946 max resid 0.1901905
## Run 26 stress 0
## ... Procrustes: rmse 0.1653415 max resid 0.2591369
## Run 27 stress 0
## ... Procrustes: rmse 0.06620031 max resid 0.09380126
## Run 28 stress 0
## ... Procrustes: rmse 0.09435951 max resid 0.1414318
## Run 29 stress 0
## ... Procrustes: rmse 0.2557863 max resid 0.3244601
## Run 30 stress 0
## ... Procrustes: rmse 0.1776251 max resid 0.2842381
## Run 31 stress 0
## ... Procrustes: rmse 0.08095828 max resid 0.1177775
## Run 32 stress 0
## ... Procrustes: rmse 0.1193847 max resid 0.169996
## Run 33 stress 9.851182e-05
## ... Procrustes: rmse 0.1804999 max resid 0.2741336
## Run 34 stress 0
## ... Procrustes: rmse 0.1853188 max resid 0.294299
## Run 35 stress 0
## ... Procrustes: rmse 0.155317 max resid 0.2169893
## Run 36 stress 0
## ... Procrustes: rmse 0.1905336 max resid 0.2492254
## Run 37 stress 0
## ... Procrustes: rmse 0.2625223 max resid 0.32063
## Run 38 stress 0
## ... Procrustes: rmse 0.1209292 max resid 0.1876638
## Run 39 stress 8.045562e-05
## ... Procrustes: rmse 0.2101744 max resid 0.3565697
## Run 40 stress 0
## ... Procrustes: rmse 0.008296387 max resid 0.01064712
## Run 41 stress 0
## ... Procrustes: rmse 0.2343557 max resid 0.2872688
## Run 42 stress 0
## ... Procrustes: rmse 0.178198 max resid 0.2806533
## Run 43 stress 0
## ... Procrustes: rmse 0.08955994 max resid 0.1285858
## Run 44 stress 0
## ... Procrustes: rmse 0.1979979 max resid 0.2458895
## Run 45 stress 0
## ... Procrustes: rmse 0.1133959 max resid 0.1901531
## Run 46 stress 0
## ... Procrustes: rmse 0.1776495 max resid 0.2970633
## Run 47 stress 0
## ... Procrustes: rmse 0.121691 max resid 0.1641822
## Run 48 stress 0
## ... Procrustes: rmse 0.1079861 max resid 0.1373512
## Run 49 stress 0
## ... Procrustes: rmse 0.06784239 max resid 0.09351869
## Run 50 stress 8.386076e-05
## ... Procrustes: rmse 0.207499 max resid 0.3524288
## Run 51 stress 0
## ... Procrustes: rmse 0.1244201 max resid 0.1703134
## Run 52 stress 0
## ... Procrustes: rmse 0.1436562 max resid 0.2399449
## Run 53 stress 0
## ... Procrustes: rmse 0.1934067 max resid 0.3274486
## Run 54 stress 6.199671e-05
## ... Procrustes: rmse 0.2086058 max resid 0.3552815
## Run 55 stress 0
## ... Procrustes: rmse 0.08907276 max resid 0.1186157
## Run 56 stress 0
## ... Procrustes: rmse 0.02416039 max resid 0.03561097
## Run 57 stress 0
## ... Procrustes: rmse 0.1076634 max resid 0.1614127
## Run 58 stress 0
## ... Procrustes: rmse 0.1112955 max resid 0.1557655
## Run 59 stress 0
## ... Procrustes: rmse 0.1932159 max resid 0.324431
## Run 60 stress 0
## ... Procrustes: rmse 0.08165017 max resid 0.1125655
## Run 61 stress 0
## ... Procrustes: rmse 0.1300655 max resid 0.1838735
## Run 62 stress 0
## ... Procrustes: rmse 0.07156856 max resid 0.1185204
## Run 63 stress 0
## ... Procrustes: rmse 0.1771945 max resid 0.1931521
## Run 64 stress 0
## ... Procrustes: rmse 0.0855544 max resid 0.1194953
## Run 65 stress 0
## ... Procrustes: rmse 0.05858111 max resid 0.09745135
## Run 66 stress 3.518934e-05
## ... Procrustes: rmse 0.1783995 max resid 0.2652453
## Run 67 stress 0
## ... Procrustes: rmse 0.1206426 max resid 0.1669646
## Run 68 stress 0
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## Run 69 stress 0
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## Run 70 stress 0
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## Run 71 stress 0
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## Run 72 stress 0
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## Run 73 stress 0
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## Run 74 stress 0
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## Run 75 stress 0
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## Run 76 stress 0
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## Run 77 stress 8.213619e-05
## ... Procrustes: rmse 0.1749898 max resid 0.2281657
## Run 78 stress 0
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## Run 79 stress 0
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## Run 80 stress 0
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## Run 81 stress 0
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## Run 82 stress 0
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## Run 83 stress 0
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## Run 84 stress 0
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## Run 85 stress 0
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## Run 86 stress 0
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## Run 87 stress 0
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## Run 88 stress 0
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## Run 89 stress 0
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## Run 90 stress 0
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## Run 91 stress 0
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## Run 92 stress 0
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## Run 93 stress 0
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## Run 94 stress 0
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## Run 95 stress 0
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## Run 96 stress 0
## ... Procrustes: rmse 0.1968524 max resid 0.3321646
## Run 97 stress 8.419512e-05
## ... Procrustes: rmse 0.1956631 max resid 0.3286516
## Run 98 stress 0
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## Run 99 stress 0
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## Run 100 stress 0
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## Run 101 stress 0
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## Run 102 stress 0
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## Run 103 stress 0
## ... Procrustes: rmse 0.08848936 max resid 0.1119793
## Run 104 stress 0
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## Run 105 stress 0
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## Run 106 stress 0
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## Run 107 stress 8.550826e-05
## ... Procrustes: rmse 0.2122989 max resid 0.3602434
## Run 108 stress 0
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## Run 109 stress 0
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## Run 110 stress 0
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## Run 111 stress 0
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## Run 112 stress 0
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## Run 113 stress 0
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## Run 114 stress 0
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## Run 115 stress 0
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## Run 116 stress 0
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## Run 117 stress 0
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## Run 118 stress 0
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## Run 119 stress 0
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## Run 120 stress 0
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## Run 121 stress 0
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## Run 122 stress 0
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## Run 123 stress 0
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## Run 124 stress 0
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## Run 125 stress 0
## ... Procrustes: rmse 0.08677814 max resid 0.1196839
## Run 126 stress 8.088044e-05
## ... Procrustes: rmse 0.1996356 max resid 0.3330351
## Run 127 stress 0
## ... Procrustes: rmse 0.1695592 max resid 0.2893127
## Run 128 stress 0
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## Run 129 stress 0
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## Run 130 stress 0
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## Run 131 stress 0
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## Run 132 stress 0
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## Run 133 stress 1.389619e-05
## ... Procrustes: rmse 0.2001437 max resid 0.3152675
## Run 134 stress 0
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## Run 135 stress 0
## ... Procrustes: rmse 0.1359388 max resid 0.1903313
## Run 136 stress 4.163063e-05
## ... Procrustes: rmse 0.2288478 max resid 0.278221
## Run 137 stress 0
## ... Procrustes: rmse 0.1114494 max resid 0.1392633
## Run 138 stress 0
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## Run 139 stress 0
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## Run 140 stress 8.104635e-05
## ... Procrustes: rmse 0.2084406 max resid 0.3539322
## Run 141 stress 0
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## Run 142 stress 0
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## Run 143 stress 0
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## Run 144 stress 0
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## Run 145 stress 0
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## Run 146 stress 0
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## Run 147 stress 0
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## Run 148 stress 0
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## Run 149 stress 0
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## Run 150 stress 0
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## Run 151 stress 0
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## Run 152 stress 0
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## Run 153 stress 0
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## Run 154 stress 0
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## Run 155 stress 0
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## Run 156 stress 0
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## Run 157 stress 0
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## Run 158 stress 0
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## Run 159 stress 0
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## Run 160 stress 0
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## Run 161 stress 0
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## Run 162 stress 0
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## Run 163 stress 0
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## Run 164 stress 0
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## Run 165 stress 0
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## Run 166 stress 0
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## Run 167 stress 9.544079e-05
## ... Procrustes: rmse 0.1769447 max resid 0.2541542
## Run 168 stress 0
## ... Procrustes: rmse 0.1441879 max resid 0.2471662
## Run 169 stress 7.691673e-05
## ... Procrustes: rmse 0.194462 max resid 0.3202064
## Run 170 stress 0
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## Run 171 stress 0
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## Run 172 stress 0
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## Run 173 stress 0
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## Run 174 stress 0
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## Run 175 stress 0
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## Run 176 stress 0
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## Run 177 stress 0
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## Run 178 stress 0
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## Run 179 stress 0
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## Run 180 stress 0
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## Run 181 stress 0
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## Run 182 stress 0
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## Run 183 stress 0
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## Run 184 stress 0
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## Run 185 stress 0
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## Run 186 stress 0
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## Run 187 stress 0
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## Run 188 stress 0
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## Run 189 stress 0
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## Run 190 stress 0
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## Run 191 stress 0
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## Run 192 stress 0
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## Run 193 stress 0
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## Run 194 stress 8.740858e-05
## ... Procrustes: rmse 0.1346688 max resid 0.1657225
## Run 195 stress 0
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## Run 196 stress 0
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## Run 197 stress 0
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## Run 198 stress 0
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## Run 199 stress 0
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## Run 200 stress 0
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## Run 201 stress 0
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## Run 202 stress 0
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## Run 203 stress 0
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## Run 204 stress 0
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## Run 205 stress 0
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## Run 206 stress 6.132916e-05
## ... Procrustes: rmse 0.1917775 max resid 0.3135694
## Run 207 stress 0
## ... Procrustes: rmse 0.1231357 max resid 0.1657643
## Run 208 stress 5.491418e-05
## ... Procrustes: rmse 0.1807396 max resid 0.307648
## Run 209 stress 0
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## Run 210 stress 0
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## Run 211 stress 0
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## Run 212 stress 0
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## Run 213 stress 0
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## Run 214 stress 0
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## Run 215 stress 0
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## Run 216 stress 0
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## Run 217 stress 0
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## Run 218 stress 0
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## Run 219 stress 7.642093e-05
## ... Procrustes: rmse 0.1896394 max resid 0.3181286
## Run 220 stress 0
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## Run 221 stress 0
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## Run 222 stress 0
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## Run 223 stress 0
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## Run 224 stress 0
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## Run 225 stress 0
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## Run 226 stress 0
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## Run 227 stress 0
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## Run 228 stress 0
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## Run 229 stress 0
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## Run 230 stress 0
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## Run 231 stress 0
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## Run 232 stress 0
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## Run 233 stress 0
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## Run 234 stress 0
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## Run 235 stress 0
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## Run 236 stress 5.357073e-05
## ... Procrustes: rmse 0.1952463 max resid 0.3342447
## Run 237 stress 0
## ... Procrustes: rmse 0.1923054 max resid 0.3061805
## Run 238 stress 0
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## Run 239 stress 0
## ... Procrustes: rmse 0.07949875 max resid 0.1094151
## Run 240 stress 0
## ... Procrustes: rmse 0.2016538 max resid 0.2738107
## Run 241 stress 8.86414e-05
## ... Procrustes: rmse 0.2041202 max resid 0.3479794
## Run 242 stress 0
## ... Procrustes: rmse 0.08958457 max resid 0.1406113
## Run 243 stress 0
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## Run 244 stress 0
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## Run 245 stress 0
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## Run 246 stress 0
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## Run 247 stress 0
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## Run 248 stress 0
## ... Procrustes: rmse 0.1016355 max resid 0.1467215
## Run 249 stress 0
## ... Procrustes: rmse 0.213194 max resid 0.296303
## Run 250 stress 0
## ... Procrustes: rmse 0.1500627 max resid 0.2400592
## Run 251 stress 0
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## Run 252 stress 0
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## Run 253 stress 0
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## Run 254 stress 0
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## Run 255 stress 0
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## Run 256 stress 8.18367e-05
## ... Procrustes: rmse 0.1886307 max resid 0.2889958
## Run 257 stress 0
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## Run 258 stress 0
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## Run 259 stress 0
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## Run 260 stress 0
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## Run 261 stress 0
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## Run 262 stress 0
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## Run 263 stress 0
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## Run 264 stress 0
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## Run 265 stress 0
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## Run 266 stress 0
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## Run 267 stress 0
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## Run 268 stress 0
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## Run 269 stress 0
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## Run 270 stress 0
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## Run 271 stress 0
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## Run 272 stress 0
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## Run 273 stress 0
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## Run 274 stress 0
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## Run 275 stress 0
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## Run 276 stress 0
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## Run 277 stress 0
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## Run 278 stress 0
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## Run 279 stress 0
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## Run 280 stress 0
## ... Procrustes: rmse 0.1217213 max resid 0.1609152
## Run 281 stress 6.332277e-05
## ... Procrustes: rmse 0.1230189 max resid 0.194346
## Run 282 stress 0
## ... Procrustes: rmse 0.2274039 max resid 0.2858565
## Run 283 stress 0
## ... Procrustes: rmse 0.1441118 max resid 0.2036282
## Run 284 stress 3.644736e-05
## ... Procrustes: rmse 0.2111511 max resid 0.3581346
## Run 285 stress 0
## ... Procrustes: rmse 0.08775219 max resid 0.1424212
## Run 286 stress 0
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## Run 287 stress 0
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## Run 288 stress 0
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## Run 289 stress 0
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## Run 290 stress 0
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## Run 291 stress 0
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## Run 292 stress 0
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## Run 293 stress 0
## ... Procrustes: rmse 0.09130739 max resid 0.1240604
## Run 294 stress 0
## ... Procrustes: rmse 0.1124021 max resid 0.1506135
## Run 295 stress 7.249731e-05
## ... Procrustes: rmse 0.1947423 max resid 0.3283804
## Run 296 stress 0
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## Run 297 stress 0
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## Run 298 stress 0
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## Run 299 stress 0
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## Run 300 stress 0
## ... Procrustes: rmse 0.1163356 max resid 0.1608127
## Run 301 stress 8.514694e-05
## ... Procrustes: rmse 0.2124826 max resid 0.3605826
## Run 302 stress 0
## ... Procrustes: rmse 0.1326271 max resid 0.1787376
## Run 303 stress 0
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## Run 304 stress 0
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## Run 305 stress 0
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## Run 306 stress 0
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## Run 307 stress 0
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## Run 308 stress 0
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## Run 309 stress 0
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## Run 310 stress 0
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## Run 311 stress 0
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## Run 312 stress 0
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## Run 313 stress 0
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## Run 314 stress 0
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## Run 315 stress 0
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## Run 316 stress 6.834323e-05
## ... Procrustes: rmse 0.1991392 max resid 0.3357647
## Run 317 stress 0
## ... Procrustes: rmse 0.06605116 max resid 0.08911046
## Run 318 stress 0
## ... Procrustes: rmse 0.1337595 max resid 0.1819636
## Run 319 stress 8.553715e-05
## ... Procrustes: rmse 0.2062394 max resid 0.3478129
## Run 320 stress 0
## ... Procrustes: rmse 0.1846948 max resid 0.2545051
## Run 321 stress 0
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## Run 322 stress 0
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## Run 323 stress 0
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## Run 324 stress 0
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## Run 325 stress 0
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## Run 326 stress 0
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## Run 327 stress 0
## ... Procrustes: rmse 0.08663101 max resid 0.118708
## Run 328 stress 0
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## Run 329 stress 0
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## Run 330 stress 0
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## Run 331 stress 9.989655e-05
## ... Procrustes: rmse 0.2028498 max resid 0.3406068
## Run 332 stress 0
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## Run 333 stress 0
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## Run 334 stress 0
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## Run 335 stress 0
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## Run 336 stress 0
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## Run 337 stress 0
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## Run 338 stress 0
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## Run 339 stress 0
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## Run 340 stress 0
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## Run 341 stress 0
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## Run 342 stress 0
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## Run 343 stress 0
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## Run 344 stress 0
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## Run 345 stress 8.298919e-05
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## Run 346 stress 7.780507e-05
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## Run 347 stress 0
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## Run 348 stress 0
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## Run 349 stress 0
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## Run 350 stress 0
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## Run 351 stress 0
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## Run 353 stress 0
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## Run 354 stress 8.174369e-05
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## Run 355 stress 0
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## Run 357 stress 0
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## Run 358 stress 0
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## Run 360 stress 0
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## Run 361 stress 0
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## Run 362 stress 0
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## Run 363 stress 9.112699e-05
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## Run 364 stress 0
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## Run 365 stress 0
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## Run 366 stress 0
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## Run 367 stress 9.742467e-05
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## Run 368 stress 0
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## Run 369 stress 0
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## Run 370 stress 0
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## Run 371 stress 0
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## Run 372 stress 0
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## Run 373 stress 8.585526e-05
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## Run 374 stress 0
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## Run 375 stress 0
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## Run 376 stress 0
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## Run 377 stress 0
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## Run 378 stress 0
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## Run 379 stress 0
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## Run 380 stress 0
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## Run 381 stress 0
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## Run 382 stress 0
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## Run 383 stress 0
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## Run 384 stress 0
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## Run 385 stress 7.54964e-05
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## Run 386 stress 0
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## Run 387 stress 8.409167e-05
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## Run 388 stress 0
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## Run 389 stress 0
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## Run 390 stress 0
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## Run 391 stress 0
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## Run 392 stress 0
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## Run 393 stress 0
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## Run 394 stress 0
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## Run 395 stress 0
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## Run 396 stress 0
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## Run 397 stress 0
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## Run 398 stress 0
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## Run 399 stress 0
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## Run 400 stress 0
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## Run 401 stress 0
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## Run 403 stress 0
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## Run 404 stress 0
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## Run 407 stress 0
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## Run 408 stress 0
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## Run 416 stress 0
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## Run 417 stress 8.489759e-05
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## Run 418 stress 0
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## Run 420 stress 0
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## Run 423 stress 0
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## Run 434 stress 0
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## Run 435 stress 6.79907e-05
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## Run 440 stress 0
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## Run 441 stress 8.540475e-05
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## Run 442 stress 0
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## Run 443 stress 7.434205e-05
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## Run 444 stress 8.118809e-05
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## Run 445 stress 0
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## Run 446 stress 9.279126e-05
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## Run 458 stress 0
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## Run 459 stress 8.542939e-05
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## Run 464 stress 9.3919e-05
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## Run 473 stress 8.544146e-05
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## Run 478 stress 9.512417e-05
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## Run 491 stress 8.861911e-05
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## Run 493 stress 8.593622e-05
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## Run 512 stress 9.168393e-05
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## Run 514 stress 0
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## Run 600 stress 0
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## Run 601 stress 7.18359e-05
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## Run 602 stress 0
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## Run 603 stress 3.011814e-05
## ... Procrustes: rmse 0.1901444 max resid 0.3213848
## Run 604 stress 0
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## Run 605 stress 0
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## Run 606 stress 0
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## Run 607 stress 0
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## Run 608 stress 0
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## Run 609 stress 0
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## Run 610 stress 0
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## Run 611 stress 0
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## Run 612 stress 0
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## Run 613 stress 0
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## Run 614 stress 0
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## Run 615 stress 0
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## Run 616 stress 0
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## Run 617 stress 0
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## Run 618 stress 0
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## Run 619 stress 0
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## Run 620 stress 0
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## Run 621 stress 0
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## Run 622 stress 8.43731e-05
## ... Procrustes: rmse 0.196002 max resid 0.3355929
## Run 623 stress 0
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## Run 624 stress 0
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## Run 625 stress 7.681548e-05
## ... Procrustes: rmse 0.2050153 max resid 0.3455272
## Run 626 stress 0
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## Run 627 stress 0
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## Run 628 stress 0
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## Run 629 stress 0
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## Run 630 stress 0
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## Run 631 stress 0
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## Run 632 stress 0
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## Run 633 stress 0
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## Run 634 stress 0
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## Run 635 stress 0
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## Run 636 stress 0
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## Run 637 stress 9.3397e-05
## ... Procrustes: rmse 0.2009695 max resid 0.3367649
## Run 638 stress 0
## ... Procrustes: rmse 0.07025718 max resid 0.09979141
## Run 639 stress 0
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## Run 640 stress 0
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## Run 641 stress 0
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## Run 642 stress 0
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## Run 643 stress 0
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## Run 644 stress 0
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## Run 645 stress 0
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## Run 646 stress 0
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## Run 647 stress 0
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## Run 648 stress 8.49803e-05
## ... Procrustes: rmse 0.213496 max resid 0.3625628
## Run 649 stress 0
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## Run 650 stress 0
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## Run 651 stress 0
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## Run 652 stress 0
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## Run 653 stress 0
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## Run 654 stress 0
## ... Procrustes: rmse 0.08516655 max resid 0.1210262
## Run 655 stress 7.959653e-05
## ... Procrustes: rmse 0.2033883 max resid 0.344751
## Run 656 stress 0
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## Run 657 stress 0
## ... Procrustes: rmse 0.1805289 max resid 0.2261359
## Run 658 stress 3.600168e-07
## ... Procrustes: rmse 0.1567629 max resid 0.1877419
## Run 659 stress 0
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## Run 660 stress 0
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## Run 661 stress 0
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## Run 662 stress 0
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## Run 663 stress 0
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## Run 664 stress 0
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## Run 665 stress 0
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## Run 666 stress 0
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## Run 667 stress 0
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## Run 668 stress 0
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## Run 669 stress 0
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## Run 670 stress 0
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## Run 671 stress 0
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## Run 672 stress 0
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## Run 673 stress 0
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## Run 674 stress 0
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## Run 675 stress 0
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## Run 676 stress 0
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## Run 677 stress 0
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## Run 678 stress 0
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## Run 679 stress 0
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## Run 680 stress 0
## ... Procrustes: rmse 0.0906371 max resid 0.1330991
## Run 681 stress 7.784548e-05
## ... Procrustes: rmse 0.2127369 max resid 0.3610813
## Run 682 stress 0
## ... Procrustes: rmse 0.0504719 max resid 0.06625186
## Run 683 stress 0
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## Run 684 stress 0
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## Run 685 stress 0
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## Run 687 stress 0
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## Run 688 stress 0
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## Run 689 stress 0
## ... Procrustes: rmse 0.1343421 max resid 0.2191134
## Run 690 stress 0
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## Run 691 stress 0
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## Run 692 stress 0
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## Run 693 stress 0
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## Run 694 stress 0
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## Run 695 stress 0
## ... Procrustes: rmse 0.1622293 max resid 0.2055059
## Run 696 stress 9.177127e-05
## ... Procrustes: rmse 0.2095263 max resid 0.356664
## Run 697 stress 8.463612e-05
## ... Procrustes: rmse 0.1990362 max resid 0.3333398
## Run 698 stress 0
## ... Procrustes: rmse 0.09003674 max resid 0.1027199
## Run 699 stress 0
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## Run 700 stress 0
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## Run 701 stress 0
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## Run 702 stress 0
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## Run 703 stress 0
## ... Procrustes: rmse 0.09629485 max resid 0.1202599
## Run 704 stress 9.73953e-05
## ... Procrustes: rmse 0.1956039 max resid 0.323147
## Run 705 stress 0
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## Run 706 stress 0
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## Run 707 stress 0
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## Run 710 stress 0
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## Run 713 stress 0
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## Run 717 stress 0
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## Run 718 stress 0
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## Run 719 stress 0
## ... Procrustes: rmse 0.1993595 max resid 0.3198828
## Run 720 stress 9.780952e-05
## ... Procrustes: rmse 0.2062912 max resid 0.3495799
## Run 721 stress 0
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## Run 722 stress 0
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## ... Procrustes: rmse 0.1190863 max resid 0.1682765
## Run 724 stress 6.751894e-05
## ... Procrustes: rmse 0.1826535 max resid 0.3129461
## Run 725 stress 0
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## Run 726 stress 0
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## Run 727 stress 0
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## Run 728 stress 0
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## Run 729 stress 0
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## Run 731 stress 0
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## Run 732 stress 0
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## Run 733 stress 0
## ... Procrustes: rmse 0.16018 max resid 0.2616273
## Run 734 stress 9.767028e-05
## ... Procrustes: rmse 0.2089555 max resid 0.3534904
## Run 735 stress 0
## ... Procrustes: rmse 0.08167984 max resid 0.09652324
## Run 736 stress 9.01629e-05
## ... Procrustes: rmse 0.2082508 max resid 0.3520375
## Run 737 stress 0
## ... Procrustes: rmse 0.1011741 max resid 0.1410687
## Run 738 stress 0
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## Run 739 stress 0
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## Run 740 stress 0
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## Run 741 stress 0
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## Run 742 stress 0
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## Run 750 stress 0
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## Run 751 stress 9.634555e-05
## ... Procrustes: rmse 0.1908646 max resid 0.3103801
## Run 752 stress 0
## ... Procrustes: rmse 0.1056683 max resid 0.15816
## Run 753 stress 0
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## Run 755 stress 0
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## Run 764 stress 0
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## Run 765 stress 0
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## ... Procrustes: rmse 0.1534176 max resid 0.2448894
## Run 767 stress 8.809959e-05
## ... Procrustes: rmse 0.2001044 max resid 0.3341301
## Run 768 stress 0
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## Run 769 stress 0
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## Run 771 stress 0
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## Run 772 stress 0
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## ... Procrustes: rmse 0.114948 max resid 0.1466526
## Run 786 stress 8.108649e-05
## ... Procrustes: rmse 0.1688691 max resid 0.2760319
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## Run 788 stress 0
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## Run 790 stress 2.685664e-05
## ... Procrustes: rmse 0.1801042 max resid 0.2514425
## Run 791 stress 9.55367e-05
## ... Procrustes: rmse 0.2099943 max resid 0.3556128
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## ... Procrustes: rmse 0.2104223 max resid 0.3575093
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## Run 820 stress 0
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## Run 822 stress 8.678318e-05
## ... Procrustes: rmse 0.2086297 max resid 0.3311949
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## ... Procrustes: rmse 0.1675119 max resid 0.2228722
## Run 829 stress 4.206002e-05
## ... Procrustes: rmse 0.1903957 max resid 0.3232889
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## Run 850 stress 0
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## Run 856 stress 0
## ... Procrustes: rmse 0.1192982 max resid 0.1596406
## Run 857 stress 8.391896e-05
## ... Procrustes: rmse 0.1890131 max resid 0.3049587
## Run 858 stress 0
## ... Procrustes: rmse 0.1061115 max resid 0.1617494
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## ... Procrustes: rmse 0.1976072 max resid 0.2940698
## Run 860 stress 0
## ... Procrustes: rmse 0.1099046 max resid 0.1499014
## Run 861 stress 0
## ... Procrustes: rmse 0.168537 max resid 0.2577382
## Run 862 stress 3.181434e-05
## ... Procrustes: rmse 0.2080459 max resid 0.3529385
## Run 863 stress 0
## ... Procrustes: rmse 0.1026138 max resid 0.1345294
## Run 864 stress 8.680167e-05
## ... Procrustes: rmse 0.2014923 max resid 0.3412998
## Run 865 stress 0
## ... Procrustes: rmse 0.2080019 max resid 0.2531327
## Run 866 stress 0
## ... Procrustes: rmse 0.1041621 max resid 0.1473748
## Run 867 stress 0
## ... Procrustes: rmse 0.2314082 max resid 0.3125411
## Run 868 stress 0
## ... Procrustes: rmse 0.09257779 max resid 0.1289006
## Run 869 stress 0
## ... Procrustes: rmse 0.1642013 max resid 0.2244519
## Run 870 stress 0
## ... Procrustes: rmse 0.1347939 max resid 0.1855246
## Run 871 stress 0
## ... Procrustes: rmse 0.1883524 max resid 0.3003818
## Run 872 stress 0
## ... Procrustes: rmse 0.1174405 max resid 0.1894898
## Run 873 stress 9.106276e-05
## ... Procrustes: rmse 0.1988958 max resid 0.3401332
## Run 874 stress 0
## ... Procrustes: rmse 0.1069415 max resid 0.1526625
## Run 875 stress 6.519598e-05
## ... Procrustes: rmse 0.08160445 max resid 0.1291413
## Run 876 stress 0
## ... Procrustes: rmse 0.1439941 max resid 0.2042811
## Run 877 stress 0
## ... Procrustes: rmse 0.07201518 max resid 0.1182784
## Run 878 stress 0
## ... Procrustes: rmse 0.1899791 max resid 0.3224683
## Run 879 stress 0
## ... Procrustes: rmse 0.1185893 max resid 0.1869057
## Run 880 stress 0
## ... Procrustes: rmse 0.1377689 max resid 0.2031453
## Run 881 stress 0
## ... Procrustes: rmse 0.09402018 max resid 0.1120569
## Run 882 stress 0
## ... Procrustes: rmse 0.0746272 max resid 0.1255474
## Run 883 stress 0
## ... Procrustes: rmse 0.1813403 max resid 0.2850518
## Run 884 stress 0
## ... Procrustes: rmse 0.1020141 max resid 0.1296668
## Run 885 stress 0
## ... Procrustes: rmse 0.06405996 max resid 0.1042046
## Run 886 stress 0
## ... Procrustes: rmse 0.06528374 max resid 0.0929568
## Run 887 stress 0
## ... Procrustes: rmse 0.1213221 max resid 0.1412732
## Run 888 stress 0
## ... Procrustes: rmse 0.1602016 max resid 0.2701383
## Run 889 stress 0
## ... Procrustes: rmse 0.05435324 max resid 0.08725522
## Run 890 stress 0
## ... Procrustes: rmse 0.02607606 max resid 0.03794636
## Run 891 stress 0
## ... Procrustes: rmse 0.1318932 max resid 0.2010963
## Run 892 stress 0
## ... Procrustes: rmse 0.1509485 max resid 0.2077992
## Run 893 stress 0
## ... Procrustes: rmse 0.1483295 max resid 0.1978731
## Run 894 stress 0
## ... Procrustes: rmse 0.1892937 max resid 0.2997714
## Run 895 stress 0
## ... Procrustes: rmse 0.12914 max resid 0.1692145
## Run 896 stress 0
## ... Procrustes: rmse 0.08674304 max resid 0.1172038
## Run 897 stress 0
## ... Procrustes: rmse 0.2306638 max resid 0.3111762
## Run 898 stress 0
## ... Procrustes: rmse 0.130019 max resid 0.2033467
## Run 899 stress 9.754085e-05
## ... Procrustes: rmse 0.172372 max resid 0.2548739
## Run 900 stress 0
## ... Procrustes: rmse 0.06789419 max resid 0.07935174
## Run 901 stress 0
## ... Procrustes: rmse 0.1501795 max resid 0.2284964
## Run 902 stress 0
## ... Procrustes: rmse 0.1952814 max resid 0.3287208
## Run 903 stress 0
## ... Procrustes: rmse 0.158777 max resid 0.2539601
## Run 904 stress 0
## ... Procrustes: rmse 0.1669132 max resid 0.2518411
## Run 905 stress 0
## ... Procrustes: rmse 0.08535636 max resid 0.1359656
## Run 906 stress 0
## ... Procrustes: rmse 0.091141 max resid 0.1248613
## Run 907 stress 0
## ... Procrustes: rmse 0.1654379 max resid 0.2281467
## Run 908 stress 0
## ... Procrustes: rmse 0.1100984 max resid 0.1524679
## Run 909 stress 0
## ... Procrustes: rmse 0.1410808 max resid 0.2012927
## Run 910 stress 0
## ... Procrustes: rmse 0.1681111 max resid 0.2666483
## Run 911 stress 0
## ... Procrustes: rmse 0.1136155 max resid 0.1569719
## Run 912 stress 0
## ... Procrustes: rmse 0.08579733 max resid 0.1385
## Run 913 stress 0
## ... Procrustes: rmse 0.06488037 max resid 0.1011356
## Run 914 stress 9.641546e-05
## ... Procrustes: rmse 0.1800365 max resid 0.2721576
## Run 915 stress 0
## ... Procrustes: rmse 0.1380656 max resid 0.1985157
## Run 916 stress 0
## ... Procrustes: rmse 0.04545416 max resid 0.06528524
## Run 917 stress 0
## ... Procrustes: rmse 0.1196933 max resid 0.1797676
## Run 918 stress 0
## ... Procrustes: rmse 0.1659023 max resid 0.2153377
## Run 919 stress 0
## ... Procrustes: rmse 0.1460163 max resid 0.2235798
## Run 920 stress 5.037588e-05
## ... Procrustes: rmse 0.2221129 max resid 0.30632
## Run 921 stress 0
## ... Procrustes: rmse 0.1072939 max resid 0.1711047
## Run 922 stress 0
## ... Procrustes: rmse 0.05622792 max resid 0.08022603
## Run 923 stress 0
## ... Procrustes: rmse 0.1520415 max resid 0.1857611
## Run 924 stress 0
## ... Procrustes: rmse 0.0691361 max resid 0.08211009
## Run 925 stress 0
## ... Procrustes: rmse 0.1314061 max resid 0.1719482
## Run 926 stress 0
## ... Procrustes: rmse 0.2282619 max resid 0.3655915
## Run 927 stress 0
## ... Procrustes: rmse 0.05373877 max resid 0.05884258
## Run 928 stress 0
## ... Procrustes: rmse 0.2212144 max resid 0.355682
## Run 929 stress 0
## ... Procrustes: rmse 0.1127018 max resid 0.1528254
## Run 930 stress 7.47436e-05
## ... Procrustes: rmse 0.2093783 max resid 0.3544229
## Run 931 stress 0
## ... Procrustes: rmse 0.1357753 max resid 0.1824004
## Run 932 stress 7.548801e-05
## ... Procrustes: rmse 0.2052734 max resid 0.3457434
## Run 933 stress 0
## ... Procrustes: rmse 0.2111736 max resid 0.256934
## Run 934 stress 0
## ... Procrustes: rmse 0.1625265 max resid 0.2405877
## Run 935 stress 0
## ... Procrustes: rmse 0.1793783 max resid 0.267099
## Run 936 stress 9.965684e-05
## ... Procrustes: rmse 0.1495553 max resid 0.2093671
## Run 937 stress 0
## ... Procrustes: rmse 0.1144623 max resid 0.1907772
## Run 938 stress 0
## ... Procrustes: rmse 0.2022169 max resid 0.2533838
## Run 939 stress 8.859814e-05
## ... Procrustes: rmse 0.1968358 max resid 0.3079143
## Run 940 stress 0
## ... Procrustes: rmse 0.1343151 max resid 0.1910967
## Run 941 stress 0
## ... Procrustes: rmse 0.1040487 max resid 0.1449599
## Run 942 stress 0
## ... Procrustes: rmse 0.1439036 max resid 0.1900108
## Run 943 stress 0
## ... Procrustes: rmse 0.1441011 max resid 0.192297
## Run 944 stress 0
## ... Procrustes: rmse 0.1213357 max resid 0.1635469
## Run 945 stress 9.546911e-05
## ... Procrustes: rmse 0.2126771 max resid 0.3609619
## Run 946 stress 0
## ... Procrustes: rmse 0.1019011 max resid 0.1368001
## Run 947 stress 0
## ... Procrustes: rmse 0.1663472 max resid 0.2016123
## Run 948 stress 0
## ... Procrustes: rmse 0.1421913 max resid 0.2057548
## Run 949 stress 0
## ... Procrustes: rmse 0.06381044 max resid 0.09074989
## Run 950 stress 0
## ... Procrustes: rmse 0.1239047 max resid 0.1803061
## Run 951 stress 0
## ... Procrustes: rmse 0.09872257 max resid 0.144266
## Run 952 stress 0
## ... Procrustes: rmse 0.1509941 max resid 0.212917
## Run 953 stress 0
## ... Procrustes: rmse 0.05099448 max resid 0.08501765
## Run 954 stress 0
## ... Procrustes: rmse 0.1337666 max resid 0.2090792
## Run 955 stress 0
## ... Procrustes: rmse 0.129709 max resid 0.1743894
## Run 956 stress 0
## ... Procrustes: rmse 0.06480706 max resid 0.07965637
## Run 957 stress 0
## ... Procrustes: rmse 0.178231 max resid 0.2880385
## Run 958 stress 0
## ... Procrustes: rmse 0.1020914 max resid 0.13237
## Run 959 stress 0
## ... Procrustes: rmse 0.1189357 max resid 0.1597158
## Run 960 stress 0
## ... Procrustes: rmse 0.162752 max resid 0.2052627
## Run 961 stress 0
## ... Procrustes: rmse 0.100301 max resid 0.1463464
## Run 962 stress 4.349162e-05
## ... Procrustes: rmse 0.1956424 max resid 0.3357252
## Run 963 stress 0
## ... Procrustes: rmse 0.1638999 max resid 0.2291104
## Run 964 stress 0
## ... Procrustes: rmse 0.1819994 max resid 0.2429549
## Run 965 stress 0
## ... Procrustes: rmse 0.0937026 max resid 0.1388833
## Run 966 stress 0
## ... Procrustes: rmse 0.09102959 max resid 0.1323845
## Run 967 stress 0
## ... Procrustes: rmse 0.08162651 max resid 0.131428
## Run 968 stress 0
## ... Procrustes: rmse 0.1264997 max resid 0.1572579
## Run 969 stress 0
## ... Procrustes: rmse 0.1143801 max resid 0.1504298
## Run 970 stress 0
## ... Procrustes: rmse 0.155472 max resid 0.2291109
## Run 971 stress 0
## ... Procrustes: rmse 0.1083866 max resid 0.1459828
## Run 972 stress 0
## ... Procrustes: rmse 0.1038751 max resid 0.1382455
## Run 973 stress 0
## ... Procrustes: rmse 0.1261412 max resid 0.1753003
## Run 974 stress 6.030289e-05
## ... Procrustes: rmse 0.1102317 max resid 0.1569785
## Run 975 stress 8.412609e-05
## ... Procrustes: rmse 0.1856652 max resid 0.294277
## Run 976 stress 0
## ... Procrustes: rmse 0.08772029 max resid 0.12704
## Run 977 stress 0
## ... Procrustes: rmse 0.1524784 max resid 0.2602892
## Run 978 stress 0
## ... Procrustes: rmse 0.06789293 max resid 0.1008646
## Run 979 stress 0
## ... Procrustes: rmse 0.2084379 max resid 0.3547313
## Run 980 stress 9.390683e-05
## ... Procrustes: rmse 0.1786138 max resid 0.2649652
## Run 981 stress 0
## ... Procrustes: rmse 0.0992052 max resid 0.13346
## Run 982 stress 9.666082e-05
## ... Procrustes: rmse 0.2005406 max resid 0.3419877
## Run 983 stress 0
## ... Procrustes: rmse 0.1535811 max resid 0.2374147
## Run 984 stress 0
## ... Procrustes: rmse 0.1378295 max resid 0.166184
## Run 985 stress 8.244324e-05
## ... Procrustes: rmse 0.2018231 max resid 0.3381003
## Run 986 stress 0
## ... Procrustes: rmse 0.06380489 max resid 0.09960946
## Run 987 stress 8.261318e-05
## ... Procrustes: rmse 0.1755542 max resid 0.2635342
## Run 988 stress 0
## ... Procrustes: rmse 0.126936 max resid 0.1543024
## Run 989 stress 0
## ... Procrustes: rmse 0.1049089 max resid 0.1363105
## Run 990 stress 0
## ... Procrustes: rmse 0.1616843 max resid 0.2350799
## Run 991 stress 0
## ... Procrustes: rmse 0.0766104 max resid 0.128143
## Run 992 stress 0
## ... Procrustes: rmse 0.1541914 max resid 0.2612486
## Run 993 stress 0
## ... Procrustes: rmse 0.203293 max resid 0.3109193
## Run 994 stress 0
## ... Procrustes: rmse 0.08767086 max resid 0.09186579
## Run 995 stress 0
## ... Procrustes: rmse 0.1764802 max resid 0.227425
## Run 996 stress 0
## ... Procrustes: rmse 0.1408518 max resid 0.2127481
## Run 997 stress 0
## ... Procrustes: rmse 0.1864554 max resid 0.3145292
## Run 998 stress 0
## ... Procrustes: rmse 0.1584367 max resid 0.2066814
## Run 999 stress 0
## ... Procrustes: rmse 0.133102 max resid 0.1703071
## Run 1000 stress 0
## ... Procrustes: rmse 0.1094523 max resid 0.1414146
## *** No convergence -- monoMDS stopping criteria:
## 1000: stress < smin
nmds_2<- metaMDS(dist_ano_2, trymax = 1000)
## Run 0 stress 0
## Run 1 stress 0
## ... Procrustes: rmse 0.05101318 max resid 0.07792902
## Run 2 stress 0
## ... Procrustes: rmse 0.3453466 max resid 0.4662627
## Run 3 stress 0
## ... Procrustes: rmse 0.06131855 max resid 0.1016324
## Run 4 stress 0
## ... Procrustes: rmse 0.1357846 max resid 0.2212667
## Run 5 stress 0
## ... Procrustes: rmse 0.1485504 max resid 0.1926733
## Run 6 stress 0
## ... Procrustes: rmse 0.0976395 max resid 0.1461112
## Run 7 stress 0
## ... Procrustes: rmse 0.05230734 max resid 0.07236596
## Run 8 stress 0
## ... Procrustes: rmse 0.09422467 max resid 0.1359496
## Run 9 stress 0
## ... Procrustes: rmse 0.2368645 max resid 0.3394639
## Run 10 stress 0
## ... Procrustes: rmse 0.124668 max resid 0.1434344
## Run 11 stress 0
## ... Procrustes: rmse 0.1134385 max resid 0.1923229
## Run 12 stress 0
## ... Procrustes: rmse 0.125054 max resid 0.2007606
## Run 13 stress 0
## ... Procrustes: rmse 0.3287186 max resid 0.4485923
## Run 14 stress 0
## ... Procrustes: rmse 0.2404093 max resid 0.3525609
## Run 15 stress 0
## ... Procrustes: rmse 0.08311118 max resid 0.1212581
## Run 16 stress 0
## ... Procrustes: rmse 0.0736051 max resid 0.1214414
## Run 17 stress 0
## ... Procrustes: rmse 0.1050709 max resid 0.1359828
## Run 18 stress 0
## ... Procrustes: rmse 0.1171892 max resid 0.1954198
## Run 19 stress 9.825759e-05
## ... Procrustes: rmse 0.3312491 max resid 0.408241
## Run 20 stress 0
## ... Procrustes: rmse 0.1179359 max resid 0.1480028
## Run 21 stress 0
## ... Procrustes: rmse 0.1598914 max resid 0.179226
## Run 22 stress 0
## ... Procrustes: rmse 0.07211291 max resid 0.1061801
## Run 23 stress 0
## ... Procrustes: rmse 0.1489661 max resid 0.1728527
## Run 24 stress 0
## ... Procrustes: rmse 0.05536678 max resid 0.08256874
## Run 25 stress 0
## ... Procrustes: rmse 0.05962433 max resid 0.09509794
## Run 26 stress 0
## ... Procrustes: rmse 0.277696 max resid 0.3830727
## Run 27 stress 0
## ... Procrustes: rmse 0.04820533 max resid 0.06352689
## Run 28 stress 0
## ... Procrustes: rmse 0.02630433 max resid 0.0347313
## Run 29 stress 0
## ... Procrustes: rmse 0.07790382 max resid 0.1076815
## Run 30 stress 0
## ... Procrustes: rmse 0.1464068 max resid 0.2371154
## Run 31 stress 0
## ... Procrustes: rmse 0.1367305 max resid 0.2269175
## Run 32 stress 0
## ... Procrustes: rmse 0.05187587 max resid 0.05701944
## Run 33 stress 0
## ... Procrustes: rmse 0.2467719 max resid 0.3593653
## Run 34 stress 0
## ... Procrustes: rmse 0.03581618 max resid 0.04836052
## Run 35 stress 0
## ... Procrustes: rmse 0.3316573 max resid 0.4542827
## Run 36 stress 0
## ... Procrustes: rmse 0.1249403 max resid 0.2086553
## Run 37 stress 0
## ... Procrustes: rmse 0.05532723 max resid 0.08445348
## Run 38 stress 0
## ... Procrustes: rmse 0.02951688 max resid 0.03668667
## Run 39 stress 0
## ... Procrustes: rmse 0.07144518 max resid 0.1127979
## Run 40 stress 0
## ... Procrustes: rmse 0.05215705 max resid 0.08702596
## Run 41 stress 0
## ... Procrustes: rmse 0.2603945 max resid 0.3760361
## Run 42 stress 0
## ... Procrustes: rmse 0.1019453 max resid 0.1703868
## Run 43 stress 0
## ... Procrustes: rmse 0.12413 max resid 0.192261
## Run 44 stress 8.580682e-05
## ... Procrustes: rmse 0.3266397 max resid 0.3502078
## Run 45 stress 1.158375e-05
## ... Procrustes: rmse 0.3214999 max resid 0.3670524
## Run 46 stress 0
## ... Procrustes: rmse 0.1064418 max resid 0.1823053
## Run 47 stress 0
## ... Procrustes: rmse 0.03746745 max resid 0.0460819
## Run 48 stress 0
## ... Procrustes: rmse 0.07064053 max resid 0.1141036
## Run 49 stress 0
## ... Procrustes: rmse 0.1051964 max resid 0.1101784
## Run 50 stress 0
## ... Procrustes: rmse 0.06320942 max resid 0.09257977
## Run 51 stress 0
## ... Procrustes: rmse 0.1583465 max resid 0.2493612
## Run 52 stress 0
## ... Procrustes: rmse 0.1354039 max resid 0.1887778
## Run 53 stress 0
## ... Procrustes: rmse 0.08012963 max resid 0.1205833
## Run 54 stress 0
## ... Procrustes: rmse 0.1018799 max resid 0.1482426
## Run 55 stress 0
## ... Procrustes: rmse 0.3129831 max resid 0.4121576
## Run 56 stress 0
## ... Procrustes: rmse 0.1319038 max resid 0.2052092
## Run 57 stress 0
## ... Procrustes: rmse 0.1122832 max resid 0.1702814
## Run 58 stress 0
## ... Procrustes: rmse 0.08959935 max resid 0.1534707
## Run 59 stress 0
## ... Procrustes: rmse 0.1251897 max resid 0.2059294
## Run 60 stress 0
## ... Procrustes: rmse 0.04550396 max resid 0.06787742
## Run 61 stress 0
## ... Procrustes: rmse 0.1437313 max resid 0.1989279
## Run 62 stress 0
## ... Procrustes: rmse 0.04638677 max resid 0.07295364
## Run 63 stress 0
## ... Procrustes: rmse 0.09848618 max resid 0.1358434
## Run 64 stress 0
## ... Procrustes: rmse 0.2489495 max resid 0.3564026
## Run 65 stress 0
## ... Procrustes: rmse 0.165684 max resid 0.2441702
## Run 66 stress 8.237483e-05
## ... Procrustes: rmse 0.3275187 max resid 0.3658676
## Run 67 stress 0
## ... Procrustes: rmse 0.1855178 max resid 0.2483112
## Run 68 stress 0
## ... Procrustes: rmse 0.2896606 max resid 0.4102198
## Run 69 stress 9.644006e-05
## ... Procrustes: rmse 0.2317164 max resid 0.3251044
## Run 70 stress 0
## ... Procrustes: rmse 0.1138369 max resid 0.1880024
## Run 71 stress 0
## ... Procrustes: rmse 0.1007267 max resid 0.1582391
## Run 72 stress 0
## ... Procrustes: rmse 0.09635996 max resid 0.1112575
## Run 73 stress 0
## ... Procrustes: rmse 0.2923699 max resid 0.3893457
## Run 74 stress 0
## ... Procrustes: rmse 0.06994999 max resid 0.1019526
## Run 75 stress 0
## ... Procrustes: rmse 0.0458138 max resid 0.06827105
## Run 76 stress 0
## ... Procrustes: rmse 0.08450872 max resid 0.129477
## Run 77 stress 0
## ... Procrustes: rmse 0.2232523 max resid 0.3151881
## Run 78 stress 0
## ... Procrustes: rmse 0.09972287 max resid 0.1204966
## Run 79 stress 0
## ... Procrustes: rmse 0.1172899 max resid 0.1959327
## Run 80 stress 0
## ... Procrustes: rmse 0.08354696 max resid 0.1202307
## Run 81 stress 0
## ... Procrustes: rmse 0.08072243 max resid 0.1304925
## Run 82 stress 0
## ... Procrustes: rmse 0.3026992 max resid 0.3084197
## Run 83 stress 0
## ... Procrustes: rmse 0.05721194 max resid 0.07334608
## Run 84 stress 0
## ... Procrustes: rmse 0.3261397 max resid 0.4411091
## Run 85 stress 0
## ... Procrustes: rmse 0.1035601 max resid 0.1695433
## Run 86 stress 0
## ... Procrustes: rmse 0.3433746 max resid 0.4640415
## Run 87 stress 0
## ... Procrustes: rmse 0.08325367 max resid 0.1231858
## Run 88 stress 0
## ... Procrustes: rmse 0.1512777 max resid 0.2267534
## Run 89 stress 0
## ... Procrustes: rmse 0.1833468 max resid 0.2107628
## Run 90 stress 0
## ... Procrustes: rmse 0.06427616 max resid 0.1005195
## Run 91 stress 0
## ... Procrustes: rmse 0.1628121 max resid 0.2157024
## Run 92 stress 9.673715e-05
## ... Procrustes: rmse 0.3286329 max resid 0.3819951
## Run 93 stress 0
## ... Procrustes: rmse 0.183163 max resid 0.2492557
## Run 94 stress 0
## ... Procrustes: rmse 0.1194188 max resid 0.1484619
## Run 95 stress 0
## ... Procrustes: rmse 0.04306537 max resid 0.05962085
## Run 96 stress 0
## ... Procrustes: rmse 0.116938 max resid 0.1984595
## Run 97 stress 9.947173e-05
## ... Procrustes: rmse 0.2025046 max resid 0.2909347
## Run 98 stress 8.037377e-05
## ... Procrustes: rmse 0.2603634 max resid 0.3580982
## Run 99 stress 0
## ... Procrustes: rmse 0.08547674 max resid 0.1035168
## Run 100 stress 0
## ... Procrustes: rmse 0.33425 max resid 0.4555796
## Run 101 stress 0
## ... Procrustes: rmse 0.1115194 max resid 0.1855201
## Run 102 stress 0
## ... Procrustes: rmse 0.1520746 max resid 0.2371492
## Run 103 stress 0
## ... Procrustes: rmse 0.06804868 max resid 0.108408
## Run 104 stress 0
## ... Procrustes: rmse 0.05564431 max resid 0.08809735
## Run 105 stress 0
## ... Procrustes: rmse 0.3167881 max resid 0.4348008
## Run 106 stress 0
## ... Procrustes: rmse 0.04012575 max resid 0.05021484
## Run 107 stress 0
## ... Procrustes: rmse 0.0704587 max resid 0.1087758
## Run 108 stress 0
## ... Procrustes: rmse 0.1314912 max resid 0.2113757
## Run 109 stress 0
## ... Procrustes: rmse 0.2589509 max resid 0.3750721
## Run 110 stress 0
## ... Procrustes: rmse 0.0358046 max resid 0.04556483
## Run 111 stress 0
## ... Procrustes: rmse 0.08048698 max resid 0.1167118
## Run 112 stress 0
## ... Procrustes: rmse 0.06362508 max resid 0.08516602
## Run 113 stress 0
## ... Procrustes: rmse 0.1268748 max resid 0.1970537
## Run 114 stress 0
## ... Procrustes: rmse 0.1278491 max resid 0.200377
## Run 115 stress 0
## ... Procrustes: rmse 0.1209495 max resid 0.1935824
## Run 116 stress 0
## ... Procrustes: rmse 0.3149567 max resid 0.4263501
## Run 117 stress 8.929136e-05
## ... Procrustes: rmse 0.3274422 max resid 0.3645604
## Run 118 stress 0
## ... Procrustes: rmse 0.09995455 max resid 0.1576648
## Run 119 stress 0
## ... Procrustes: rmse 0.1330177 max resid 0.2045295
## Run 120 stress 0
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## Run 121 stress 0
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## Run 122 stress 0
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## Run 123 stress 0
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## Run 124 stress 0
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## Run 125 stress 0
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## Run 126 stress 0
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## Run 127 stress 0
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## Run 128 stress 0
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## Run 129 stress 0
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## Run 130 stress 0
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## Run 131 stress 0
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## Run 132 stress 0
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## Run 133 stress 0
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## Run 134 stress 0.0008723211
## Run 135 stress 0
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## Run 136 stress 0
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## Run 137 stress 9.975693e-05
## ... Procrustes: rmse 0.3262292 max resid 0.332341
## Run 138 stress 0
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## Run 139 stress 0
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## Run 140 stress 0
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## Run 141 stress 0
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## Run 142 stress 0
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## Run 143 stress 0
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## Run 144 stress 0
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## Run 145 stress 0
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## Run 146 stress 0
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## Run 147 stress 0
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## Run 148 stress 0
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## Run 149 stress 0
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## Run 150 stress 8.702475e-05
## ... Procrustes: rmse 0.0822992 max resid 0.1246311
## Run 151 stress 0
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## Run 152 stress 0
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## Run 153 stress 0
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## Run 154 stress 0
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## Run 155 stress 0
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## Run 156 stress 0
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## Run 157 stress 0
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## Run 158 stress 0
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## Run 159 stress 0
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## Run 160 stress 0
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## Run 161 stress 0
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## Run 162 stress 0
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## Run 163 stress 0
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## Run 164 stress 0
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## Run 165 stress 0
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## Run 166 stress 0
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## Run 167 stress 0
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## Run 168 stress 0
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## Run 169 stress 9.450555e-05
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## Run 170 stress 0
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## Run 171 stress 0
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## Run 172 stress 8.723784e-05
## ... Procrustes: rmse 0.3281544 max resid 0.3742008
## Run 173 stress 0
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## Run 174 stress 0
## ... Procrustes: rmse 0.08933467 max resid 0.1114211
## Run 175 stress 7.500906e-05
## ... Procrustes: rmse 0.0640054 max resid 0.089007
## Run 176 stress 0
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## Run 177 stress 0
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## Run 178 stress 0
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## Run 179 stress 0
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## Run 180 stress 0
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## Run 181 stress 0
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## Run 182 stress 0
## ... Procrustes: rmse 0.08262317 max resid 0.1378677
## Run 183 stress 8.570306e-05
## ... Procrustes: rmse 0.3280782 max resid 0.377658
## Run 184 stress 0
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## Run 185 stress 0
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## Run 186 stress 0
## ... Procrustes: rmse 0.161351 max resid 0.2544144
## Run 187 stress 8.763279e-05
## ... Procrustes: rmse 0.2595108 max resid 0.3572941
## Run 188 stress 0
## ... Procrustes: rmse 0.08796666 max resid 0.143933
## Run 189 stress 0
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## Run 190 stress 0
## ... Procrustes: rmse 0.1263751 max resid 0.1467185
## Run 191 stress 8.678304e-05
## ... Procrustes: rmse 0.3276961 max resid 0.3702971
## Run 192 stress 0
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## Run 193 stress 0
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## Run 194 stress 0
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## Run 195 stress 0
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## Run 196 stress 0
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## Run 197 stress 0
## ... Procrustes: rmse 0.1852188 max resid 0.2583693
## Run 198 stress 2.974384e-05
## ... Procrustes: rmse 0.1162249 max resid 0.1932928
## Run 199 stress 0
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## Run 200 stress 0
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## Run 201 stress 0
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## Run 202 stress 0
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## Run 203 stress 0
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## Run 204 stress 0
## ... Procrustes: rmse 0.2972855 max resid 0.3824085
## Run 205 stress 6.494833e-05
## ... Procrustes: rmse 0.06271649 max resid 0.08350462
## Run 206 stress 0
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## Run 207 stress 0
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## Run 208 stress 0
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## Run 209 stress 0
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## Run 210 stress 0
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## Run 211 stress 3.482458e-05
## ... Procrustes: rmse 0.2450599 max resid 0.3404893
## Run 212 stress 0
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## Run 213 stress 0
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## Run 214 stress 0
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## Run 215 stress 0
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## Run 216 stress 0
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## Run 217 stress 0
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## Run 218 stress 9.420047e-05
## ... Procrustes: rmse 0.3280898 max resid 0.3733087
## Run 219 stress 0
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## Run 220 stress 0
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## Run 221 stress 0
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## Run 222 stress 0
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## Run 223 stress 0
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## Run 224 stress 0
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## Run 225 stress 0
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## Run 226 stress 0
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## Run 227 stress 0
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## Run 228 stress 0
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## Run 229 stress 0
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## Run 230 stress 1.797579e-06
## ... Procrustes: rmse 0.3429885 max resid 0.4582725
## Run 231 stress 0
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## Run 232 stress 0
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## Run 233 stress 0
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## Run 234 stress 0
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## Run 235 stress 9.097895e-05
## ... Procrustes: rmse 0.2051326 max resid 0.2939428
## Run 236 stress 0
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## Run 237 stress 0
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## Run 238 stress 0
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## Run 239 stress 0
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## Run 240 stress 0
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## Run 241 stress 0
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## Run 242 stress 0
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## Run 243 stress 0
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## Run 244 stress 0
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## Run 245 stress 0
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## Run 246 stress 0
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## Run 247 stress 0
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## Run 248 stress 0
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## Run 249 stress 0
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## Run 250 stress 0
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## Run 251 stress 0
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## Run 252 stress 0
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## Run 253 stress 0
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## Run 254 stress 0
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## Run 255 stress 0
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## Run 256 stress 0
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## Run 257 stress 0
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## Run 258 stress 0
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## Run 259 stress 0
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## Run 260 stress 0
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## Run 261 stress 0
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## Run 262 stress 0
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## Run 263 stress 0
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## Run 264 stress 0
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## Run 265 stress 0
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## Run 266 stress 0
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## Run 267 stress 0
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## Run 268 stress 0
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## Run 269 stress 0
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## Run 270 stress 0
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## Run 271 stress 0
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## Run 272 stress 0
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## Run 273 stress 0
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## Run 274 stress 0
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## Run 275 stress 0
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## Run 276 stress 0
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## Run 277 stress 0
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## Run 278 stress 0
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## Run 279 stress 0
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## Run 280 stress 0
## ... Procrustes: rmse 0.09583175 max resid 0.1297768
## Run 281 stress 6.732232e-05
## ... Procrustes: rmse 0.06336491 max resid 0.08615909
## Run 282 stress 0
## ... Procrustes: rmse 0.06422092 max resid 0.09938915
## Run 283 stress 1.187171e-05
## ... Procrustes: rmse 0.2908397 max resid 0.3602223
## Run 284 stress 0
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## Run 285 stress 0
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## Run 286 stress 0
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## Run 287 stress 0
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## Run 288 stress 0
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## Run 289 stress 0
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## Run 290 stress 0
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## Run 291 stress 0
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## Run 292 stress 0
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## Run 293 stress 0
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## Run 294 stress 0
## ... Procrustes: rmse 0.08997692 max resid 0.111442
## Run 295 stress 6.679743e-05
## ... Procrustes: rmse 0.3327697 max resid 0.4132592
## Run 296 stress 0
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## Run 297 stress 0
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## Run 298 stress 0
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## Run 299 stress 0
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## Run 300 stress 0
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## Run 301 stress 0
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## Run 302 stress 0
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## Run 303 stress 0
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## Run 304 stress 0
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## Run 305 stress 0
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## Run 306 stress 0
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## Run 307 stress 0
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## Run 308 stress 0
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## Run 309 stress 0
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## Run 310 stress 0
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## Run 311 stress 0
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## Run 312 stress 0
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## Run 313 stress 0
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## Run 314 stress 0
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## Run 315 stress 0
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## Run 316 stress 0
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## Run 317 stress 0
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## Run 318 stress 0
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## Run 319 stress 0
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## Run 320 stress 0
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## Run 321 stress 0
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## Run 322 stress 0
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## Run 323 stress 0
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## Run 324 stress 0
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## Run 325 stress 0
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## Run 326 stress 0
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## Run 327 stress 0
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## Run 328 stress 0
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## Run 329 stress 0
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## Run 330 stress 0
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## Run 331 stress 0
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## Run 332 stress 0
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## Run 333 stress 0
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## Run 334 stress 0
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## Run 335 stress 0
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## Run 336 stress 0
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## Run 337 stress 0
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## Run 338 stress 0
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## Run 339 stress 0
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## Run 340 stress 0
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## Run 341 stress 0
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## Run 342 stress 0
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## Run 343 stress 0
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## Run 344 stress 0
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## Run 345 stress 0
## ... Procrustes: rmse 0.05489095 max resid 0.08418155
## Run 346 stress 9.628005e-05
## ... Procrustes: rmse 0.2690922 max resid 0.3683083
## Run 347 stress 0
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## Run 348 stress 0
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## Run 349 stress 0
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## Run 350 stress 5.819008e-05
## ... Procrustes: rmse 0.2453108 max resid 0.3318984
## Run 351 stress 0
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## Run 352 stress 0
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## Run 353 stress 0
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## Run 354 stress 0
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## Run 355 stress 0
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## Run 356 stress 0
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## Run 357 stress 0
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## Run 358 stress 0
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## Run 359 stress 0
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## Run 360 stress 0
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## Run 361 stress 0
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## Run 362 stress 0
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## Run 363 stress 0
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## Run 364 stress 0
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## Run 365 stress 0
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## Run 366 stress 0
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## Run 367 stress 0
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## Run 368 stress 1.942198e-06
## ... Procrustes: rmse 0.06643549 max resid 0.09654482
## Run 369 stress 0
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## Run 370 stress 0
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## Run 371 stress 7.642527e-05
## ... Procrustes: rmse 0.3301031 max resid 0.3933043
## Run 372 stress 0
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## Run 373 stress 0
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## Run 374 stress 0
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## Run 375 stress 0
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## Run 376 stress 0
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## Run 377 stress 0
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## Run 378 stress 0
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## Run 379 stress 0
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## Run 380 stress 0
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## Run 381 stress 0
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## Run 382 stress 0
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## Run 383 stress 0
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## Run 384 stress 0
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## Run 385 stress 0
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## Run 386 stress 0
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## Run 387 stress 0
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## Run 405 stress 1.05621e-05
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## Run 412 stress 7.434603e-05
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## Run 414 stress 0
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## Run 415 stress 9.764656e-05
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## Run 423 stress 0
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## Run 424 stress 9.548601e-05
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## Run 432 stress 0
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## Run 440 stress 0
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## Run 443 stress 0
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## Run 444 stress 0
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## Run 445 stress 5.359357e-05
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## Run 450 stress 0
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## Run 452 stress 0
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## Run 453 stress 0
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## Run 454 stress 0
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## Run 455 stress 0
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## Run 470 stress 4.606783e-05
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## Run 472 stress 9.811743e-05
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## Run 474 stress 9.458355e-05
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## Run 478 stress 0
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## Run 489 stress 0
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## Run 504 stress 9.978932e-05
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## Run 513 stress 6.9632e-05
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## Run 667 stress 3.432514e-05
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## Run 668 stress 8.834113e-05
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## Run 680 stress 0
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## Run 689 stress 0
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## Run 690 stress 0
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## Run 706 stress 7.930562e-05
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## ... Procrustes: rmse 0.1349896 max resid 0.2060772
## Run 736 stress 7.878941e-05
## ... Procrustes: rmse 0.07543587 max resid 0.1152296
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## Run 750 stress 9.916134e-05
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## Run 769 stress 9.82776e-05
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## ... Procrustes: rmse 0.3144552 max resid 0.4110519
## Run 913 stress 0
## ... Procrustes: rmse 0.104376 max resid 0.1785502
## Run 914 stress 0
## ... Procrustes: rmse 0.106435 max resid 0.1251671
## Run 915 stress 0
## ... Procrustes: rmse 0.2892996 max resid 0.3797312
## Run 916 stress 9.855787e-05
## ... Procrustes: rmse 0.2508929 max resid 0.3473763
## Run 917 stress 0
## ... Procrustes: rmse 0.08605566 max resid 0.1401171
## Run 918 stress 0
## ... Procrustes: rmse 0.1530334 max resid 0.1854695
## Run 919 stress 0
## ... Procrustes: rmse 0.04538574 max resid 0.05847881
## Run 920 stress 0
## ... Procrustes: rmse 0.2914894 max resid 0.4124576
## Run 921 stress 0
## ... Procrustes: rmse 0.06260596 max resid 0.1023189
## Run 922 stress 0
## ... Procrustes: rmse 0.1282929 max resid 0.1333603
## Run 923 stress 0
## ... Procrustes: rmse 0.2418219 max resid 0.3491192
## Run 924 stress 0
## ... Procrustes: rmse 0.143062 max resid 0.2271631
## Run 925 stress 0
## ... Procrustes: rmse 0.3207338 max resid 0.4460479
## Run 926 stress 0
## ... Procrustes: rmse 0.1135668 max resid 0.1882017
## Run 927 stress 0
## ... Procrustes: rmse 0.09052851 max resid 0.1026696
## Run 928 stress 0
## ... Procrustes: rmse 0.04765296 max resid 0.07105028
## Run 929 stress 0
## ... Procrustes: rmse 0.3254718 max resid 0.446946
## Run 930 stress 0
## ... Procrustes: rmse 0.3331205 max resid 0.4366481
## Run 931 stress 0
## ... Procrustes: rmse 0.04247165 max resid 0.06097702
## Run 932 stress 0
## ... Procrustes: rmse 0.05197084 max resid 0.06349433
## Run 933 stress 0
## ... Procrustes: rmse 0.1042135 max resid 0.1506143
## Run 934 stress 0
## ... Procrustes: rmse 0.1407778 max resid 0.2217839
## Run 935 stress 0
## ... Procrustes: rmse 0.2755168 max resid 0.3831792
## Run 936 stress 0
## ... Procrustes: rmse 0.1729147 max resid 0.2156474
## Run 937 stress 0
## ... Procrustes: rmse 0.08826206 max resid 0.1194706
## Run 938 stress 0
## ... Procrustes: rmse 0.04543971 max resid 0.07003008
## Run 939 stress 0
## ... Procrustes: rmse 0.1073199 max resid 0.1674123
## Run 940 stress 0
## ... Procrustes: rmse 0.05534106 max resid 0.07828218
## Run 941 stress 0
## ... Procrustes: rmse 0.1032506 max resid 0.1764345
## Run 942 stress 0
## ... Procrustes: rmse 0.1138244 max resid 0.1884376
## Run 943 stress 4.657839e-05
## ... Procrustes: rmse 0.3261485 max resid 0.332447
## Run 944 stress 0
## ... Procrustes: rmse 0.05163706 max resid 0.07747059
## Run 945 stress 0
## ... Procrustes: rmse 0.1071815 max resid 0.1223574
## Run 946 stress 0
## ... Procrustes: rmse 0.3060886 max resid 0.3791608
## Run 947 stress 0
## ... Procrustes: rmse 0.1710077 max resid 0.2542757
## Run 948 stress 0
## ... Procrustes: rmse 0.07160985 max resid 0.09855616
## Run 949 stress 0
## ... Procrustes: rmse 0.02767979 max resid 0.0361027
## Run 950 stress 0
## ... Procrustes: rmse 0.1000144 max resid 0.1705667
## Run 951 stress 0
## ... Procrustes: rmse 0.3265347 max resid 0.45098
## Run 952 stress 0
## ... Procrustes: rmse 0.03309326 max resid 0.04588211
## Run 953 stress 0
## ... Procrustes: rmse 0.07592769 max resid 0.1201744
## Run 954 stress 0
## ... Procrustes: rmse 0.09582687 max resid 0.1379785
## Run 955 stress 0
## ... Procrustes: rmse 0.05943023 max resid 0.09562323
## Run 956 stress 0
## ... Procrustes: rmse 0.06449403 max resid 0.09487493
## Run 957 stress 0
## ... Procrustes: rmse 0.2876068 max resid 0.3169127
## Run 958 stress 0
## ... Procrustes: rmse 0.04947584 max resid 0.07169876
## Run 959 stress 0
## ... Procrustes: rmse 0.100855 max resid 0.1726613
## Run 960 stress 0
## ... Procrustes: rmse 0.1235727 max resid 0.1974056
## Run 961 stress 0
## ... Procrustes: rmse 0.1140151 max resid 0.1854241
## Run 962 stress 0
## ... Procrustes: rmse 0.04587064 max resid 0.06725551
## Run 963 stress 0
## ... Procrustes: rmse 0.1282374 max resid 0.1781113
## Run 964 stress 0
## ... Procrustes: rmse 0.1212758 max resid 0.1629539
## Run 965 stress 0
## ... Procrustes: rmse 0.07711803 max resid 0.1306554
## Run 966 stress 0
## ... Procrustes: rmse 0.3156608 max resid 0.4378473
## Run 967 stress 0
## ... Procrustes: rmse 0.2960443 max resid 0.4111196
## Run 968 stress 0
## ... Procrustes: rmse 0.1196055 max resid 0.1890477
## Run 969 stress 0
## ... Procrustes: rmse 0.08204226 max resid 0.1317144
## Run 970 stress 0
## ... Procrustes: rmse 0.08314953 max resid 0.1394962
## Run 971 stress 8.41841e-05
## ... Procrustes: rmse 0.326629 max resid 0.3826285
## Run 972 stress 0
## ... Procrustes: rmse 0.06840866 max resid 0.1024178
## Run 973 stress 0
## ... Procrustes: rmse 0.09569894 max resid 0.1605443
## Run 974 stress 9.059461e-05
## ... Procrustes: rmse 0.1371188 max resid 0.21306
## Run 975 stress 0
## ... Procrustes: rmse 0.09621759 max resid 0.1614901
## Run 976 stress 0
## ... Procrustes: rmse 0.1240356 max resid 0.1978344
## Run 977 stress 0
## ... Procrustes: rmse 0.3122166 max resid 0.3872399
## Run 978 stress 0
## ... Procrustes: rmse 0.08909072 max resid 0.1179085
## Run 979 stress 0
## ... Procrustes: rmse 0.05950234 max resid 0.08945019
## Run 980 stress 8.868435e-05
## ... Procrustes: rmse 0.2656403 max resid 0.3643322
## Run 981 stress 0.0001844339
## ... Procrustes: rmse 0.3313798 max resid 0.4042591
## Run 982 stress 1.262028e-06
## ... Procrustes: rmse 0.2936307 max resid 0.3653352
## Run 983 stress 0
## ... Procrustes: rmse 0.07072977 max resid 0.1006557
## Run 984 stress 0
## ... Procrustes: rmse 0.04234947 max resid 0.06272532
## Run 985 stress 0
## ... Procrustes: rmse 0.3122868 max resid 0.423801
## Run 986 stress 0
## ... Procrustes: rmse 0.2286671 max resid 0.3111728
## Run 987 stress 0
## ... Procrustes: rmse 0.08978163 max resid 0.139532
## Run 988 stress 0
## ... Procrustes: rmse 0.07109975 max resid 0.1174518
## Run 989 stress 0
## ... Procrustes: rmse 0.1127473 max resid 0.1932025
## Run 990 stress 0
## ... Procrustes: rmse 0.2995327 max resid 0.4138977
## Run 991 stress 0
## ... Procrustes: rmse 0.09615075 max resid 0.1578662
## Run 992 stress 0
## ... Procrustes: rmse 0.3208797 max resid 0.4084703
## Run 993 stress 0
## ... Procrustes: rmse 0.1031478 max resid 0.1161255
## Run 994 stress 6.723699e-05
## ... Procrustes: rmse 0.06451207 max resid 0.09049909
## Run 995 stress 0
## ... Procrustes: rmse 0.08074403 max resid 0.1102818
## Run 996 stress 0
## ... Procrustes: rmse 0.1178784 max resid 0.1975086
## Run 997 stress 0
## ... Procrustes: rmse 0.3092356 max resid 0.432542
## Run 998 stress 0
## ... Procrustes: rmse 0.03387277 max resid 0.04482488
## Run 999 stress 0
## ... Procrustes: rmse 0.05520581 max resid 0.08131016
## Run 1000 stress 0
## ... Procrustes: rmse 0.09586213 max resid 0.1477476
## *** No convergence -- monoMDS stopping criteria:
## 5: no. of iterations >= maxit
## 995: stress < smin
pro_nmds<-procrustes(X = nmds_0, Y = nmds_2, symmetric = FALSE)
protest(X = nmds_0, Y = nmds_2, scores = "sites", permutations = 10000)
##
## Call:
## protest(X = nmds_0, Y = nmds_2, scores = "sites", permutations = 10000)
##
## Procrustes Sum of Squares (m12 squared): 0.07438
## Correlation in a symmetric Procrustes rotation: 0.9621
## Significance: 0.041667
##
## Permutation: free
## Number of permutations: 23
plot(pro_nmds, kind = 1, type = "text",
xlab="Dimensão 1", ylab="Dimensão 2", main = " ")
plot(pro_nmds, kind = 2)
Após isso, calculamos a correlação entre a matriz de composição de espécie e as matrizes correspondentes a ambos proxies: estrutura vegetacional (deterministic) e distância (estocástico).
# Distância geográfica como proxy de estocasticidade
blocos_totalmente<-read_excel("pi_matrix_dados_especiais.xlsx")
blocos_totalmente %>%
filter(Name==c(4, 5, 8, 9)) %>%
group_by(Name) %>%
sample_n(2, replace = T) %>%
geodist()->geodist_proxy_stoc_model_eight
dist(geodist_proxy_stoc_model_eight)->proxy_stoc_model_eight
# Estrutura da vegetação como proxy de nicho ecológico
dist_nicho <- read_excel("dist_nicho.xlsx")
dist_nicho %>%
mutate(Local=as.factor(Local),
Factor=c(rep(4, 12), rep(5, 12), rep(9, 12), rep(8, 12),
rep("4C", 1), rep("5C", 1), rep("8C", 1), rep("9C", 1))) %>%
group_by(Factor) %>%
summarise(Estat_media=mean(Metrica)) %>%
dist(method = "euclidean")->proxy_det_model
mantel.partial(dist_geral_0_a_2_anos, proxy_det_model, proxy_stoc_model_eight, method = "pearson")
##
## Partial Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel.partial(xdis = dist_geral_0_a_2_anos, ydis = proxy_det_model, zdis = proxy_stoc_model_eight, method = "pearson")
##
## Mantel statistic r: 0.05359
## Significance: 0.357
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.238 0.335 0.374 0.435
## Permutation: free
## Number of permutations: 999
mantel.partial(dist_geral_0_a_2_anos, proxy_stoc_model_eight, proxy_det_model, method = "pearson")
##
## Partial Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel.partial(xdis = dist_geral_0_a_2_anos, ydis = proxy_stoc_model_eight, zdis = proxy_det_model, method = "pearson")
##
## Mantel statistic r: 0.5673
## Significance: 0.003
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.353 0.409 0.481 0.537
## Permutation: free
## Number of permutations: 999