Descriptive stats

Remove localities

sp <- read.csv("Spectral parameters Diasporus 2018.csv")[, -1]

sp$Species <- gsub("D.v", "V", sp$Species) 
sp$Species <- gsub("D.d", "D", sp$Species) 
sp$Species <- gsub("D.h", "H", sp$Species)


spf <- sp[!(sp$Species == "Diastema" & sp$Locality %in% c("Crucitas", "Milpas")), ] 

spf <- spf[!(spf$Species == "Hylaeformis" & spf$Locality %in% c("Ena", "Utyum")), ] 

spf <- spf[!(spf$Species == "Vocator" & spf$Locality %in% c("Tinamastes", "Uvita", "Altamira")), ] 


spf <- spf[, grep("fun$", names(spf), invert = TRUE)]

spf <- spf[complete.cases(spf),]

Variables measured

names(sp)[-c(1,2, 32:34)]
##  [1] "duration"    "meanfreq"    "sd"          "freq.median" "freq.Q25"   
##  [6] "freq.Q75"    "freq.IQR"    "time.median" "time.Q25"    "time.Q75"   
## [11] "time.IQR"    "skew"        "kurt"        "sp.ent"      "time.ent"   
## [16] "entropy"     "sfm"         "meanfun"     "minfun"      "maxfun"     
## [21] "meandom"     "mindom"      "maxdom"      "dfrange"     "modindx"    
## [26] "startdom"    "enddom"      "dfslope"     "meanpeakf"

Number of calls

Diastema Hylaeformis Vocator
Golfito 72 70
La Selva 65
AguaBuena 64
Guaria 41
Uvita 41
Piro 40
Guayacan 36
Tinamastes 32
Cahuita 28
Tenorio 23
Arenal 21
Fortuna 18
Bijagua 16
Manzanillo 8
Tirimbina 7
Monserrat 158
Dantas 150
Tapanti 92
Poas 53
Queveri 46
Monteverde 32
CerroIncognita 7
Agua Buena 47
Altamira
Crucitas
Ena
Milpas
Paraguas 74
Utyum

Number of recordings

Diastema Hylaeformis Vocator
La Selva 10
AguaBuena 9
Golfito 9 9
Guaria 9
Guayacan 9
Cahuita 8
Fortuna 7
Tirimbina 6
Uvita 6
Arenal 5
Piro 5
Bijagua 4
Tenorio 4
Tinamastes 4
Manzanillo 3
Dantas 22
Monserrat 20
Tapanti 13
Poas 7
Queveri 6
Monteverde 4
CerroIncognita 1
Agua Buena 6
Altamira
Crucitas
Ena
Milpas
Paraguas 10
Utyum

Data formating

Correlation among variables

## [1] "original parameters after removing fundamental frequency related parameters"
##  [1] "duration"    "meanfreq"    "sd"          "freq.median" "freq.Q25"   
##  [6] "freq.Q75"    "freq.IQR"    "time.median" "time.Q25"    "time.Q75"   
## [11] "time.IQR"    "skew"        "kurt"        "sp.ent"      "time.ent"   
## [16] "entropy"     "sfm"         "meandom"     "mindom"      "maxdom"     
## [21] "dfrange"     "modindx"     "startdom"    "enddom"      "dfslope"    
## [26] "meanpeakf"

## [1] "non colinear  parameters"
##  [1] "duration"    "meanfreq"    "sd"          "freq.IQR"    "time.median"
##  [6] "time.Q25"    "time.IQR"    "kurt"        "sp.ent"      "time.ent"   
## [11] "entropy"     "sfm"         "mindom"      "maxdom"      "dfrange"    
## [16] "modindx"     "startdom"    "enddom"      "dfslope"

Correlation after removing collinear variables

Random Forest by species-locality

## [1] "Accuracy at best number of trees Spectral Parameters"
##   mtry Accuracy    Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5    5 0.890728 0.883161      0.849974      0.923579     0.129139
##   AccuracyPValue McnemarPValue
## 5   1.03324e-197           NaN
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##       0.874464       0.865738       0.851467       0.895062       0.127682 
## AccuracyPValue  McnemarPValue 
##       0.000000            NaN

Test data error rate

## [1] 0.165018

Variable importance

Random forest for single species

D. diastema

## [1] "Accuracy at best number of trees Spectral Parameters"
##   mtry Accuracy    Kappa AccuracyLower AccuracyUpper AccuracyNull
## 3    3    0.864 0.849919      0.791202      0.918735        0.144
##   AccuracyPValue McnemarPValue
## 3    3.70116e-72           NaN
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    7.85530e-01    7.64284e-01    7.41233e-01    8.25396e-01    1.39535e-01 
## AccuracyPValue  McnemarPValue 
##   4.43035e-180            NaN

Test data error rate

## [1] 0.220635

Variable importance

D. hylaeformis

## [1] "Accuracy at best number of trees Spectral Parameters"
##   mtry Accuracy    Kappa AccuracyLower AccuracyUpper AccuracyNull
## 5    5 0.946565 0.931618      0.893002      0.978249      0.29771
##   AccuracyPValue McnemarPValue
## 5    5.42064e-56           NaN
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    9.00000e-01    8.71439e-01    8.66322e-01    9.27594e-01    2.97500e-01 
## AccuracyPValue  McnemarPValue 
##   4.33058e-141            NaN

Test data error rate

## [1] 0.0671912

Variable importance

D. Vocator

## Warning: Ignoring unknown parameters: width

## [1] "Accuracy at best number of trees Spectral Parameters"
##   mtry Accuracy Kappa AccuracyLower AccuracyUpper AccuracyNull
## 1    1        1     1      0.922938             1     0.391304
##   AccuracyPValue McnemarPValue
## 1    1.80167e-19           NaN
##       Accuracy          Kappa  AccuracyLower  AccuracyUpper   AccuracyNull 
##    9.72414e-01    9.57775e-01    9.30876e-01    9.92434e-01    3.86207e-01 
## AccuracyPValue  McnemarPValue 
##    1.40795e-52            NaN

Test data error rate

## [1] 0.000193931

Variable importance

Predictions

Model accuracy

Proximity matrices

All

Vocator-Agua Buena Vocator-Golfito Diastema-AguaBuena Diastema-Arenal Diastema-Cahuita Diastema-Fortuna Diastema-Golfito Diastema-Guaria Diastema-Guayacan Diastema-Bijagua Diastema-Manzanillo Diastema-Piro Diastema-La Selva Diastema-Tenorio Diastema-Tinamastes Diastema-Tirimbina Diastema-Uvita Hylaeformis-Dantas Hylaeformis-Monserrat Hylaeformis-Monteverde Hylaeformis-Poas Hylaeformis-Queveri Hylaeformis-Tapanti Hylaeformis-CerroIncognita Vocator-Paraguas
Vocator-Agua Buena 1e+00 0.0020 0.0000 0.0000 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0004 0.0000 0.0000 0.0000 0.0000 0.0001 0.0000 0.0000 0e+00 0.0004 0.0000 0.0000 0 0.0001 0.0000
Vocator-Golfito 2e-03 1.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0e+00 0.0000 0.0000 0.0001 0 0.0000 0.0652
Diastema-AguaBuena 0e+00 0.0000 1.0000 0.0005 0.0000 0.0000 0.1384 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0006 0.0017 0.0000 0.0134 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-Arenal 0e+00 0.0000 0.0005 1.0000 0.0020 0.0003 0.0000 0.0000 0.0001 0.0047 0.0000 0.0038 0.0000 0.0241 0.0007 0.0002 0.0001 0.0000 0e+00 0.0001 0.0000 0.0000 0 0.0000 0.0000
Diastema-Cahuita 1e-04 0.0000 0.0000 0.0020 1.0000 0.0001 0.0000 0.0019 0.1493 0.0102 0.0099 0.0000 0.0088 0.0000 0.0000 0.1415 0.0000 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0014
Diastema-Fortuna 0e+00 0.0000 0.0000 0.0003 0.0001 1.0000 0.0000 0.0003 0.0000 0.0000 0.0002 0.0006 0.0065 0.0052 0.0000 0.0000 0.0000 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-Golfito 0e+00 0.0000 0.1384 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 0.0003 0.0000 0.0007 0.0013 0.0000 0.0040 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-Guaria 0e+00 0.0000 0.0000 0.0000 0.0019 0.0003 0.0000 1.0000 0.0001 0.0029 0.0172 0.0000 0.0176 0.0000 0.0000 0.0121 0.0000 0.0000 0e+00 0.0000 0.0000 0.0001 0 0.0000 0.0000
Diastema-Guayacan 0e+00 0.0000 0.0000 0.0001 0.1493 0.0000 0.0000 0.0001 1.0000 0.0475 0.0125 0.0000 0.0000 0.0000 0.0000 0.2105 0.0000 0.0000 0e+00 0.0000 0.0000 0.0001 0 0.0000 0.0084
Diastema-Bijagua 0e+00 0.0000 0.0000 0.0047 0.0102 0.0000 0.0000 0.0029 0.0475 1.0000 0.0000 0.0001 0.0002 0.0000 0.0000 0.0285 0.0000 0.0000 0e+00 0.0000 0.0000 0.0192 0 0.0000 0.0003
Diastema-Manzanillo 4e-04 0.0000 0.0000 0.0000 0.0099 0.0002 0.0000 0.0172 0.0125 0.0000 1.0000 0.0000 0.0037 0.0000 0.0000 0.0317 0.0000 0.0000 0e+00 0.0000 0.0000 0.0004 0 0.0000 0.0016
Diastema-Piro 0e+00 0.0000 0.0000 0.0038 0.0000 0.0006 0.0003 0.0000 0.0000 0.0001 0.0000 1.0000 0.0000 0.0014 0.0004 0.0000 0.0010 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-La Selva 0e+00 0.0000 0.0000 0.0000 0.0088 0.0065 0.0000 0.0176 0.0000 0.0002 0.0037 0.0000 1.0000 0.0071 0.0000 0.0008 0.0000 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-Tenorio 0e+00 0.0000 0.0006 0.0241 0.0000 0.0052 0.0007 0.0000 0.0000 0.0000 0.0000 0.0014 0.0071 1.0000 0.0001 0.0000 0.0001 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Diastema-Tinamastes 0e+00 0.0000 0.0017 0.0007 0.0000 0.0000 0.0013 0.0000 0.0000 0.0000 0.0000 0.0004 0.0000 0.0001 1.0000 0.0000 0.0097 0.0000 0e+00 0.0010 0.0000 0.0000 0 0.0051 0.0000
Diastema-Tirimbina 1e-04 0.0000 0.0000 0.0002 0.1415 0.0000 0.0000 0.0121 0.2105 0.0285 0.0317 0.0000 0.0008 0.0000 0.0000 1.0000 0.0000 0.0000 0e+00 0.0000 0.0000 0.0021 0 0.0000 0.0015
Diastema-Uvita 0e+00 0.0000 0.0134 0.0001 0.0000 0.0000 0.0040 0.0000 0.0000 0.0000 0.0000 0.0010 0.0000 0.0001 0.0097 0.0000 1.0000 0.0000 0e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Hylaeformis-Dantas 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 9e-04 0.0174 0.0129 0.0000 0 0.0127 0.0000
Hylaeformis-Monserrat 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0009 1e+00 0.0000 0.0000 0.0000 0 0.0000 0.0000
Hylaeformis-Monteverde 4e-04 0.0000 0.0000 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0010 0.0000 0.0000 0.0174 0e+00 1.0000 0.0004 0.0000 0 0.0058 0.0000
Hylaeformis-Poas 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0129 0e+00 0.0004 1.0000 0.0000 0 0.0178 0.0000
Hylaeformis-Queveri 0e+00 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0001 0.0001 0.0192 0.0004 0.0000 0.0000 0.0000 0.0000 0.0021 0.0000 0.0000 0e+00 0.0000 0.0000 1.0000 0 0.0000 0.0063
Hylaeformis-Tapanti 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0e+00 0.0000 0.0000 0.0000 1 0.0000 0.0000
Hylaeformis-CerroIncognita 1e-04 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0051 0.0000 0.0000 0.0127 0e+00 0.0058 0.0178 0.0000 0 1.0000 0.0000
Vocator-Paraguas 0e+00 0.0652 0.0000 0.0000 0.0014 0.0000 0.0000 0.0000 0.0084 0.0003 0.0016 0.0000 0.0000 0.0000 0.0000 0.0015 0.0000 0.0000 0e+00 0.0000 0.0000 0.0063 0 0.0000 1.0000

Diastema

AguaBuena Arenal Cahuita Fortuna Golfito Guaria Guayacan Bijagua Manzanillo Piro La Selva Tenorio Tinamastes Tirimbina Uvita
AguaBuena 1.0000 0.0013 0.0000 0.0002 0.0634 0.0000 0.0000 0.0000 0.0000 0.1470 0.0000 0.0001 0.0006 0.0000 0.0126
Arenal 0.0013 1.0000 0.0029 0.0001 0.0022 0.0002 0.0011 0.0014 0.0000 0.0034 0.0000 0.0217 0.0000 0.0004 0.0002
Cahuita 0.0000 0.0029 1.0000 0.0002 0.0000 0.0010 0.0143 0.0047 0.0002 0.0000 0.0139 0.0007 0.0000 0.0133 0.0000
Fortuna 0.0002 0.0001 0.0002 1.0000 0.0000 0.0149 0.0000 0.0005 0.0001 0.0001 0.0167 0.0014 0.0000 0.0000 0.0000
Golfito 0.0634 0.0022 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 0.0046 0.0000 0.0000 0.0043 0.0000 0.0551
Guaria 0.0000 0.0002 0.0010 0.0149 0.0000 1.0000 0.0029 0.0000 0.0140 0.0000 0.0010 0.0061 0.0000 0.0047 0.0000
Guayacan 0.0000 0.0011 0.0143 0.0000 0.0000 0.0029 1.0000 0.0969 0.0035 0.0000 0.0017 0.0000 0.0000 0.1140 0.0000
Bijagua 0.0000 0.0014 0.0047 0.0005 0.0000 0.0000 0.0969 1.0000 0.0000 0.0000 0.0010 0.0000 0.0000 0.0217 0.0000
Manzanillo 0.0000 0.0000 0.0002 0.0001 0.0000 0.0140 0.0035 0.0000 1.0000 0.0000 0.0008 0.0001 0.0000 0.0067 0.0000
Piro 0.1470 0.0034 0.0000 0.0001 0.0046 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0053 0.0005 0.0000 0.0051
La Selva 0.0000 0.0000 0.0139 0.0167 0.0000 0.0010 0.0017 0.0010 0.0008 0.0000 1.0000 0.0089 0.0000 0.0000 0.0000
Tenorio 0.0001 0.0217 0.0007 0.0014 0.0000 0.0061 0.0000 0.0000 0.0001 0.0053 0.0089 1.0000 0.0000 0.0000 0.0000
Tinamastes 0.0006 0.0000 0.0000 0.0000 0.0043 0.0000 0.0000 0.0000 0.0000 0.0005 0.0000 0.0000 1.0000 0.0000 0.0051
Tirimbina 0.0000 0.0004 0.0133 0.0000 0.0000 0.0047 0.1140 0.0217 0.0067 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000
Uvita 0.0126 0.0002 0.0000 0.0000 0.0551 0.0000 0.0000 0.0000 0.0000 0.0051 0.0000 0.0000 0.0051 0.0000 1.0000

Hylaeformis

Dantas Monserrat Monteverde Poas Queveri Tapanti
Dantas 1.0000 4e-04 0.0002 0.0063 0.0000 0
Monserrat 0.0004 1e+00 0.0000 0.0000 0.0000 0
Monteverde 0.0002 0e+00 1.0000 0.0026 0.0047 0
Poas 0.0063 0e+00 0.0026 1.0000 0.0000 0
Queveri 0.0000 0e+00 0.0047 0.0000 1.0000 0
Tapanti 0.0000 0e+00 0.0000 0.0000 0.0000 1

Vocator

Agua Buena Golfito Paraguas
Agua Buena 1.0000 0.0116 0.0000
Golfito 0.0116 1.0000 0.0138
Paraguas 0.0000 0.0138 1.0000

Predicting CerroIncognito

## [1] "Predicted:"
##      1213      1214      1215      1216      1217      1218      1219 
##    Dantas    Dantas Monserrat Monserrat Monserrat    Dantas    Dantas 
## Levels: Dantas Monserrat Monteverde Poas Queveri Tapanti

Unsupervised random forest per species

Correlation to SNR

In this case removing noise variables should produce more robust models

##    duration    meanfreq          sd    freq.IQR time.median    time.Q25 
##  -0.2144573  -0.0793392  -0.4817546  -0.4275289  -0.1187021  -0.0281593 
##    time.IQR        kurt      sp.ent    time.ent     entropy         sfm 
##  -0.2283864   0.0716331  -0.5737095   0.1988142  -0.5370427  -0.6753948 
##      mindom      maxdom     dfrange     modindx    startdom      enddom 
##  -0.0421630  -0.0375370   0.0267182  -0.0646219  -0.0607716  -0.0123189 
##     dfslope         SNR 
##   0.0878456   1.0000000

OOB error rate

## [1] "Vocator"
## [1] 0
## [1] "Diastema"
## [1] 0
## [1] "Hylaeformis"
## [1] 0

Variable importance by species

## [[1]]

## 
## [[2]]

## 
## [[3]]

Proximity matrices (unsuperv RF)

Diastema

AguaBuena Arenal Cahuita Fortuna Golfito Guaria Guayacan Bijagua Manzanillo Piro La Selva Tenorio Tinamastes Tirimbina Uvita
AguaBuena 1.000000 0.052182 0.029401 0.046324 0.158201 0.022209 0.017166 0.026353 0.011311 0.154279 0.043678 0.055934 0.114323 0.027343 0.210498
Arenal 0.052182 1.000000 0.083387 0.092384 0.072550 0.080509 0.069526 0.109745 0.051483 0.072257 0.073837 0.158723 0.059079 0.070976 0.052293
Cahuita 0.029401 0.083387 1.000000 0.101621 0.026744 0.136158 0.172829 0.134069 0.156347 0.029362 0.155053 0.093902 0.017442 0.143877 0.021832
Fortuna 0.046324 0.092384 0.101621 1.000000 0.041130 0.161617 0.085487 0.091710 0.121694 0.042813 0.156682 0.128560 0.022809 0.116958 0.034247
Golfito 0.158201 0.072550 0.026744 0.041130 1.000000 0.025966 0.022309 0.037012 0.013607 0.169269 0.036422 0.063360 0.191337 0.032897 0.193600
Guaria 0.022209 0.080509 0.136158 0.161617 0.025966 1.000000 0.153314 0.135126 0.223576 0.022299 0.165706 0.127563 0.012411 0.170605 0.016095
Guayacan 0.017166 0.069526 0.172829 0.085487 0.022309 0.153314 1.000000 0.190815 0.207572 0.024178 0.121592 0.081088 0.017146 0.183502 0.014374
Bijagua 0.026353 0.109745 0.134069 0.091710 0.037012 0.135126 0.190815 1.000000 0.125105 0.038696 0.127615 0.113605 0.032131 0.160161 0.023810
Manzanillo 0.011311 0.051483 0.156347 0.121694 0.013607 0.223576 0.207572 0.125105 1.000000 0.011609 0.130358 0.075763 0.005918 0.182440 0.007177
Piro 0.154279 0.072257 0.029362 0.042813 0.169269 0.022299 0.024178 0.038696 0.011609 1.000000 0.038330 0.059334 0.173772 0.031019 0.182240
La Selva 0.043678 0.073837 0.155053 0.156682 0.036422 0.165706 0.121592 0.127615 0.130358 0.038330 1.000000 0.123018 0.020418 0.154698 0.030912
Tenorio 0.055934 0.158723 0.093902 0.128560 0.063360 0.127563 0.081088 0.113605 0.075763 0.059334 0.123018 1.000000 0.036681 0.109488 0.045484
Tinamastes 0.114323 0.059079 0.017442 0.022809 0.191337 0.012411 0.017146 0.032131 0.005918 0.173772 0.020418 0.036681 1.000000 0.021824 0.188589
Tirimbina 0.027343 0.070976 0.143877 0.116958 0.032897 0.170605 0.183502 0.160161 0.182440 0.031019 0.154698 0.109488 0.021824 1.000000 0.022974
Uvita 0.210498 0.052293 0.021832 0.034247 0.193600 0.016095 0.014374 0.023810 0.007177 0.182240 0.030912 0.045484 0.188589 0.022974 1.000000

Hylaeformis

Dantas Monserrat Monteverde Poas Queveri Tapanti CerroIncognita
Dantas 1.000000 0.131428 0.105029 0.172354 0.045465 0.035757 0.163634
Monserrat 0.131428 1.000000 0.079244 0.093898 0.026676 0.064984 0.101164
Monteverde 0.105029 0.079244 1.000000 0.099837 0.235384 0.016331 0.109445
Poas 0.172354 0.093898 0.099837 1.000000 0.073201 0.025030 0.201363
Queveri 0.045465 0.026676 0.235384 0.073201 1.000000 0.007386 0.072254
Tapanti 0.035757 0.064984 0.016331 0.025030 0.007386 1.000000 0.024933
CerroIncognita 0.163634 0.101164 0.109445 0.201363 0.072254 0.024933 1.000000

Vocator

Agua Buena Golfito Paraguas
Agua Buena 1.000000 0.109582 0.048391
Golfito 0.109582 1.000000 0.077840
Paraguas 0.048391 0.077840 1.000000

Mantel test for site signature

## [1] "Diastema"
## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## vegan::mantel(xdis = 1 - X, ydis = bm, permutations = 10000) 
## 
## Mantel statistic r: 0.336 
##       Significance: 9.999e-05 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0193 0.0258 0.0319 0.0378 
## Permutation: free
## Number of permutations: 10000
## 
## [1] "Hylaeformis"
## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## vegan::mantel(xdis = 1 - X, ydis = bm, permutations = 10000) 
## 
## Mantel statistic r: 0.54 
##       Significance: 9.999e-05 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0293 0.0395 0.0476 0.0599 
## Permutation: free
## Number of permutations: 10000
## Warning: Removed 1 rows containing missing values (geom_path).

To load the list containing all proximities run:

proxms <- readRDS("Proximities by site unsupervised RF.RDS")



# <img src="/home/m/Downloads/grone.jpeg" alt="R" height="700" width="800"