R Notebook
FV
2023-10-17
packages
# install if required
if(!require(tidyverse)){install.packages("tidyverse")}
if(!require(googlesheets4)){install.packages("googlesheets4")}
if(!require(GGally)){install.packages("GGally")}
if(!require(reshape2)){install.packages("reshape2")}
if(!require(lme4)){install.packages("lme4")}
if(!require(compiler)){install.packages("compiler")}
if(!require(parallel)){install.packages("parallel")}
if(!require(boot)){install.packages("boot")}
if(!require(lattice)){install.packages("lattice")}
if(!require(car)){install.packages("car")}
if(!require(ggpubr)){install.packages("ggpubr")}
if(!require(vegan)){install.packages("vegan")}
if(!require(ggsci)){install.packages("ggsci")}
if(!require(ggrepel)){install.packages("ggrepel")}
if(!require(ggforce)){install.packages("ggforce")}
if(!require(plotly)){install.packages("plotly")}
if(!require(rgl)){install.packages("rgl")}
if(!require(mgcv)){install.packages("mgcv")}
if(!require(factoextra)){install.packages("factoextra")}
if(!require(devtools)){install.packages("devtools")}
if(!require(gridExtra)){install.packages("gridExtra")}
if(!require(psych)){install.packages("psych")}
if(!require(klaR)){install.packages("klaR")}
if(!require(BiodiversityR)){install.packages("BiodiversityR")}
# Load
library(tidyverse)
library(googlesheets4); gs4_deauth()
library(googledrive)
library(GGally)
library(reshape2)
library(lme4)
library(compiler)
library(parallel)
library(boot)
library(lattice)
library(car)
library(ggpubr)
library(vegan)
library(readxl)
library(ggsci)
library(ggrepel)
library(ggforce)
library(plotly)
library(rgl)
library(mgcv)
library(dplyr)
library(factoextra)
library(devtools)
library(gridExtra)
library(psych)
library(klaR)Dataset
Datos asociados al estudio de Condit et al. 2002. Beta-diversity in tropical forest trees. Science 295: 666-669. Supplementary material [data] (https://www.davidzeleny.net/anadat-r/doku.php/en:data:bci)
data(BCI)
BCI.env <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/bci.env.txt', row.names = 1)
BCI.soil <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/bci.soil.txt')Matrices
Se fabrica una sola matriz ambiental (i.e., M2) combinando las variables ambientales per se y las variables de química de suelo.
M1 <- BCI
M2 <- cbind(BCI.env[,3:7], BCI.soil[,c(3:13,15)])
# checking, rownames
check.datasets(M1, M2)## OKOrdination Model
estandarización de la matriz de especies
M1 <- decostand(M1, method="hellinger")Análisis de gradientes indirecto
Utilizar la función correcta para obtener los resultados que se muestran en el resto del documento (pregunta 1 del cuestionario).
ord.model1 <- vegan::______(M1, scale=TRUE)Objetivos:
Determinar los principales “paquetes” o grupos de variables de especies que se asocian entre sí y responden de manera conjunta a gradientes ambientales que aún no se han identificado.
Identificar un grupo de especies que muestre asociación (positiva o negativa) a un gradiente de “desnivel del terreno” (“slope”).
Formatos .long para ggplot
plot2 <- ordiplot(ord.model1, choices = c(1,2) , scaling=0)
sites.long2 <- sites.long(plot2, env.data=M2)
species.long2 <- species.long(plot2)
axis.long <- axis.long(ord.model1, choices = c(1,2))env.fit
spec.envfit <- envfit(plot2, env=M1)
spec.data.envfit <- data.frame(r=spec.envfit$vectors$r, p=spec.envfit$vectors$pvals)
species.long2 <- species.long(plot2, spec.data=spec.data.envfit)
species.long2[order(abs(species.long2$axis1), decreasing = TRUE),]## r p axis1 axis2
## Elaeis.oleifera 0.5743402984 0.001 0.1750452983 -2.422217e-02
## Poulsenia.armata 0.4318085109 0.001 -0.1697704568 2.358422e-02
## Coussarea.curvigemma 0.4094606346 0.001 0.1660386027 -1.844440e-02
## Vochysia.ferruginea 0.5282156247 0.001 0.1614107846 -3.168177e-02
## Quararibea.asterolepis 0.4867649953 0.001 -0.1592313697 -7.310259e-02
## Virola.sebifera 0.4502548808 0.001 -0.1579249042 7.401872e-02
## Ocotea.whitei 0.3092742529 0.002 -0.1544270387 -1.518698e-02
## Lindackeria.laurina 0.4088268419 0.001 0.1449941702 -1.735568e-02
## Virola.surinamensis 0.3646009428 0.001 -0.1430544300 -2.639048e-02
## Cupania.rufescens 0.2950454821 0.002 0.1415609580 -1.458830e-02
## Pouteria.reticulata 0.3812622676 0.001 0.1412971694 -1.399892e-02
## Beilschmiedia.pendula 0.1948097717 0.009 -0.1363101574 3.032761e-02
## Protium.costaricense 0.2850773746 0.001 -0.1291459950 5.333699e-02
## Guatteria.dumetorum 0.2996591540 0.001 -0.1291284203 7.013894e-02
## Spondias.mombin 0.3494606904 0.001 0.1253903065 2.379019e-02
## Ocotea.cernua 0.2978658586 0.001 0.1250630240 5.510329e-02
## Unonopsis.pittieri 0.5106996908 0.001 -0.1229588261 1.240272e-01
## Maquira.guianensis.costaricana 0.3483481332 0.001 -0.1205822579 5.174429e-02
## Lacmellea.panamensis 0.2698085970 0.004 0.1204393150 2.514050e-03
## Terminalia.amazonia 0.3467417794 0.002 0.1200120665 9.847974e-04
## Miconia.argentea 0.2283824680 0.005 0.1177370779 2.543419e-02
## Tetrathylacium.johansenii 0.3122834571 0.003 0.1162650028 -4.667923e-02
## Maclura.tinctoria 0.2457037823 0.026 0.1126750485 -1.998185e-02
## Oenocarpus.mapora 0.3357133516 0.001 0.1111138074 7.795840e-02
## Cassipourea.guianensis 0.3767127819 0.001 0.1110714612 4.992722e-03
## Annona.spraguei 0.2920273871 0.002 0.1092142537 7.327653e-02
## Talisia.nervosa 0.2223831099 0.042 0.1080446385 -1.211168e-02
## Alibertia.edulis 0.2223831099 0.042 0.1080446385 -1.211168e-02
## Chimarrhis.parviflora 0.2223831099 0.042 0.1080446385 -1.211168e-02
## Sterculia.apetala 0.2987032253 0.003 0.1043124862 -4.902388e-02
## Trichilia.pallida 0.1447594208 0.032 0.1042798962 1.122792e-02
## Ficus.insipida 0.2185800223 0.007 0.1025017388 -4.390477e-02
## Chamguava.schippii 0.2231101992 0.009 0.1025007513 -1.322618e-02
## Coccoloba.manzinellensis 0.1908958954 0.010 0.1021293872 -1.961479e-02
## Randia.armata 0.1906419943 0.010 0.1013510699 -5.342017e-02
## Guarea.fuzzy 0.1445172349 0.039 -0.0968378329 -3.948847e-02
## Sloanea.terniflora 0.2249469971 0.004 -0.0952348317 -6.112694e-02
## Trophis.caucana 0.2136703991 0.006 -0.0942323645 -6.097842e-02
## Tabernaemontana.arborea 0.3883349102 0.001 0.0930303713 1.298078e-01
## Ficus.tonduzii 0.1655926156 0.012 -0.0914932988 2.771867e-02
## Luehea.seemannii 0.2940209468 0.001 0.0891368560 -1.037661e-01
## Faramea.occidentalis 0.0717964585 0.164 0.0877737007 -4.596480e-04
## Garcinia.intermedia 0.2046214059 0.005 0.0841182311 -7.293547e-02
## Inga.laurina 0.1235024421 0.049 0.0831292521 -8.665913e-03
## Chrysophyllum.cainito 0.1509596300 0.015 0.0815832614 -3.943790e-02
## Virola.multiflora 0.1413280809 0.028 -0.0811343253 -4.365545e-02
## Guarea.guidonia 0.4924769828 0.001 -0.0806231849 -1.727302e-01
## Inga.cocleensis 0.5118631946 0.001 0.0796131871 1.721308e-01
## Symphonia.globulifera 0.1673098572 0.017 -0.0795102191 5.017713e-02
## Apeiba.tibourbou 0.1057374294 0.083 0.0786355908 2.325283e-02
## Laetia.thamnia 0.4773244045 0.001 0.0776052616 1.524141e-01
## Drypetes.standleyi 0.2274287662 0.002 -0.0752226210 -1.398280e-01
## Ocotea.oblonga 0.0980271372 0.092 -0.0746455527 -4.048272e-02
## Attalea.butyracea 0.1693883399 0.014 0.0733751479 -6.009243e-02
## Inga.pezizifera 0.2093073814 0.009 -0.0731020578 -9.126350e-02
## Tetragastris.panamensis 0.0924930369 0.106 0.0727810644 -4.480816e-03
## Astrocaryum.standleyanum 0.2134155279 0.008 0.0716500753 -1.158528e-01
## Triplaris.cumingiana 0.3421202672 0.001 0.0714133408 -1.515940e-01
## Guazuma.ulmifolia 0.0740024508 0.141 0.0712406513 -2.213165e-02
## Aegiphila.panamensis 0.0601029310 0.204 0.0709489500 2.163965e-02
## Lonchocarpus.heptaphyllus 0.1784344372 0.016 0.0707196338 8.843497e-02
## Laetia.procera 0.2205888736 0.003 0.0705046956 8.467786e-02
## Sapium.broadleaf 0.1458920245 0.030 -0.0703730221 -5.741856e-02
## Inga.nobilis 0.1284084864 0.033 -0.0702827864 -2.469086e-02
## Alchornea.costaricensis 0.0480148920 0.327 -0.0702305454 -1.262950e-02
## Eugenia.nesiotica 0.0575173798 0.234 0.0697839145 -2.542026e-02
## Platypodium.elegans 0.1535580918 0.022 0.0691581947 7.737352e-02
## Inga.semialata 0.0998839926 0.072 -0.0690117013 1.207646e-02
## Ficus.trigonata 0.1780511840 0.010 -0.0686884703 -7.503453e-02
## Socratea.exorrhiza 0.3136720464 0.003 -0.0683370975 1.536010e-01
## Protium.tenuifolium 0.1840739209 0.014 -0.0682415828 -8.199485e-02
## Hasseltia.floribunda 0.1977229436 0.009 -0.0681638038 8.316996e-02
## Eugenia.florida 0.0506581345 0.305 0.0673215011 -4.317959e-02
## Pouteria.stipitata 0.1224446760 0.056 0.0667317804 3.791848e-02
## Prioria.copaifera 0.0398493058 0.382 0.0667013811 1.430565e-02
## Aspidosperma.desmanthum 0.2380503789 0.004 -0.0657856039 -1.020737e-01
## Hieronyma.alchorneoides 0.0935189836 0.112 0.0655087227 -1.778066e-02
## Cordia.lasiocalyx 0.3588973441 0.001 -0.0653782245 -1.296529e-01
## Erythrina.costaricensis 0.0754098518 0.171 -0.0651969386 -1.157962e-07
## Inga.goldmanii 0.0761731571 0.164 0.0638845315 9.107447e-03
## Psychotria.grandis 0.0851298658 0.091 0.0623792112 -2.708979e-02
## Banara.guianensis 0.0851298658 0.091 0.0623792112 -2.708979e-02
## Inga.ruiziana 0.1387963901 0.048 0.0619536996 -3.017346e-02
## Casearia.guianensis 0.0807639976 0.126 0.0615877149 -2.263684e-02
## Ficus.costaricana 0.0510002998 0.266 0.0608160750 -2.045126e-02
## Croton.billbergianus 0.1012373651 0.086 0.0603353823 2.323696e-02
## Xylopia.macrantha 0.1320962044 0.033 -0.0579294211 -5.404743e-02
## Casearia.sylvestris 0.0528237699 0.282 0.0571309347 -3.434255e-02
## Platymiscium.pinnatum 0.0711951022 0.176 0.0562791843 3.817568e-02
## Terminalia.oblonga 0.1203535444 0.043 -0.0556480036 -7.338606e-02
## Marila.laxiflora 0.0537182530 0.259 -0.0537234528 -1.937800e-02
## Pterocarpus.rohrii 0.0998822688 0.095 0.0535050229 -6.666815e-02
## Dipteryx.oleifera 0.1774182198 0.009 -0.0523996035 8.928197e-02
## Swartzia.simplex.continentalis 0.0569659457 0.270 0.0522649788 -5.828558e-02
## Dendropanax.arboreus 0.2798537867 0.003 0.0518272796 1.223163e-01
## Lafoensia.punicifolia 0.0990106742 0.079 0.0516733981 6.287667e-02
## Theobroma.cacao 0.0580340265 0.239 -0.0515421458 4.145704e-03
## Turpinia.occidentalis 0.1083477025 0.058 -0.0513503487 8.123746e-02
## Swartzia.simplex.var.grandiflora 0.0791221627 0.138 0.0506430921 -4.361232e-02
## Jacaranda.copaia 0.4362878461 0.001 0.0504901693 1.603070e-01
## Picramnia.latifolia 0.1872462137 0.015 -0.0500996298 -8.921384e-02
## Trophis.racemosa 0.0495868897 0.308 0.0497380359 -7.727703e-03
## Enterolobium.schomburgkii 0.0727005483 0.164 0.0492873753 4.198689e-02
## Nectandra.cissiflora 0.3491868448 0.001 -0.0491554361 1.307182e-01
## Hirtella.americana 0.0628148536 0.176 0.0482519696 -2.884972e-02
## Siparuna.pauciflora 0.1901941527 0.016 -0.0478577201 8.811169e-02
## Cecropia.obtusifolia 0.0514721496 0.280 0.0446206850 3.284906e-02
## Cupania.cinerea 0.0737157226 0.189 0.0440996686 4.803182e-02
## Miconia.elata 0.0737157226 0.189 0.0440996686 4.803182e-02
## Ceiba.pentandra 0.0697279465 0.183 0.0436830091 3.959766e-02
## Posoqueria.latifolia 0.1142619833 0.061 0.0434313319 -5.879332e-02
## Hirtella.triandra 0.1526227327 0.021 -0.0432338588 -7.039971e-02
## Handroanthus.guayacan 0.0280194421 0.542 0.0430708562 -3.435238e-03
## Cordia.alliodora 0.0591587681 0.283 0.0418869600 4.783553e-02
## Cupania.seemannii 0.2884415711 0.001 0.0416622112 1.104988e-01
## Sorocea.affinis 0.0429467165 0.350 -0.0407821917 8.533019e-04
## Eugenia.oerstediana 0.0404185523 0.389 0.0407007091 -1.378367e-03
## Brosimum.alicastrum 0.0262985452 0.527 -0.0405634681 -3.839712e-02
## Cedrela.odorata 0.0618829747 0.214 -0.0403773030 4.255082e-02
## Apeiba.glabra 0.1944708464 0.006 -0.0403256476 9.978655e-02
## Heisteria.acuminata 0.0338804617 0.451 -0.0402468854 1.221643e-02
## Pseudobombax.septenatum 0.0431840509 0.382 0.0400316963 -3.167864e-02
## Cespedesia.spathulata 0.0432970170 0.325 -0.0399922748 -2.890882e-02
## Hampea.appendiculata 0.0763846201 0.166 -0.0385265888 4.623842e-02
## Zanthoxylum.ekmanii 0.3187543453 0.001 -0.0384216484 1.323333e-01
## Miconia.hondurensis 0.1541378352 0.019 0.0372348125 9.908023e-02
## Zuelania.guidonia 0.0366998782 0.424 0.0366892787 -4.042668e-02
## Cordia.bicolor 0.5869093190 0.001 -0.0362468397 1.904636e-01
## Maytenus.schippii 0.0237026108 0.586 -0.0350860298 2.282744e-03
## Zanthoxylum.juniperinum 0.2101766481 0.005 0.0349768243 9.794369e-02
## Inga.acuminata 0.0719186780 0.147 -0.0349753506 -7.536064e-02
## Pourouma.bicolor 0.1341284712 0.047 -0.0347600423 1.018298e-01
## Thevetia.ahouai 0.0437200706 0.325 0.0343683297 -3.893363e-02
## Hura.crepitans 0.4428451003 0.001 -0.0340111731 -1.813414e-01
## Gustavia.superba 0.0325241173 0.431 0.0330421055 -7.411106e-02
## Mosannona.garwoodii 0.0254275738 0.566 0.0325710333 1.738218e-02
## Cecropia.insignis 0.4817599431 0.001 -0.0312504354 1.660203e-01
## Quassia.amara 0.0536646803 0.240 0.0309751327 -4.098348e-02
## Inga.umbellifera 0.1551457615 0.020 -0.0307224297 8.437132e-02
## Margaritaria.nobilis 0.0187378567 0.633 -0.0306538849 -1.040378e-02
## Tocoyena.pittieri 0.0204485417 0.650 -0.0306134737 -9.901149e-03
## Casearia.arborea 0.2916917045 0.002 -0.0304118103 1.208241e-01
## Allophylus.psilospermus 0.0526478968 0.278 0.0303087161 -6.076434e-02
## Alseis.blackiana 0.0255369322 0.540 0.0302698491 -2.379486e-02
## Trichilia.tuberculata 0.0052680412 0.886 0.0299278005 1.516868e-02
## Cinnamomum.triplinerve 0.0462946056 0.337 0.0292687631 4.502334e-02
## Licania.hypoleuca 0.1686690252 0.014 0.0290688031 9.295951e-02
## Macrocnemum.roseum 0.1303347260 0.031 -0.0281310092 -1.174269e-01
## Inga.punctata 0.0142007460 0.719 -0.0277735003 1.074637e-03
## Casearia.commersoniana 0.1828388286 0.015 -0.0261146888 1.032987e-01
## Perebea.xanthochyma 0.2683649467 0.003 -0.0260880154 1.539287e-01
## Lacistema.aggregatum 0.0310007161 0.469 -0.0259584563 3.863916e-02
## Cavanillesia.platanifolia 0.2276341819 0.002 -0.0256566354 -1.244015e-01
## Ocotea.puberula 0.2561671254 0.002 0.0254156718 1.134156e-01
## Talisia.princeps 0.0132811451 0.732 -0.0254077531 -9.629117e-03
## Pachira.sessilis 0.0128353223 0.731 0.0244528940 9.870914e-03
## Piper.reticulatum 0.0169547535 0.665 -0.0242126493 -2.619437e-02
## Chrysochlamys.eclipes 0.0187732271 0.605 -0.0240510361 -2.250821e-02
## Sapium.glandulosum 0.0191651531 0.623 0.0240219491 -4.059383e-02
## Calophyllum.longifolium 0.0151730835 0.692 0.0239973207 1.153496e-02
## Myrospermum.frutescens 0.0298670809 0.489 0.0230495616 -2.316543e-02
## Ficus.maxima 0.0104634547 0.783 -0.0227373242 -7.815251e-03
## Inga.sapindoides 0.0147685896 0.733 -0.0226155704 -1.587855e-03
## Solanum.hayesii 0.0442118384 0.365 -0.0224614260 3.537622e-02
## Abarema.macradenia 0.0818658547 0.092 -0.0220071621 6.729056e-02
## Chrysophyllum.argenteum 0.0962148822 0.097 -0.0218645215 7.186403e-02
## Ficus.obtusifolia 0.0117197250 0.792 0.0215667055 -1.615799e-02
## Ficus.yoponensis 0.0106929705 0.800 0.0212861278 1.129907e-02
## Genipa.americana 0.0091247533 0.780 0.0208008745 -1.751104e-02
## Celtis.schippii 0.0128593550 0.742 -0.0206307748 -2.517406e-02
## Andira.inermis 0.0265908353 0.529 -0.0204866451 -3.437513e-02
## Colubrina.glandulosa 0.0084130911 0.827 0.0203146240 -6.286080e-03
## Vismia.baccifera 0.0134365623 0.710 -0.0197040380 -1.951676e-02
## Guarea.grandifolia 0.0948223843 0.095 -0.0195017238 6.209977e-02
## Inga.oerstediana 0.0072555170 0.849 -0.0190201374 -6.963230e-04
## Nectandra.purpurea 0.0068677447 0.848 0.0184766330 -6.068963e-03
## Anacardium.excelsum 0.0943869032 0.103 0.0182557826 -6.523981e-02
## Senna.dariensis 0.0179457158 0.600 -0.0175760023 -2.747162e-02
## Zanthoxylum.setulosum 0.0179457158 0.600 -0.0175760023 -2.747162e-02
## Siparuna.guianensis 0.1053293028 0.085 0.0175456726 7.626172e-02
## Pachira.quinata 0.0067815801 0.877 0.0173641154 8.269896e-03
## Cupania.latifolia 0.0173987438 0.663 -0.0172364388 -2.107104e-02
## Diospyros.artanthifolia 0.0168949811 0.668 0.0169727296 2.519683e-02
## Psidium.friedrichsthalianum 0.0577084408 0.257 0.0166899965 -5.727416e-02
## Brosimum.guianense 0.0236665088 0.567 0.0161826933 -3.414685e-02
## Trichanthera.gigantea 0.0076726118 0.832 0.0155485050 1.393713e-02
## Amaioua.corymbosa 0.0491233172 0.245 0.0152226294 -5.080944e-02
## Schizolobium.parahyba 0.0045688983 0.911 0.0151128960 3.873780e-03
## Miconia.affinis 0.1023931662 0.065 0.0148855646 7.705917e-02
## Coccoloba.coronata 0.1608562486 0.015 -0.0142891062 8.789727e-02
## Zanthoxylum.panamense 0.2531143764 0.004 -0.0140191038 1.125730e-01
## Licania.platypus 0.0939800057 0.095 -0.0136657484 -6.779036e-02
## Ochroma.pyramidale 0.1433380509 0.034 -0.0131491727 1.046750e-01
## Guettarda.foliacea 0.0362604960 0.461 0.0130522392 3.933901e-02
## Nectandra.lineata 0.0046010516 0.888 0.0127530631 -1.139109e-02
## Simarouba.amara 0.4219095977 0.001 -0.0125558751 1.550294e-01
## Casearia.aculeata 0.0524696830 0.257 0.0122157614 -5.788775e-02
## Guapira.myrtiflora 0.0368518852 0.402 0.0116779209 -4.189418e-02
## Tachigali.versicolor 0.0349587467 0.443 0.0113669575 3.300130e-02
## Ormosia.coccinea 0.0249054053 0.557 0.0105660321 -3.704089e-02
## Trema.micrantha 0.0047114119 0.903 -0.0104557559 -1.118998e-02
## Vachellia.melanoceras 0.0181534028 0.658 -0.0100181937 -3.418234e-02
## Ormosia.macrocalyx 0.0198790327 0.633 0.0099569326 -3.329718e-02
## Eugenia.galalonensis 0.0142332359 0.714 -0.0099244620 -1.603039e-02
## Desmopsis.panamensis 0.0281150197 0.459 -0.0096711713 1.461482e-02
## Pouteria.fossicola 0.0018984359 0.963 -0.0096461336 1.535504e-03
## Spondias.radlkoferi 0.0513955672 0.299 0.0081013189 3.279737e-02
## Protium.panamense 0.0574927644 0.245 0.0075073301 4.740557e-02
## Astronium.graveolens 0.0003951352 0.986 0.0074223999 -4.928057e-03
## Heisteria.concinna 0.1189181994 0.044 0.0073486195 -9.307281e-02
## Ficus.colubrinae 0.0369464457 0.420 -0.0063026714 4.746963e-02
## Myrcia.gatunensis 0.1176781935 0.055 0.0061593941 8.602427e-02
## Spachea.membranacea 0.0093541071 0.789 0.0057215724 3.710014e-02
## Acalypha.diversifolia 0.0476250929 0.305 0.0044404478 -5.429103e-02
## Tabebuia.rosea 0.1417904199 0.030 -0.0042574804 -9.465251e-02
## Trichospermum.galeottii 0.0747811266 0.146 -0.0040676744 6.808693e-02
## Acalypha.macrostachya 0.0066674293 0.900 -0.0035649548 -2.000366e-02
## Ficus.popenoei 0.0100186720 0.789 -0.0025032225 -2.472993e-02
## Adelia.triloba 0.0354352289 0.439 0.0017871098 -6.220665e-02
## Garcinia.madruno 0.0968700899 0.088 0.0017133841 8.203762e-02
## Inga.spectabilis 0.1451984832 0.030 -0.0015181153 9.030762e-02
## Trattinnickia.aspera 0.0453219383 0.342 0.0010721599 7.060280e-02
## Erythroxylum.macrophyllum 0.0419357890 0.380 -0.0009639826 5.283014e-02
## Alchornea.latifolia 0.0021933676 0.981 0.0009093084 1.164347e-02
## Ormosia.amazonica 0.0001628752 1.000 0.0004181332 3.151841e-03
## labels
## Elaeis.oleifera Elaeis.oleifera
## Poulsenia.armata Poulsenia.armata
## Coussarea.curvigemma Coussarea.curvigemma
## Vochysia.ferruginea Vochysia.ferruginea
## Quararibea.asterolepis Quararibea.asterolepis
## Virola.sebifera Virola.sebifera
## Ocotea.whitei Ocotea.whitei
## Lindackeria.laurina Lindackeria.laurina
## Virola.surinamensis Virola.surinamensis
## Cupania.rufescens Cupania.rufescens
## Pouteria.reticulata Pouteria.reticulata
## Beilschmiedia.pendula Beilschmiedia.pendula
## Protium.costaricense Protium.costaricense
## Guatteria.dumetorum Guatteria.dumetorum
## Spondias.mombin Spondias.mombin
## Ocotea.cernua Ocotea.cernua
## Unonopsis.pittieri Unonopsis.pittieri
## Maquira.guianensis.costaricana Maquira.guianensis.costaricana
## Lacmellea.panamensis Lacmellea.panamensis
## Terminalia.amazonia Terminalia.amazonia
## Miconia.argentea Miconia.argentea
## Tetrathylacium.johansenii Tetrathylacium.johansenii
## Maclura.tinctoria Maclura.tinctoria
## Oenocarpus.mapora Oenocarpus.mapora
## Cassipourea.guianensis Cassipourea.guianensis
## Annona.spraguei Annona.spraguei
## Talisia.nervosa Talisia.nervosa
## Alibertia.edulis Alibertia.edulis
## Chimarrhis.parviflora Chimarrhis.parviflora
## Sterculia.apetala Sterculia.apetala
## Trichilia.pallida Trichilia.pallida
## Ficus.insipida Ficus.insipida
## Chamguava.schippii Chamguava.schippii
## Coccoloba.manzinellensis Coccoloba.manzinellensis
## Randia.armata Randia.armata
## Guarea.fuzzy Guarea.fuzzy
## Sloanea.terniflora Sloanea.terniflora
## Trophis.caucana Trophis.caucana
## Tabernaemontana.arborea Tabernaemontana.arborea
## Ficus.tonduzii Ficus.tonduzii
## Luehea.seemannii Luehea.seemannii
## Faramea.occidentalis Faramea.occidentalis
## Garcinia.intermedia Garcinia.intermedia
## Inga.laurina Inga.laurina
## Chrysophyllum.cainito Chrysophyllum.cainito
## Virola.multiflora Virola.multiflora
## Guarea.guidonia Guarea.guidonia
## Inga.cocleensis Inga.cocleensis
## Symphonia.globulifera Symphonia.globulifera
## Apeiba.tibourbou Apeiba.tibourbou
## Laetia.thamnia Laetia.thamnia
## Drypetes.standleyi Drypetes.standleyi
## Ocotea.oblonga Ocotea.oblonga
## Attalea.butyracea Attalea.butyracea
## Inga.pezizifera Inga.pezizifera
## Tetragastris.panamensis Tetragastris.panamensis
## Astrocaryum.standleyanum Astrocaryum.standleyanum
## Triplaris.cumingiana Triplaris.cumingiana
## Guazuma.ulmifolia Guazuma.ulmifolia
## Aegiphila.panamensis Aegiphila.panamensis
## Lonchocarpus.heptaphyllus Lonchocarpus.heptaphyllus
## Laetia.procera Laetia.procera
## Sapium.broadleaf Sapium.broadleaf
## Inga.nobilis Inga.nobilis
## Alchornea.costaricensis Alchornea.costaricensis
## Eugenia.nesiotica Eugenia.nesiotica
## Platypodium.elegans Platypodium.elegans
## Inga.semialata Inga.semialata
## Ficus.trigonata Ficus.trigonata
## Socratea.exorrhiza Socratea.exorrhiza
## Protium.tenuifolium Protium.tenuifolium
## Hasseltia.floribunda Hasseltia.floribunda
## Eugenia.florida Eugenia.florida
## Pouteria.stipitata Pouteria.stipitata
## Prioria.copaifera Prioria.copaifera
## Aspidosperma.desmanthum Aspidosperma.desmanthum
## Hieronyma.alchorneoides Hieronyma.alchorneoides
## Cordia.lasiocalyx Cordia.lasiocalyx
## Erythrina.costaricensis Erythrina.costaricensis
## Inga.goldmanii Inga.goldmanii
## Psychotria.grandis Psychotria.grandis
## Banara.guianensis Banara.guianensis
## Inga.ruiziana Inga.ruiziana
## Casearia.guianensis Casearia.guianensis
## Ficus.costaricana Ficus.costaricana
## Croton.billbergianus Croton.billbergianus
## Xylopia.macrantha Xylopia.macrantha
## Casearia.sylvestris Casearia.sylvestris
## Platymiscium.pinnatum Platymiscium.pinnatum
## Terminalia.oblonga Terminalia.oblonga
## Marila.laxiflora Marila.laxiflora
## Pterocarpus.rohrii Pterocarpus.rohrii
## Dipteryx.oleifera Dipteryx.oleifera
## Swartzia.simplex.continentalis Swartzia.simplex.continentalis
## Dendropanax.arboreus Dendropanax.arboreus
## Lafoensia.punicifolia Lafoensia.punicifolia
## Theobroma.cacao Theobroma.cacao
## Turpinia.occidentalis Turpinia.occidentalis
## Swartzia.simplex.var.grandiflora Swartzia.simplex.var.grandiflora
## Jacaranda.copaia Jacaranda.copaia
## Picramnia.latifolia Picramnia.latifolia
## Trophis.racemosa Trophis.racemosa
## Enterolobium.schomburgkii Enterolobium.schomburgkii
## Nectandra.cissiflora Nectandra.cissiflora
## Hirtella.americana Hirtella.americana
## Siparuna.pauciflora Siparuna.pauciflora
## Cecropia.obtusifolia Cecropia.obtusifolia
## Cupania.cinerea Cupania.cinerea
## Miconia.elata Miconia.elata
## Ceiba.pentandra Ceiba.pentandra
## Posoqueria.latifolia Posoqueria.latifolia
## Hirtella.triandra Hirtella.triandra
## Handroanthus.guayacan Handroanthus.guayacan
## Cordia.alliodora Cordia.alliodora
## Cupania.seemannii Cupania.seemannii
## Sorocea.affinis Sorocea.affinis
## Eugenia.oerstediana Eugenia.oerstediana
## Brosimum.alicastrum Brosimum.alicastrum
## Cedrela.odorata Cedrela.odorata
## Apeiba.glabra Apeiba.glabra
## Heisteria.acuminata Heisteria.acuminata
## Pseudobombax.septenatum Pseudobombax.septenatum
## Cespedesia.spathulata Cespedesia.spathulata
## Hampea.appendiculata Hampea.appendiculata
## Zanthoxylum.ekmanii Zanthoxylum.ekmanii
## Miconia.hondurensis Miconia.hondurensis
## Zuelania.guidonia Zuelania.guidonia
## Cordia.bicolor Cordia.bicolor
## Maytenus.schippii Maytenus.schippii
## Zanthoxylum.juniperinum Zanthoxylum.juniperinum
## Inga.acuminata Inga.acuminata
## Pourouma.bicolor Pourouma.bicolor
## Thevetia.ahouai Thevetia.ahouai
## Hura.crepitans Hura.crepitans
## Gustavia.superba Gustavia.superba
## Mosannona.garwoodii Mosannona.garwoodii
## Cecropia.insignis Cecropia.insignis
## Quassia.amara Quassia.amara
## Inga.umbellifera Inga.umbellifera
## Margaritaria.nobilis Margaritaria.nobilis
## Tocoyena.pittieri Tocoyena.pittieri
## Casearia.arborea Casearia.arborea
## Allophylus.psilospermus Allophylus.psilospermus
## Alseis.blackiana Alseis.blackiana
## Trichilia.tuberculata Trichilia.tuberculata
## Cinnamomum.triplinerve Cinnamomum.triplinerve
## Licania.hypoleuca Licania.hypoleuca
## Macrocnemum.roseum Macrocnemum.roseum
## Inga.punctata Inga.punctata
## Casearia.commersoniana Casearia.commersoniana
## Perebea.xanthochyma Perebea.xanthochyma
## Lacistema.aggregatum Lacistema.aggregatum
## Cavanillesia.platanifolia Cavanillesia.platanifolia
## Ocotea.puberula Ocotea.puberula
## Talisia.princeps Talisia.princeps
## Pachira.sessilis Pachira.sessilis
## Piper.reticulatum Piper.reticulatum
## Chrysochlamys.eclipes Chrysochlamys.eclipes
## Sapium.glandulosum Sapium.glandulosum
## Calophyllum.longifolium Calophyllum.longifolium
## Myrospermum.frutescens Myrospermum.frutescens
## Ficus.maxima Ficus.maxima
## Inga.sapindoides Inga.sapindoides
## Solanum.hayesii Solanum.hayesii
## Abarema.macradenia Abarema.macradenia
## Chrysophyllum.argenteum Chrysophyllum.argenteum
## Ficus.obtusifolia Ficus.obtusifolia
## Ficus.yoponensis Ficus.yoponensis
## Genipa.americana Genipa.americana
## Celtis.schippii Celtis.schippii
## Andira.inermis Andira.inermis
## Colubrina.glandulosa Colubrina.glandulosa
## Vismia.baccifera Vismia.baccifera
## Guarea.grandifolia Guarea.grandifolia
## Inga.oerstediana Inga.oerstediana
## Nectandra.purpurea Nectandra.purpurea
## Anacardium.excelsum Anacardium.excelsum
## Senna.dariensis Senna.dariensis
## Zanthoxylum.setulosum Zanthoxylum.setulosum
## Siparuna.guianensis Siparuna.guianensis
## Pachira.quinata Pachira.quinata
## Cupania.latifolia Cupania.latifolia
## Diospyros.artanthifolia Diospyros.artanthifolia
## Psidium.friedrichsthalianum Psidium.friedrichsthalianum
## Brosimum.guianense Brosimum.guianense
## Trichanthera.gigantea Trichanthera.gigantea
## Amaioua.corymbosa Amaioua.corymbosa
## Schizolobium.parahyba Schizolobium.parahyba
## Miconia.affinis Miconia.affinis
## Coccoloba.coronata Coccoloba.coronata
## Zanthoxylum.panamense Zanthoxylum.panamense
## Licania.platypus Licania.platypus
## Ochroma.pyramidale Ochroma.pyramidale
## Guettarda.foliacea Guettarda.foliacea
## Nectandra.lineata Nectandra.lineata
## Simarouba.amara Simarouba.amara
## Casearia.aculeata Casearia.aculeata
## Guapira.myrtiflora Guapira.myrtiflora
## Tachigali.versicolor Tachigali.versicolor
## Ormosia.coccinea Ormosia.coccinea
## Trema.micrantha Trema.micrantha
## Vachellia.melanoceras Vachellia.melanoceras
## Ormosia.macrocalyx Ormosia.macrocalyx
## Eugenia.galalonensis Eugenia.galalonensis
## Desmopsis.panamensis Desmopsis.panamensis
## Pouteria.fossicola Pouteria.fossicola
## Spondias.radlkoferi Spondias.radlkoferi
## Protium.panamense Protium.panamense
## Astronium.graveolens Astronium.graveolens
## Heisteria.concinna Heisteria.concinna
## Ficus.colubrinae Ficus.colubrinae
## Myrcia.gatunensis Myrcia.gatunensis
## Spachea.membranacea Spachea.membranacea
## Acalypha.diversifolia Acalypha.diversifolia
## Tabebuia.rosea Tabebuia.rosea
## Trichospermum.galeottii Trichospermum.galeottii
## Acalypha.macrostachya Acalypha.macrostachya
## Ficus.popenoei Ficus.popenoei
## Adelia.triloba Adelia.triloba
## Garcinia.madruno Garcinia.madruno
## Inga.spectabilis Inga.spectabilis
## Trattinnickia.aspera Trattinnickia.aspera
## Erythroxylum.macrophyllum Erythroxylum.macrophyllum
## Alchornea.latifolia Alchornea.latifolia
## Ormosia.amazonica Ormosia.amazonica## Vector Fit
vectors.envfit <- envfit(plot2, env= M2)
vectors.long3 <- vectorfit.long(vectors.envfit)
vectors.long3[order(vectors.long3$r, decreasing = TRUE),]## vector axis1 axis2 r p
## pH pH -0.6733827 -0.7392941 0.749067498 0.001
## B B -0.6715563 -0.7409536 0.608960844 0.001
## Zn Zn -0.4375430 -0.8991975 0.588198669 0.001
## K K -0.6564503 -0.7543692 0.581789521 0.001
## Ca Ca -0.6512359 -0.7588754 0.476065968 0.001
## Cu Cu -0.9272676 -0.3743993 0.417551384 0.001
## Mn Mn -0.9706953 -0.2403138 0.402845746 0.001
## slope slope -0.9430936 -0.3325273 0.402264254 0.001
## Al Al 0.7996414 0.6004778 0.399878301 0.001
## Mg Mg -0.4999652 -0.8660455 0.348792534 0.001
## P P 0.8910532 -0.4538988 0.288904483 0.001
## Fe Fe -0.4256258 -0.9048993 0.287705405 0.002
## convex convex 0.1408759 -0.9900273 0.261094388 0.001
## N N -0.5529926 -0.8331862 0.243798010 0.002
## aspectEW aspectEW -0.8886350 -0.4586152 0.117310488 0.062
## aspectNS aspectNS 0.5534512 -0.8328816 0.051645183 0.267
## elevation elevation -0.9929408 -0.1186111 0.001034524 0.977### Spec r > 0.4
species.long3 <- species.long2[species.long2$r >= 0.4, ]
species.long3## r p axis1 axis2
## Cecropia.insignis 0.4817599 0.001 -0.03125044 0.16602026
## Cordia.bicolor 0.5869093 0.001 -0.03624684 0.19046364
## Coussarea.curvigemma 0.4094606 0.001 0.16603860 -0.01844440
## Elaeis.oleifera 0.5743403 0.001 0.17504530 -0.02422217
## Guarea.guidonia 0.4924770 0.001 -0.08062318 -0.17273016
## Hura.crepitans 0.4428451 0.001 -0.03401117 -0.18134145
## Inga.cocleensis 0.5118632 0.001 0.07961319 0.17213078
## Jacaranda.copaia 0.4362878 0.001 0.05049017 0.16030697
## Laetia.thamnia 0.4773244 0.001 0.07760526 0.15241413
## Lindackeria.laurina 0.4088268 0.001 0.14499417 -0.01735568
## Poulsenia.armata 0.4318085 0.001 -0.16977046 0.02358422
## Quararibea.asterolepis 0.4867650 0.001 -0.15923137 -0.07310259
## Simarouba.amara 0.4219096 0.001 -0.01255588 0.15502936
## Unonopsis.pittieri 0.5106997 0.001 -0.12295883 0.12402724
## Virola.sebifera 0.4502549 0.001 -0.15792490 0.07401872
## Vochysia.ferruginea 0.5282156 0.001 0.16141078 -0.03168177
## labels
## Cecropia.insignis Cecropia.insignis
## Cordia.bicolor Cordia.bicolor
## Coussarea.curvigemma Coussarea.curvigemma
## Elaeis.oleifera Elaeis.oleifera
## Guarea.guidonia Guarea.guidonia
## Hura.crepitans Hura.crepitans
## Inga.cocleensis Inga.cocleensis
## Jacaranda.copaia Jacaranda.copaia
## Laetia.thamnia Laetia.thamnia
## Lindackeria.laurina Lindackeria.laurina
## Poulsenia.armata Poulsenia.armata
## Quararibea.asterolepis Quararibea.asterolepis
## Simarouba.amara Simarouba.amara
## Unonopsis.pittieri Unonopsis.pittieri
## Virola.sebifera Virola.sebifera
## Vochysia.ferruginea Vochysia.ferruginea### Var Ambientales r >= 0.4
vectors.long3 <- vectors.long3[vectors.long3$r >= 0.4, ]
vectors.long3## vector axis1 axis2 r p
## slope slope -0.9430936 -0.3325273 0.4022643 0.001
## B B -0.6715563 -0.7409536 0.6089608 0.001
## Ca Ca -0.6512359 -0.7588754 0.4760660 0.001
## Cu Cu -0.9272676 -0.3743993 0.4175514 0.001
## K K -0.6564503 -0.7543692 0.5817895 0.001
## Mn Mn -0.9706953 -0.2403138 0.4028457 0.001
## Zn Zn -0.4375430 -0.8991975 0.5881987 0.001
## pH pH -0.6733827 -0.7392941 0.7490675 0.001plots
f = 1
plotgg2 <- ggplot() +
geom_vline(xintercept = c(0), color = "grey70", linetype = 2) +
geom_hline(yintercept = c(0), color = "grey70", linetype = 2) +
#xlab(axis.long[1, "label"]) +
# ylab(axis.long[2, "label"]) +
scale_x_continuous(sec.axis = dup_axis(labels=NULL, name=NULL)) +
scale_y_continuous(sec.axis = dup_axis(labels=NULL, name=NULL)) +
geom_point(data=sites.long2,
aes(x=axis1, y=axis2),
size=1, shape=1) +
### species
geom_point(data=species.long3,aes(x=axis1*f, y=axis2*f)) +
geom_segment(data=species.long3,aes(x=0, y=0, xend=axis1*f, yend=axis2*f),colour="darkred", linewidth=0.7, arrow=arrow(angle=20)) +
geom_text_repel(data=species.long3,aes(x=axis1*f, y=axis2*f, label=labels),colour="darkred") +
### env
#geom_segment(data=vectors.long3,aes(x=0, y=0, xend=axis1*f, yend=axis2*f),colour="blue", linewidth=0.7, arrow=arrow(angle=20)) +
#geom_text_repel(data=vectors.long3,aes(x=axis1*f, y=axis2*f, label=vector),colour="blue") +
### groups
#geom_polygon(data=AgeCat.ellipses.long,
# aes(x=axis1, y=axis2, colour= AgeCat.ellipses.long$Age.Cat,
# fill=after_scale(alpha(colour, 0.2))),
# linewidth=0.2, show.legend=TRUE) +
#geom_point(data=centroids.long1,
# aes(x=axis1c,y=axis2c, col=centroids.long1$Centroid)) +
ggsci::scale_color_cosmic() +
coord_fixed(ratio=1)
plotgg2
Ordisurf
plot2 <- ordiplot(ord.model1, choices = c(1,2), display = "sites" , scaling=1)
ordisurf(plot2, y=as.numeric(M2$slope), add=FALSE, col="blue", bubble=5)