R/getTraits.R
In LimaRAF/TreeCo: An R Package to Manage TreeCo Database
Defines functions
getTraits
Documented in
getTraits
#' @title Get TreeCo Species Traits
#'
#' @description To be included
#'
#' @param tree.data a data frame with the species names
#' @param spp.name character. The name of the column containing the
#' species names. Defaults to "Name_submitted"
#' @param trait.cons a data frame with the extra, consensual species
#' information
#' @param trait.sp data frame with the species trait information
#' averaged by species
#' @param trait.gen data frame with the species trait information
#' averaged by genus
#' @param trait.fam data frame with the species trait information
#' averaged by family
#' @param generaliza a list containing the vectors of traits which can
#' be generalized at genera and family levels, respectively.
#' Defaults to list(c("wsg_gcm3","LeafType","SeedMass_g"),c("wsg_gcm3"))
#' @param add.spp data frame with species to be added to the trait
#' retrieval
#' @param rm.colunas vector of extra columns names that will be
#' removed from the original dataframe. Default is NULL but a vector
#' is provided with the most commonly removed columns
#' @param inc.colunas vector of columns names that should be included
#' contained in the vector of often-excluded columns. Default is
#' NULL (i.e. keep the vector of often-excluded columns the same)
#' @return To be described
#'
#' @details To be included
#'
#' @author Renato A. F. de Lima
#'
#'
#'
getTraits <- function(tree.data = NULL,
spp.name = "Name_submitted",
trait.cons = NULL,
trait.sp = NULL,
trait.gen = NULL,
trait.fam = NULL,
generaliza = list(c("wsg_gcm3","LeafType","SeedMass_g"),
c("wsg_gcm3")),
add.spp = NULL,
rm.colunas = NULL,
inc.colunas = NULL) {
## Checking input
# #### TRANFORMING THE VARIABLES ###
# tree.data$ordem = as.character(tree.data$ordem)
# tree.data$Name_submitted = as.character(tree.data$Name_submitted)
#
# #### CREATING THE DOCUMENT WITH THE LIST OF DECISIONS TAKES AT EACH STEP ####
# notas = NULL
#
# #### CREATING THE LIST OF TAXA INSIDE THE ABUNDANCE DATASET ####
# taxa = tree.data[,c("Name_submitted","family","genus","taxon.rank")]
# taxa = taxa[!duplicated(taxa$Name_submitted),]
# taxa = taxa[order(taxa$Name_submitted),]
# taxa = taxa[!taxa$taxon.rank %in% "unidentified",]
#
# if(!is.null(add.spp)) {
# taxa1 = add.spp[,c("Name_submitted","family","genus","taxon.rank")]
# taxa = rbind.data.frame(taxa,taxa1)
# }
#
# ########################################################################
# #### TREE TRAITS AVAILABLE FROM THE SOUTH AMERICA TREE SPECIES LIST ####
# ########################################################################
# #Info: threat status, endemism, establishment, dispersal syndrome and habit
# names(trees.sa)[names(trees.sa)%in%"SpeciesKTSA"] = "Name_submitted"
# taxa = merge(taxa,trees.sa[,c("Name_submitted","establishment.AF","establishment.BR","habito","succesional.group",
# "dispersal.syndrome","geographical_distribution","status_final","status_brazil_2005",
# "status_iucn_2005","life.form.reflora","habitat.reflora","vegtype.reflora",
# "domain.reflora")],by="Name_submitted",all.x = TRUE)
#
# #### TRAIT DATA EDITING ####
# ## Species establishment (endemic or exotic/cultivated) in respect to the Atlantic Forest and to Brazil ##
# taxa$establishment.AF[is.na(taxa$establishment.AF)&!is.na(taxa$establishment.BR)] =
# taxa$establishment.BR[is.na(taxa$establishment.AF)&!is.na(taxa$establishment.BR)]
# taxa$establishment.AF[taxa$establishment.AF%in%"check"&taxa$establishment.BR%in%c("native","cultivated")] =
# taxa$establishment.BR[taxa$establishment.AF%in%"check"&taxa$establishment.BR%in%c("native","cultivated")]
# taxa$establishment.AF[taxa$establishment.AF %in% c("cultivated","naturalized","not in Brazil")] = "exotic"
# notas[1] = "The native/exotic classification is in respect to the Atlantic Forest and more broadly to Brazil"
#
# ## Extinction threat level - Brazil + IUCN (global) ##
# taxa$status_final[is.na(taxa$status_final)] = "not_evaluated_or_not_threatened"
# taxa$extinction = as.factor(gsub("_iucn|_reflora|_author|_brasil","",taxa$status_final))
# #CR=4, DD=0.5, EN=3, LC=0, NT=1, not_evaluated=0, VU=2
# niveis = c(4,0.5,3,0,1,0,2)
# names(niveis) = c("critically_endangered_CR","data_deficient_DD","endangered_EN","least_concern_LC","near_threatened_NT","not_evaluated_or_not_threatened","vulnerable_VU")
# levels(taxa$extinction) = as.character(niveis[names(niveis) %in% levels(taxa$extinction)])
# taxa$extinction = as.double(as.character(taxa$extinction))
# taxa$extinction[taxa$taxon.rank %in% c("unidentified","genus","family")] = NA
# taxa$status_final[taxa$taxon.rank %in% c("unidentified","genus","family")] = NA
# notas = c(notas,paste("The values given for CR, DD, EN, LC, NT, NE, and VU were: ",paste(niveis, collapse=","),", respectively",sep=""))
#
# ## Endemism level - in respect to the Atlantic Forest ##
# #edtiting species geographical occurrence by genus
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Artocarpus","Citrus","Coffea","Camellia","Corymbia","Cupressus",
# "Dracaena","Eucalyptus","Eriobotrya","Hovenia","Leucaena","Ligustrum",
# "Mangifera","Mimusops","Morus","Pinus","Pittosporum","Platanus",
# "Ricinus","Spathodea","Syzygium","Tamarindus","Tecoma")] = "exotic"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Neomitranthes","Salzmannia"
# )] = "eastern_south_america"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Bocagea","Hornschuchia","Tovomitopsis","Urbanodendron","Behuria",
# "Macrotorus","Andradea","Ramisia","Macrothumia","Tripterodendron"
# )] = "regional_endemic"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Kuhlmanniodendron","Paratecoma","Ophthalmoblapton","Arapatiella","Brodriguesia",
# "Grazielodendron","Harleyodendron","Hydrogaster","Curitiba","Riodocea","Melanopsidium",
# "Andreadoxa","Alatococcus","Trigoniodendron"
# )] = "local_endemic"
# #More concise classification: C/E/N/W SA=1, exotic=-1, local=3, pan./neotropical=0, regional=2, SA=0
# taxa$endemism = as.factor(taxa$geographical_distribution)
# niveis = c(1,1,-1,3,0,1,0,2,0,1,1,1)
# names(niveis) = c("central_south_america","eastern_south_america","exotic","local_endemic","neotropical","northern_south_america",
# "pantropical","regional_endemic","south_american","south_and_central_south_america","southern_south_america","western_south_america")
# levels(taxa$endemism) = as.character(niveis[names(niveis) %in% levels(taxa$endemism)])
# taxa$endemism = as.double(as.character(taxa$endemism))
# notas = c(notas,paste("The more concise values given for CSA, ESA, Exotic, Local endemic, Neotrop., NSA, Pantrop., Regional endemic, SA, SCSA, SSA and WSA were: ",paste(niveis, collapse=","),", respectively",sep=""))
# #More detailed classification: C/E/N/W SA=2, exotic=-1, local=4, pan./neotropical=0, regional=3, SA=1
# taxa$endemism1 = as.factor(taxa$geographical_distribution)
# niveis = c(2,2,-1,4,0,2,0,3,0,1,2,2)
# levels(taxa$endemism) = as.character(niveis[names(niveis) %in% levels(taxa$endemism)])
# taxa$endemism = as.double(as.character(taxa$endemism))
# notas = c(notas,paste("The more detailed values given for CSA, ESA, Exotic, Local endemic, Neotrop., NSA, Pantrop., Regional endemic, SA, SCSA, SSA and WSA were: ",paste(niveis, collapse=","),", respectively",sep=""))
# #notas = c(notas,"")
#
# ## Ecological/successional group ##
# taxa$ecological.group = taxa$succesional.group
# taxa$ecological.group[taxa$ecological.group %in% "climax"] = 4
# taxa$ecological.group[taxa$ecological.group %in% "late_secondary"] = 3
# taxa$ecological.group[taxa$ecological.group %in% c("early_secondary","early_seconday","early_secondary?")] = 2
# taxa$ecological.group[taxa$ecological.group %in% c("pioneer")] = 1
# taxa$ecological.group[taxa$ecological.group %in% c("non_pioneer")] = 2.5
# taxa$ecological.group[taxa$ecological.group %in% c("light_demanding","pioneer?")] = 1.5
# taxa$ecological.group[taxa$ecological.group %in% c("shade_tolerant","climax shade_tolerant","climax?")] = 3.5
# taxa$ecological.group = suppressWarnings(as.double(taxa$ecological.group))
# notas = c(notas,"The ecological group classification for Pioneer, Early_secondary, Late_secondary, and Climax species were 1, 2, 3, 4, respectively. In addition: Light-demanding= 1.5, Non-pioneer= 2.5 and Shade-tolerant= 3.5")
#
# ## Automatic assignment of very common pioneer, early secondary, late secondary and climax genera
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Trema","Celtis","Guazuma","Bixa","Dodonea","Heliocarpus","Tecoma","Ricinus","Leucaena",
# "Manihot","Vernonanthura","Urera","Vasconcellea","Carica","Cecropia","Vismia","Chiococca",
# "Cochlospermum","Commiphora","Curatella","Prosopis","Physocalymma","Wedelia","Chromolaena")] = 1
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Lithraea","Vismia","Schinus","Moquiniastrum","Lithraea","Clethra","Aparisthmium","Schizolobium",
# "Acrocomia","Schinopsis","Acca","Ligustrum","Alchornea","Erythrina","Annona","Sapium")] = 1.5
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Zanthoxylum","Cedrela","Maclura","Enterolobium","Lonchocarpus","Lacistema","Tapirira",
# "Cybistax","Prockia","Coutarea","Sparattosperma","Sapindus","Balfourodendron",
# "Crateva","Hura","Simarouba","Plathymenia","Dasyphyllum","Peltophorum","Rhamnidium",
# "Bowdichia","Basiloxylon","Pterogyne","Helietta","Tetrorchidium")] = 2
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Blepharocalyx","Pimenta","Galipea","Senefeldera","Schoepfia","Tetrastylidium","Amphirrhox",
# "Leretia","Platycyamus","Melanoxylon","Diploon","Sweetia")] = 3
# notas = c(notas,"Missing classification of Ecological Groups for some species was carried at genus level for some genera typically pioneer (e.g. Trema, Celtis, Guazuma, Vernonanthura, Urera, Cecropia) or late_secondary (e.g. Blepharocalyx, Senefeldera, Schoepfia, Tetrastylidium, Amphirrhox, Platycyamus, Melanoxylon, Diploon, Sweetia)")
#
# ## Final edits for ecological groups
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Myrcia citrifolia","Myrceugenia ovalifolia","Aniba intermedia")] = 3
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Citrus limon","Citrus sinensis","Coffea arabica","Bougainvillea praecox")] = 2
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Crepidospermum atlanticum","Eugenia puberula")] = 2.5
# ## Inspecting species still missing ecological groups info
# #tmp = taxa[is.na(taxa$ecological.group)&!is.na(taxa$GS),]
# #tmp1 = aggregate(tmp$N,list(tmp$species.correct),sum)
# #tmp1$GS = aggregate(tmp$GS,list(tmp$species.correct),mean)$x
# #tmp1$SuccesionalGroup = as.character(aggregate(tmp$SuccesionalGroup,list(tmp$species.correct),unique)$x)
# #tmp1[order(tmp1$x),]
# #tmp1[,c("species.correct","SuccesionalGroup","GS")]
# #tmp1[tmp1$species.correct %in% c("Myrcia citrifolia","Myrceugenia ovalifolia","Crepidospermum atlanticum","Aniba intermedia"),c("species.correct","SuccesionalGroup","GS")]
#
#
# ## Creating column for different life-forms (palms, ferns, etc)
# taxa$life.form = NA
# taxa$life.form[taxa$family %in% c("Arecaceae")] = "palm"
# taxa$life.form[taxa$family %in% c("Araceae","Asparagaceae","Laxmanniaceae","Velloziaceae")] = "palmoids"
# taxa$life.form[taxa$family %in% c("Cyatheaceae","Dicksoniaceae","Blechnaceae")] = "tree_fern"
# taxa$life.form[taxa$family %in% c("Cactaceae")] = "succulent_tree"
# taxa$life.form[taxa$family %in% c("Poaceae")] = "woody_bamboo"
# taxa$life.form[taxa$family %in% c("Convolvulaceae","Cucurbitaceae","Menispermaceae","Smilacaceae",
# "Turneraceae","Vitaceae")] = "woody_vines_and_subshrubs"
# #"Convolvulaceae" => "Ipomoea carnea" "Ipomoea pinnata"
# #"Cucurbitaceae" => "Cayaponia tayuya" "Wilbrandia"
# #"Menispermaceae" => "Abuta grandifolia" "Cissampelos ovalifolia"
# #"Smilacaceae" => "Smilax fluminensis"
# #"Turneraceae" => "Turnera blanchetiana" "Turnera calyptrocarpa" "Turnera diffusa" "Turnera macrophylla"
# #"Vitaceae"=> "Cissus pulcherrima"
# taxa$life.form[is.na(taxa$life.form)] = "woody_tree"
#
# ## Dispersal syndromes ##
# #by families
# taxa$dispersal.syndrome[!is.na(taxa$family) & is.na(taxa$dispersal.syndrome) & taxa$family %in%
# c("Myrtaceae","Lauraceae","Annonaceae","Chrysobalanaceae","Siparunaceae","Piperaceae",
# "Aquifoliaceae","Erythroxylaceae","Arecaceae","Burseraceae","Clusiaceae")] = "zoochoric"
# taxa$dispersal.syndrome[!is.na(taxa$Name_submitted) & grepl("Eucalyptus|Corymbia",taxa$Name_submitted)] = "anemochoric"
# taxa$dispersal.syndrome[!is.na(taxa$family) & taxa$family %in%
# c("Cyatheaceae")] = "anemochoric" #Asteraceae,Bignoniaceae,Vochysiaceae??
#
# #by genera
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Miconia","Leandra","Pisonia","Guapira","Myrsine","Pouteria","Solanum","Capsicum","Ficus","Mollinedia","Diospyros","Symplocos",
# "Ardisia","Cabralea","Calophyllum","Cereus","Cheiloclinium","Diploon","Dipteryx","Lantana","Ossaea","Prockia","Sideroxylon","Anacardium","Emmotum","Hyeronima","Macropeplus","Meliosma",
# "Pera","Pradosia","Pseudolmedia","Sacoglottis","Sessea","Simaba","Strychnos","Tapirira","Agonandra","Alchornea","Citronella","Heisteria","Henriettea","Jacaratia","Schinus","Tetrorchidium","Urera",
# "Vantanea","Aureliana","Bunchosia","Cecropia","Celtis","Copaifera","Coussapoa","Humiriastrum","Pourouma","Prunus","Salacia","Sapium","Stylogyne","Talisia","Brunfelsia","Citharexylum","Dendropanax",
# "Pilocarpus","Rauvolfia","Tabernaemontana","Zollernia","Cestrum","Chionanthus","Manilkara","Meriania","Micropholis","Ormosia","Virola","Lacistema","Sorocea","Vitex","Xylosma","Brosimum","Connarus",
# "Euplassa","Guarea","Matayba","Schefflera","Aegiphila","Picramnia","Chrysophyllum","Daphnopsis","Styrax","Andira","Coccoloba","Cybianthus","Neea","Mouriri","Allophylus","Ouratea","Zanthoxylum",
# "Cupania","Byrsonima","Casearia","Maytenus","Trichilia","Swartzia","Inga","Rubus","Citrus",
# "Alibertia","Amaioua","Chiococca","Chomelia","Cordiera","Coussarea","Faramea","Genipa","Guettarda","Ixora","Kutchubaea","Palicourea","Posoqueria","Psychotria","Randia","Rudgea","Tocoyena",
# "Vismia","Quiina","Quararibea","Phytolacca","Homalolepis","Simaba","Capparidastrum","Neocalyptrocalyx","Athenaea","Monteverdia"
# )] = "zoochoric"
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Gymnanthes","Galipea","Jatropha","Pachystroma","Sebastiania","Cnidoscolus","Calliandra","Cassia","Esenbeckia","Helicteres","Mabea","Metrodorea","Mimosa","Actinostemon","Manihot","Senegalia",
# "Senna","Croton","Senefeldera","Algernonia","Brasiliocroton","Stillingia"
# )] = "autochoric"
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Adenocalymma","Pachira","Peltophorum","Plathymenia","Raulinoreitzia","Bougainvillea","Cedrela","Hymenolobium","Myrocarpus","Pinus","Pterodon","Ruprechtia","Alsophila","Lafoensia","Moquiniastrum","Seguieria",
# "Symphyopappus","Triplaris","Callisthene","Centrolobium","Pterocarpus","Astronium","Cariniana","Lonchocarpus","Pseudobombax","Ceiba","Luehea","Tabebuia","Tachigali","Vernonanthura","Eriotheca","Terminalia",
# "Handroanthus","Piptocarpha","Jacaranda","Cyathea","Dalbergia","Qualea","Tibouchina","Handroanthus","Vochysia","Baccharis","Kielmeyera","Aspidosperma","Machaerium","Vernonia","Eupatorium",
# "Alseis","Bathysa","Coutarea","Rustia","Simira","Combretum","Luetzelburgia","Pleroma"
# )] = "anemochoric"
#
# #tmp = taxa[is.na(taxa$dispersal.syndrome),]
# #tmp = tmp[!grepl(" ",tmp$Name_submitted),]
# #sort(table(tmp$Name_submitted))
# #sort(table(tmp$genus))
# notas = c(notas,"Missing classification of Dispersal Syndrome for some species or morphospecies was carried at genus or family level (e.g. all Miconia are zoochorich and all ferns are anemochoric")
#
# ####################################################################
# #### MEAN TREE TRAITS AVAILABLE FROM THE TREECO TRAIT DATABASE ####
# ####################################################################
#
# #### MERGING TRAIT AT SPECIES LEVEL ####
# tmp = trait.spp[trait.spp$TAX %in% taxa$Name_submitted,]
# taxa = merge(taxa,tmp,by.x="Name_submitted",by.y="TAX",all.x=T)
#
# ##CHECK!!
# #Checkings possible problems
# #tax[!is.na(tax$wsg_gcm3)&tax$wsg_gcm3>1&tax$GS<2,c("species.correct","wsg","wsg_gcm3","SuccesionalGroup","GS")]
# #tax[!is.na(tax$wsg_gcm3)&tax$wsg_gcm3<0.6&tax$GS>=3.5,c("species.correct","wsg","wsg_gcm3","SuccesionalGroup","GS")]
#
# #### PRELIMINAR EDITING OF TRAIT DATA ####
# #### UPDATE THIS PART OF THE CODE FROM THE CODES OF THE PAPER SUBMITTED TO SCIENCE ####
# ## Seed mass ~ Seed volume
# taxa$SeedVolume = NA
# #for circular fruits
# taxa$SeedVolume[is.na(taxa$SeedLength_cm)&is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)] =
# (4/3)*pi*(as.double(taxa$SeedDiameter_cm[is.na(taxa$SeedLength_cm)&is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)^3
# #for ellipsoidal fruits
# taxa$SeedVolume[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)] =
# (4/3)*pi*(as.double(taxa$SeedDiameter_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)*
# (as.double(taxa$SeedWidth_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)*
# (as.double(taxa$SeedLength_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)
# #plot(log(taxa$SeedMass_g) ~ log(taxa$SeedVolume)); abline(0,1,lwd=2,col=2)
# #text(x=log(taxa$SeedVolume), y=log(taxa$SeedMass_g), labels=taxa$Name_submitted,cex=0.5,pos=1:3)
#
# tmp = na.omit(taxa[,c("Name_submitted","SeedMass_g","SeedVolume")])
# mod = lm(log(as.double(tmp$SeedMass_g[!tmp$Name_submitted %in% c("Miconia prasina","Myrcia pubipetala")])) ~ log(as.double(tmp$SeedVolume[!tmp$Name_submitted %in% c("Miconia prasina","Myrcia pubipetala")])))
# #abline(mod)
# ## CHECK!!
# ##RE-CHECK THE EQUATION USING ONLY SPECIES WITH ALL SEED INFO (RAW TRAIT VALUES): length/width and/or diameter and seed mass
# taxa$est_SeedMass_g = exp(coef(mod)[1] + coef(mod)[2]*log(taxa$SeedVolume))
# #plot(taxa$est_SeedMass_g ~ taxa$SeedMass_g, log="xy"); abline(0,1,lwd=2,col=2)
# #taxa$SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$est_SeedMass_g)] =
# # taxa$est_SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$est_SeedMass_g)]
#
# #seed mass <- 0.8*fruits/kg
# #plot(SeedMass_g ~ FruitMass_g, data=trait.spp, log="xy",
# # ylim=c(6.150288e-06, 1.157476e+02),
# # xlim=c(0.00001, 850)); abline(0,1,lwd=2,col=2)
# #tmp = na.omit(trait.spp[,c("SeedMass_g","FruitMass_g")])
# #mod = lm(log(tmp$SeedMass_g) ~ log(tmp$FruitMass_g))
# #abline(mod)
# #abline(-0.5,0.85)
# #text(x=trait.taxa$FruitMass_g, y=trait.taxa$SeedMass_g, labels=trait.taxa$TAX,cex=0.4,pos=1:3)
# ##RE-CHECK THE EQUATION USING ONLY SPECIES WITH ALL SEED INFO (RAW TRAIT VALUES): fruit mass and seed mass
# taxa$est_SeedMass_g[is.na(taxa$est_SeedMass_g)] = exp(coef(mod)[1] + coef(mod)[2]*log(taxa$FruitMass_g[is.na(taxa$est_SeedMass_g)]))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$FruitMass_g)] =
# taxa$est_SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$FruitMass_g)]
# notas = c(notas,"Missing information of Seed Mass was also obtained from studies providing values of number of seeds per kilogram. In additin, for some monospermic species was based on a conversion formula using Fruit_mass as an input")
#
# #### MERGING TRAIT AT GENUS LEVEL ####
# gen = as.character(trait.gen$TAX[trait.gen$TAX %in% taxa$genus])
# trait = generaliza[[1]]
# for(j in 1:length(gen)) {
# tmp = taxa[taxa$genus %in% gen[j],]
# for(i in 1:length(trait)) {
# tmp[is.na(tmp[,trait[i]]),trait[i]] = as.character(trait.gen[as.character(trait.gen$TAX) %in% gen[j],trait[i]])
# }
# taxa[taxa$genus %in% gen[j],trait] = tmp[,trait]
# }
# notas = c(notas,paste("Missing info at species level was replaced by genus-level averages for the following traits: ",paste(generaliza[[1]], collapse=","),".",sep=""))
#
# #### MERGING TRAIT AT FAMILY LEVEL ####
# fam = as.character(trait.fam$TAX[trait.fam$TAX %in% taxa$family])
# trait = generaliza[[2]]
# for(j in 1:length(fam)) {
# tmp = taxa[taxa$family %in% fam[j],]
# for(i in 1:length(trait)) {
# tmp[is.na(tmp[,trait[i]]),trait[i]] = as.character(trait.fam[as.character(trait.fam$TAX) %in% fam[j],trait[i]])
# }
# taxa[taxa$family %in% fam[j],trait] = tmp[,trait]
# }
# notas = c(notas,paste("Missing info at species level was replaced by family-level averages for the following traits: ",paste(generaliza[[2]], collapse=","),".",sep=""))
#
# #### EDITING MISSING TRAIT DATA FOR ABUNDANT OR FREQUENT SPECIES IN TREECO ###
# ## Maximum Height (m) ##
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Vellozia variabilis"] = 2
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Vellozia tubiflora"] = 2
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Ipomoea carnea"] = 2.5
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Erythroxylum nummularium"] = 4
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Cratylia mollis"] = 4
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Hyptis pachyphylla"] = 3
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Croton adenodontus"] = 3
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Eriope exaltata"] = 6
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Simaba ferruginea"] = 13
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Homalolepis ferruginea"] = 13
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Erythroxylum pauferrense"] = 6
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Ephedranthus dimerus"] = 20
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Myrcia costeira"] = 9
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Psychotria pubigera"] = 4
#
# ## Getting leaf Length and Width from the speciesLink measurements ##
# # tmp = read.csv("C://Users//renat//Documents//raflima//Pos Doc//Databases//Species traits//Atributos das espécies//leaf_size_speciesLink.csv",as.is=T)
# tmp = read.csv("E:/WD Backup.swstor/renato/NmQwODhiMTFiOWQ3NDcxOW/Volume{258b8dde-ad01-4a49-b95b-eb77d73987c4}//Users//renat//Documents//raflima//Pos Doc//Databases//Species traits//Atributos das especies//leaf_size_speciesLink.csv",as.is=T)
#
#
# tmp = tmp[!is.na(tmp$Length),]
# tmp1 = cbind.data.frame(aggregate(tmp$Length,list(tmp$species),mean),
# W=aggregate(tmp$Width,list(tmp$species),mean)$x)
# names(tmp1)[1:2] = c("species","L")
# tmp1$LA = pi*tmp1$L*tmp1$W/4
# notas = c(notas,"Missing information of Leaf Area was obtained from Leaf_length and Leaf_width using the formula of an ellipse: pi*L*W/4")
#
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Astrocaryum aculeatissimum"] = tmp1$LA[tmp1$species == "Astrocaryum aculeatissimum"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Euterpe edulis"] = tmp1$LA[tmp1$species == "Euterpe edulis"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Marlierea racemosa"] = tmp1$LA[tmp1$species == "Marlierea racemosa"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Myrcia aethusa"] = tmp1$LA[tmp1$species == "Myrcia aethusa"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Myrcia pubipetala"] = tmp1$LA[tmp1$species == "Myrcia pubipetala"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Pachystroma longifolium"] = tmp1$LA[tmp1$species == "Pachystroma longifolium"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Astrocaryum aculeatissimum"] = tmp1$LA[tmp1$species == "Astrocaryum aculeatissimum"]
#
# ## Editing LeafType data ##
# taxa$LeafType[grepl("compostas",taxa$LeafType)&!grepl("simples",taxa$LeafType)] = "compostas"
# taxa$LeafType[!grepl("compostas",taxa$LeafType)&grepl("simples",taxa$LeafType)] = "simples"
# taxa$LeafType[!grepl("compostas",taxa$LeafType)&!grepl("simples",taxa$LeafType)] = NA
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Annona",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Bauhinia rufa",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Cheiloclinium",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus fontanesianus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus gaudichaudianus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus pentandrus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Esenbeckia grandiflora",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Matayba",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Pseudobombax simplicifolium",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Roupala montana",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Swartzia simplex",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Tabebuia insignis",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Vitex mexiae",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Weinmannia humilis",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Aralia warmingiana",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Eriotheca pubescens",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Malouetia cestroides",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Joannesia princeps",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Malouetia cestroides",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Piptocarpha axillaris|Piptocarpha macropoda|Piptocarpha regnellii",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Protium heptaphyllum|Protium spruceanum|Protium widgrenii",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Schefflera calva|Schefflera macrocarpa",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Tabebuia roseoalba|Tabebuia aurea",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Vitex cymosa|Vitex megapotamica|Vitex polygama",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Zeyheria montana|Zeyheria tuberculosa",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Actinostemon",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Allophylus",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Callisthene",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Celtis",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Dendropanax",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Faramea",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Jacaranda",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Sebastiania",taxa$Name_submitted)] = "simples"
# taxa$LeafType[grepl("compostas",taxa$LeafType)&grepl("simples",taxa$LeafType)] = NA
# taxa$LeafArea[is.infinite(taxa$LeafArea)] = NA
#
# #some final edits at genus or family level
# taxa$LeafType[!is.na(taxa$family)&is.na(taxa$LeafType)&grepl("Annonaceae|Melastomataceae|Myrtaceae",taxa$family)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&is.na(taxa$LeafType)&grepl("Beilschmiedia|Mezilaurus",taxa$Name_submitted)] = "simples"
#
# #some final edits at species level (looked up in herbarium vouchers)
# taxa$LeafType[!is.na(taxa$Name_submitted) & is.na(taxa$LeafType) & taxa$Name_submitted %in%
# c("Bauhinia_longifolia","Cavanillesia_umbellata","Guapira_areolata","Pogonophora_schomburgkiana"
# )] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted) & is.na(taxa$LeafType) & taxa$Name_submitted %in%
# c("Caryocar_brasiliense","Cenostigma_bracteosum","Connarus_suberosus","Esenbeckia_febrifuga","Pachira_endecaphylla",
# "Galipea_jasminiflora","Protium_atlanticum","Protium_icicariba","Sparattosperma_leucanthum"
# )] = "compostas"
# notas = c(notas,"Missing information of Leaf Type was obtained at genus-level for some taxa. Species with both compound and simple leafs along their onthogeny (e.g. Matayba, Roupala) were treated as having compound leaves")
#
# ### Final edits: Seed size
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Actinostemon")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Sebastiania")])))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Athenaea")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Capsicum")])))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Anaxagorea")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Xylopia")])))
#
# ### Edits for very species rich genera without habit
# ##VERIFICAR A PROPORÇÃO DE ÁRVORES E ARBUSTOS POR FAMILIA E GENERO PARA FECHAR AS LISTAGEMS ABAIXO, PRINCIPALMENTE GENEROS
# #By family
# taxa$habito[!is.na(taxa$family) & is.na(taxa$habito) & taxa$family%in%
# c("Annonaceae","Burseraceae","Chrysobalanaceae","Lauraceae","Lecythidaceae","Moraceae","Myristicaceae","Myrtaceae","Proteaceae","Sapotaceae"
# )] = 1
# taxa$habito[!is.na(taxa$family) & is.na(taxa$habito) & taxa$family%in%
# c("Lacistemataceae","Loganiaceae","Pipeaceae","Siparunaceae","Violaceae"
# )] = 0.5
# #By genus
# taxa$habito[!is.na(taxa$genus) & is.na(taxa$habito) & taxa$genus%in%
# c("Alchornea","Anadenanthera"
# )] = 1
# taxa$habito[!is.na(taxa$genus) & is.na(taxa$habito) & taxa$genus%in%
# c("Athenaea","Brunfelsia","Capsicum","Piper","Eumachia","Chiococca","Stachytarpheta","Schweiggeria"
# )] = 0.5
#
# #### CHECKING COMMON SPECIES STILL WITHOUT TRAIT INFO ####
# tmp = c("establishment.AF","habito","extinction","endemism","ecological.group","dispersal.syndrome",
# "wsg_gcm3","MaxHeight_m","MaxDbh_cm",
# "SeedLength_cm","SeedWidth_cm","SeedDiameter_cm","SeedMass_g","FruitMass_g",
# "LeafArea","LeafType","SuccesionalGroup",
# "Deciduousness","LT","PericarpConsistency","SexualSystem","PollinationSyndrome","SLA_cm2_g.1")
# tmp1= NULL
# for(i in 1:length(tmp)) {
# vrvl = tmp[i]
# if(is.numeric(taxa[,vrvl])) { tmp2 = taxa$Name_submitted[is.na(taxa[,vrvl])]
# } else { tmp2 = taxa$Name_submitted[is.na(taxa[,vrvl])|(grepl("NA:",taxa[,vrvl])&!grepl("\\|",taxa[,vrvl]))]
# }
# tmp2 = tmp2[!grepl(" sp\\.",tmp2)&!is.na(tmp2)]
# tmp2 = tmp2[grepl(" ",tmp2)]
# if(is.null(tmp1)) { tmp1 = c(length(table(tmp2)),100*sum(table(tmp2))/dim(taxa)[1])
# } else { tmp1 = rbind.data.frame(tmp1,c(length(table(tmp2)),100*sum(table(tmp2))/dim(taxa)[1])) }
# }
# names(tmp1) =c("Nsp_without","prop.sp.without")
# rownames(tmp1) = tmp
# print("Check the number and proportion of species (not genera or families) without trait information.")
# print("Proportion below 40% generally results in good coverage for all individuals at the community level.")
# print(tmp1[order(tmp1$prop.sp.without),])
#
# #### FILTERING THE SELECTED METADATA (COLUMNS) ####
# colunas = c("X","species.original","Habit","Bark","LeafMargin","LeafTip","AcumenLength_cm","LeafSubtype","Leaflets",
# "LeafHairiness_upper","LeafHairiness_lower","FruitLipids","FruitWater","FruitProtein","FruitCarbo",
# "PollinationSubsyndrome","Anthesis","FlowerType","CorollaType","CorollaColour","SepalColour","CorollaLength_cm","CorollaWidth_cm",
# "ChemicalCompounds","PhysicalCompounds","Allelopathy","sem.kg","Flowers","Fruits","Seeds","LeafN","obs1","obs2","obs3",
# "GeogDist","Domain","Vegetation","TaxNotes","MinLeafLength_cm","MaxLeafLength_cm","MinLeafWidth_cm","MaxLeafWidth_cm",
# "LeafThickness_micro","FruitLength_cm","FruitWidth_cm","FruitDiameter_cm","LeafChlorophyllAB","LeafCarbon","LeafWater",
# "dry_mass_fraction","WoodCarbon_gkg.1","LeafDryMatter_mg.g","ChlorophyllContent_FCI","LeafTough_N.mm","PithProp","XylProp","BarkProp",
# "BarkProp","VesselDensity_n.mm2","VesselDiameter_microm","StomataDensity_n.mm2","StomataLength_microm","Kpot_kg.m.s.Mpa",
# "SuccesionalGroup","wsg")
# if(is.null(rm.colunas)) {colunas1 = colunas} else { colunas1 = c(colunas,rm.colunas) }
# if(is.null(inc.colunas)) {colunas1 = colunas1} else { colunas1 = colunas1[!colunas1 %in% inc.colunas] }
# if(!is.null(colunas1)) taxa = taxa[,!names(taxa) %in% colunas1]
#
# #### PREPARING AND RETURNING THE FINAL RESULTS ####
# notas = gsub("\\\n","",notas)
# notas1 = paste(">>>NOTE ",1:length(notas),": ",notas,sep="")
# resulta = list(taxa, notas1)
# names(resulta) = c("data_frame","editing_notes")
# return(resulta)
#
}
LimaRAF/TreeCo documentation built on Sept. 25, 2024, 12:41 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions getTraits
Documented in getTraits
#' @title Get TreeCo Species Traits
#'
#' @description To be included
#'
#' @param tree.data a data frame with the species names
#' @param spp.name character. The name of the column containing the
#' species names. Defaults to "Name_submitted"
#' @param trait.cons a data frame with the extra, consensual species
#' information
#' @param trait.sp data frame with the species trait information
#' averaged by species
#' @param trait.gen data frame with the species trait information
#' averaged by genus
#' @param trait.fam data frame with the species trait information
#' averaged by family
#' @param generaliza a list containing the vectors of traits which can
#' be generalized at genera and family levels, respectively.
#' Defaults to list(c("wsg_gcm3","LeafType","SeedMass_g"),c("wsg_gcm3"))
#' @param add.spp data frame with species to be added to the trait
#' retrieval
#' @param rm.colunas vector of extra columns names that will be
#' removed from the original dataframe. Default is NULL but a vector
#' is provided with the most commonly removed columns
#' @param inc.colunas vector of columns names that should be included
#' contained in the vector of often-excluded columns. Default is
#' NULL (i.e. keep the vector of often-excluded columns the same)
#' @return To be described
#'
#' @details To be included
#'
#' @author Renato A. F. de Lima
#'
#'
#'
getTraits <- function(tree.data = NULL,
spp.name = "Name_submitted",
trait.cons = NULL,
trait.sp = NULL,
trait.gen = NULL,
trait.fam = NULL,
generaliza = list(c("wsg_gcm3","LeafType","SeedMass_g"),
c("wsg_gcm3")),
add.spp = NULL,
rm.colunas = NULL,
inc.colunas = NULL) {
## Checking input
# #### TRANFORMING THE VARIABLES ###
# tree.data$ordem = as.character(tree.data$ordem)
# tree.data$Name_submitted = as.character(tree.data$Name_submitted)
#
# #### CREATING THE DOCUMENT WITH THE LIST OF DECISIONS TAKES AT EACH STEP ####
# notas = NULL
#
# #### CREATING THE LIST OF TAXA INSIDE THE ABUNDANCE DATASET ####
# taxa = tree.data[,c("Name_submitted","family","genus","taxon.rank")]
# taxa = taxa[!duplicated(taxa$Name_submitted),]
# taxa = taxa[order(taxa$Name_submitted),]
# taxa = taxa[!taxa$taxon.rank %in% "unidentified",]
#
# if(!is.null(add.spp)) {
# taxa1 = add.spp[,c("Name_submitted","family","genus","taxon.rank")]
# taxa = rbind.data.frame(taxa,taxa1)
# }
#
# ########################################################################
# #### TREE TRAITS AVAILABLE FROM THE SOUTH AMERICA TREE SPECIES LIST ####
# ########################################################################
# #Info: threat status, endemism, establishment, dispersal syndrome and habit
# names(trees.sa)[names(trees.sa)%in%"SpeciesKTSA"] = "Name_submitted"
# taxa = merge(taxa,trees.sa[,c("Name_submitted","establishment.AF","establishment.BR","habito","succesional.group",
# "dispersal.syndrome","geographical_distribution","status_final","status_brazil_2005",
# "status_iucn_2005","life.form.reflora","habitat.reflora","vegtype.reflora",
# "domain.reflora")],by="Name_submitted",all.x = TRUE)
#
# #### TRAIT DATA EDITING ####
# ## Species establishment (endemic or exotic/cultivated) in respect to the Atlantic Forest and to Brazil ##
# taxa$establishment.AF[is.na(taxa$establishment.AF)&!is.na(taxa$establishment.BR)] =
# taxa$establishment.BR[is.na(taxa$establishment.AF)&!is.na(taxa$establishment.BR)]
# taxa$establishment.AF[taxa$establishment.AF%in%"check"&taxa$establishment.BR%in%c("native","cultivated")] =
# taxa$establishment.BR[taxa$establishment.AF%in%"check"&taxa$establishment.BR%in%c("native","cultivated")]
# taxa$establishment.AF[taxa$establishment.AF %in% c("cultivated","naturalized","not in Brazil")] = "exotic"
# notas[1] = "The native/exotic classification is in respect to the Atlantic Forest and more broadly to Brazil"
#
# ## Extinction threat level - Brazil + IUCN (global) ##
# taxa$status_final[is.na(taxa$status_final)] = "not_evaluated_or_not_threatened"
# taxa$extinction = as.factor(gsub("_iucn|_reflora|_author|_brasil","",taxa$status_final))
# #CR=4, DD=0.5, EN=3, LC=0, NT=1, not_evaluated=0, VU=2
# niveis = c(4,0.5,3,0,1,0,2)
# names(niveis) = c("critically_endangered_CR","data_deficient_DD","endangered_EN","least_concern_LC","near_threatened_NT","not_evaluated_or_not_threatened","vulnerable_VU")
# levels(taxa$extinction) = as.character(niveis[names(niveis) %in% levels(taxa$extinction)])
# taxa$extinction = as.double(as.character(taxa$extinction))
# taxa$extinction[taxa$taxon.rank %in% c("unidentified","genus","family")] = NA
# taxa$status_final[taxa$taxon.rank %in% c("unidentified","genus","family")] = NA
# notas = c(notas,paste("The values given for CR, DD, EN, LC, NT, NE, and VU were: ",paste(niveis, collapse=","),", respectively",sep=""))
#
# ## Endemism level - in respect to the Atlantic Forest ##
# #edtiting species geographical occurrence by genus
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Artocarpus","Citrus","Coffea","Camellia","Corymbia","Cupressus",
# "Dracaena","Eucalyptus","Eriobotrya","Hovenia","Leucaena","Ligustrum",
# "Mangifera","Mimusops","Morus","Pinus","Pittosporum","Platanus",
# "Ricinus","Spathodea","Syzygium","Tamarindus","Tecoma")] = "exotic"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Neomitranthes","Salzmannia"
# )] = "eastern_south_america"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Bocagea","Hornschuchia","Tovomitopsis","Urbanodendron","Behuria",
# "Macrotorus","Andradea","Ramisia","Macrothumia","Tripterodendron"
# )] = "regional_endemic"
# taxa$geographical_distribution[is.na(taxa$geographical_distribution) & taxa$genus %in%
# c("Kuhlmanniodendron","Paratecoma","Ophthalmoblapton","Arapatiella","Brodriguesia",
# "Grazielodendron","Harleyodendron","Hydrogaster","Curitiba","Riodocea","Melanopsidium",
# "Andreadoxa","Alatococcus","Trigoniodendron"
# )] = "local_endemic"
# #More concise classification: C/E/N/W SA=1, exotic=-1, local=3, pan./neotropical=0, regional=2, SA=0
# taxa$endemism = as.factor(taxa$geographical_distribution)
# niveis = c(1,1,-1,3,0,1,0,2,0,1,1,1)
# names(niveis) = c("central_south_america","eastern_south_america","exotic","local_endemic","neotropical","northern_south_america",
# "pantropical","regional_endemic","south_american","south_and_central_south_america","southern_south_america","western_south_america")
# levels(taxa$endemism) = as.character(niveis[names(niveis) %in% levels(taxa$endemism)])
# taxa$endemism = as.double(as.character(taxa$endemism))
# notas = c(notas,paste("The more concise values given for CSA, ESA, Exotic, Local endemic, Neotrop., NSA, Pantrop., Regional endemic, SA, SCSA, SSA and WSA were: ",paste(niveis, collapse=","),", respectively",sep=""))
# #More detailed classification: C/E/N/W SA=2, exotic=-1, local=4, pan./neotropical=0, regional=3, SA=1
# taxa$endemism1 = as.factor(taxa$geographical_distribution)
# niveis = c(2,2,-1,4,0,2,0,3,0,1,2,2)
# levels(taxa$endemism) = as.character(niveis[names(niveis) %in% levels(taxa$endemism)])
# taxa$endemism = as.double(as.character(taxa$endemism))
# notas = c(notas,paste("The more detailed values given for CSA, ESA, Exotic, Local endemic, Neotrop., NSA, Pantrop., Regional endemic, SA, SCSA, SSA and WSA were: ",paste(niveis, collapse=","),", respectively",sep=""))
# #notas = c(notas,"")
#
# ## Ecological/successional group ##
# taxa$ecological.group = taxa$succesional.group
# taxa$ecological.group[taxa$ecological.group %in% "climax"] = 4
# taxa$ecological.group[taxa$ecological.group %in% "late_secondary"] = 3
# taxa$ecological.group[taxa$ecological.group %in% c("early_secondary","early_seconday","early_secondary?")] = 2
# taxa$ecological.group[taxa$ecological.group %in% c("pioneer")] = 1
# taxa$ecological.group[taxa$ecological.group %in% c("non_pioneer")] = 2.5
# taxa$ecological.group[taxa$ecological.group %in% c("light_demanding","pioneer?")] = 1.5
# taxa$ecological.group[taxa$ecological.group %in% c("shade_tolerant","climax shade_tolerant","climax?")] = 3.5
# taxa$ecological.group = suppressWarnings(as.double(taxa$ecological.group))
# notas = c(notas,"The ecological group classification for Pioneer, Early_secondary, Late_secondary, and Climax species were 1, 2, 3, 4, respectively. In addition: Light-demanding= 1.5, Non-pioneer= 2.5 and Shade-tolerant= 3.5")
#
# ## Automatic assignment of very common pioneer, early secondary, late secondary and climax genera
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Trema","Celtis","Guazuma","Bixa","Dodonea","Heliocarpus","Tecoma","Ricinus","Leucaena",
# "Manihot","Vernonanthura","Urera","Vasconcellea","Carica","Cecropia","Vismia","Chiococca",
# "Cochlospermum","Commiphora","Curatella","Prosopis","Physocalymma","Wedelia","Chromolaena")] = 1
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Lithraea","Vismia","Schinus","Moquiniastrum","Lithraea","Clethra","Aparisthmium","Schizolobium",
# "Acrocomia","Schinopsis","Acca","Ligustrum","Alchornea","Erythrina","Annona","Sapium")] = 1.5
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Zanthoxylum","Cedrela","Maclura","Enterolobium","Lonchocarpus","Lacistema","Tapirira",
# "Cybistax","Prockia","Coutarea","Sparattosperma","Sapindus","Balfourodendron",
# "Crateva","Hura","Simarouba","Plathymenia","Dasyphyllum","Peltophorum","Rhamnidium",
# "Bowdichia","Basiloxylon","Pterogyne","Helietta","Tetrorchidium")] = 2
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$genus %in%
# c("Blepharocalyx","Pimenta","Galipea","Senefeldera","Schoepfia","Tetrastylidium","Amphirrhox",
# "Leretia","Platycyamus","Melanoxylon","Diploon","Sweetia")] = 3
# notas = c(notas,"Missing classification of Ecological Groups for some species was carried at genus level for some genera typically pioneer (e.g. Trema, Celtis, Guazuma, Vernonanthura, Urera, Cecropia) or late_secondary (e.g. Blepharocalyx, Senefeldera, Schoepfia, Tetrastylidium, Amphirrhox, Platycyamus, Melanoxylon, Diploon, Sweetia)")
#
# ## Final edits for ecological groups
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Myrcia citrifolia","Myrceugenia ovalifolia","Aniba intermedia")] = 3
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Citrus limon","Citrus sinensis","Coffea arabica","Bougainvillea praecox")] = 2
# taxa$ecological.group[is.na(taxa$ecological.group) & taxa$species.correct %in%
# c("Crepidospermum atlanticum","Eugenia puberula")] = 2.5
# ## Inspecting species still missing ecological groups info
# #tmp = taxa[is.na(taxa$ecological.group)&!is.na(taxa$GS),]
# #tmp1 = aggregate(tmp$N,list(tmp$species.correct),sum)
# #tmp1$GS = aggregate(tmp$GS,list(tmp$species.correct),mean)$x
# #tmp1$SuccesionalGroup = as.character(aggregate(tmp$SuccesionalGroup,list(tmp$species.correct),unique)$x)
# #tmp1[order(tmp1$x),]
# #tmp1[,c("species.correct","SuccesionalGroup","GS")]
# #tmp1[tmp1$species.correct %in% c("Myrcia citrifolia","Myrceugenia ovalifolia","Crepidospermum atlanticum","Aniba intermedia"),c("species.correct","SuccesionalGroup","GS")]
#
#
# ## Creating column for different life-forms (palms, ferns, etc)
# taxa$life.form = NA
# taxa$life.form[taxa$family %in% c("Arecaceae")] = "palm"
# taxa$life.form[taxa$family %in% c("Araceae","Asparagaceae","Laxmanniaceae","Velloziaceae")] = "palmoids"
# taxa$life.form[taxa$family %in% c("Cyatheaceae","Dicksoniaceae","Blechnaceae")] = "tree_fern"
# taxa$life.form[taxa$family %in% c("Cactaceae")] = "succulent_tree"
# taxa$life.form[taxa$family %in% c("Poaceae")] = "woody_bamboo"
# taxa$life.form[taxa$family %in% c("Convolvulaceae","Cucurbitaceae","Menispermaceae","Smilacaceae",
# "Turneraceae","Vitaceae")] = "woody_vines_and_subshrubs"
# #"Convolvulaceae" => "Ipomoea carnea" "Ipomoea pinnata"
# #"Cucurbitaceae" => "Cayaponia tayuya" "Wilbrandia"
# #"Menispermaceae" => "Abuta grandifolia" "Cissampelos ovalifolia"
# #"Smilacaceae" => "Smilax fluminensis"
# #"Turneraceae" => "Turnera blanchetiana" "Turnera calyptrocarpa" "Turnera diffusa" "Turnera macrophylla"
# #"Vitaceae"=> "Cissus pulcherrima"
# taxa$life.form[is.na(taxa$life.form)] = "woody_tree"
#
# ## Dispersal syndromes ##
# #by families
# taxa$dispersal.syndrome[!is.na(taxa$family) & is.na(taxa$dispersal.syndrome) & taxa$family %in%
# c("Myrtaceae","Lauraceae","Annonaceae","Chrysobalanaceae","Siparunaceae","Piperaceae",
# "Aquifoliaceae","Erythroxylaceae","Arecaceae","Burseraceae","Clusiaceae")] = "zoochoric"
# taxa$dispersal.syndrome[!is.na(taxa$Name_submitted) & grepl("Eucalyptus|Corymbia",taxa$Name_submitted)] = "anemochoric"
# taxa$dispersal.syndrome[!is.na(taxa$family) & taxa$family %in%
# c("Cyatheaceae")] = "anemochoric" #Asteraceae,Bignoniaceae,Vochysiaceae??
#
# #by genera
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Miconia","Leandra","Pisonia","Guapira","Myrsine","Pouteria","Solanum","Capsicum","Ficus","Mollinedia","Diospyros","Symplocos",
# "Ardisia","Cabralea","Calophyllum","Cereus","Cheiloclinium","Diploon","Dipteryx","Lantana","Ossaea","Prockia","Sideroxylon","Anacardium","Emmotum","Hyeronima","Macropeplus","Meliosma",
# "Pera","Pradosia","Pseudolmedia","Sacoglottis","Sessea","Simaba","Strychnos","Tapirira","Agonandra","Alchornea","Citronella","Heisteria","Henriettea","Jacaratia","Schinus","Tetrorchidium","Urera",
# "Vantanea","Aureliana","Bunchosia","Cecropia","Celtis","Copaifera","Coussapoa","Humiriastrum","Pourouma","Prunus","Salacia","Sapium","Stylogyne","Talisia","Brunfelsia","Citharexylum","Dendropanax",
# "Pilocarpus","Rauvolfia","Tabernaemontana","Zollernia","Cestrum","Chionanthus","Manilkara","Meriania","Micropholis","Ormosia","Virola","Lacistema","Sorocea","Vitex","Xylosma","Brosimum","Connarus",
# "Euplassa","Guarea","Matayba","Schefflera","Aegiphila","Picramnia","Chrysophyllum","Daphnopsis","Styrax","Andira","Coccoloba","Cybianthus","Neea","Mouriri","Allophylus","Ouratea","Zanthoxylum",
# "Cupania","Byrsonima","Casearia","Maytenus","Trichilia","Swartzia","Inga","Rubus","Citrus",
# "Alibertia","Amaioua","Chiococca","Chomelia","Cordiera","Coussarea","Faramea","Genipa","Guettarda","Ixora","Kutchubaea","Palicourea","Posoqueria","Psychotria","Randia","Rudgea","Tocoyena",
# "Vismia","Quiina","Quararibea","Phytolacca","Homalolepis","Simaba","Capparidastrum","Neocalyptrocalyx","Athenaea","Monteverdia"
# )] = "zoochoric"
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Gymnanthes","Galipea","Jatropha","Pachystroma","Sebastiania","Cnidoscolus","Calliandra","Cassia","Esenbeckia","Helicteres","Mabea","Metrodorea","Mimosa","Actinostemon","Manihot","Senegalia",
# "Senna","Croton","Senefeldera","Algernonia","Brasiliocroton","Stillingia"
# )] = "autochoric"
# taxa$dispersal.syndrome[!is.na(taxa$genus) & is.na(taxa$dispersal.syndrome) & taxa$genus%in%
# c("Adenocalymma","Pachira","Peltophorum","Plathymenia","Raulinoreitzia","Bougainvillea","Cedrela","Hymenolobium","Myrocarpus","Pinus","Pterodon","Ruprechtia","Alsophila","Lafoensia","Moquiniastrum","Seguieria",
# "Symphyopappus","Triplaris","Callisthene","Centrolobium","Pterocarpus","Astronium","Cariniana","Lonchocarpus","Pseudobombax","Ceiba","Luehea","Tabebuia","Tachigali","Vernonanthura","Eriotheca","Terminalia",
# "Handroanthus","Piptocarpha","Jacaranda","Cyathea","Dalbergia","Qualea","Tibouchina","Handroanthus","Vochysia","Baccharis","Kielmeyera","Aspidosperma","Machaerium","Vernonia","Eupatorium",
# "Alseis","Bathysa","Coutarea","Rustia","Simira","Combretum","Luetzelburgia","Pleroma"
# )] = "anemochoric"
#
# #tmp = taxa[is.na(taxa$dispersal.syndrome),]
# #tmp = tmp[!grepl(" ",tmp$Name_submitted),]
# #sort(table(tmp$Name_submitted))
# #sort(table(tmp$genus))
# notas = c(notas,"Missing classification of Dispersal Syndrome for some species or morphospecies was carried at genus or family level (e.g. all Miconia are zoochorich and all ferns are anemochoric")
#
# ####################################################################
# #### MEAN TREE TRAITS AVAILABLE FROM THE TREECO TRAIT DATABASE ####
# ####################################################################
#
# #### MERGING TRAIT AT SPECIES LEVEL ####
# tmp = trait.spp[trait.spp$TAX %in% taxa$Name_submitted,]
# taxa = merge(taxa,tmp,by.x="Name_submitted",by.y="TAX",all.x=T)
#
# ##CHECK!!
# #Checkings possible problems
# #tax[!is.na(tax$wsg_gcm3)&tax$wsg_gcm3>1&tax$GS<2,c("species.correct","wsg","wsg_gcm3","SuccesionalGroup","GS")]
# #tax[!is.na(tax$wsg_gcm3)&tax$wsg_gcm3<0.6&tax$GS>=3.5,c("species.correct","wsg","wsg_gcm3","SuccesionalGroup","GS")]
#
# #### PRELIMINAR EDITING OF TRAIT DATA ####
# #### UPDATE THIS PART OF THE CODE FROM THE CODES OF THE PAPER SUBMITTED TO SCIENCE ####
# ## Seed mass ~ Seed volume
# taxa$SeedVolume = NA
# #for circular fruits
# taxa$SeedVolume[is.na(taxa$SeedLength_cm)&is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)] =
# (4/3)*pi*(as.double(taxa$SeedDiameter_cm[is.na(taxa$SeedLength_cm)&is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)^3
# #for ellipsoidal fruits
# taxa$SeedVolume[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)] =
# (4/3)*pi*(as.double(taxa$SeedDiameter_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)*
# (as.double(taxa$SeedWidth_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)*
# (as.double(taxa$SeedLength_cm[!is.na(taxa$SeedLength_cm)&!is.na(taxa$SeedWidth_cm)&!is.na(taxa$SeedDiameter_cm)])/2)
# #plot(log(taxa$SeedMass_g) ~ log(taxa$SeedVolume)); abline(0,1,lwd=2,col=2)
# #text(x=log(taxa$SeedVolume), y=log(taxa$SeedMass_g), labels=taxa$Name_submitted,cex=0.5,pos=1:3)
#
# tmp = na.omit(taxa[,c("Name_submitted","SeedMass_g","SeedVolume")])
# mod = lm(log(as.double(tmp$SeedMass_g[!tmp$Name_submitted %in% c("Miconia prasina","Myrcia pubipetala")])) ~ log(as.double(tmp$SeedVolume[!tmp$Name_submitted %in% c("Miconia prasina","Myrcia pubipetala")])))
# #abline(mod)
# ## CHECK!!
# ##RE-CHECK THE EQUATION USING ONLY SPECIES WITH ALL SEED INFO (RAW TRAIT VALUES): length/width and/or diameter and seed mass
# taxa$est_SeedMass_g = exp(coef(mod)[1] + coef(mod)[2]*log(taxa$SeedVolume))
# #plot(taxa$est_SeedMass_g ~ taxa$SeedMass_g, log="xy"); abline(0,1,lwd=2,col=2)
# #taxa$SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$est_SeedMass_g)] =
# # taxa$est_SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$est_SeedMass_g)]
#
# #seed mass <- 0.8*fruits/kg
# #plot(SeedMass_g ~ FruitMass_g, data=trait.spp, log="xy",
# # ylim=c(6.150288e-06, 1.157476e+02),
# # xlim=c(0.00001, 850)); abline(0,1,lwd=2,col=2)
# #tmp = na.omit(trait.spp[,c("SeedMass_g","FruitMass_g")])
# #mod = lm(log(tmp$SeedMass_g) ~ log(tmp$FruitMass_g))
# #abline(mod)
# #abline(-0.5,0.85)
# #text(x=trait.taxa$FruitMass_g, y=trait.taxa$SeedMass_g, labels=trait.taxa$TAX,cex=0.4,pos=1:3)
# ##RE-CHECK THE EQUATION USING ONLY SPECIES WITH ALL SEED INFO (RAW TRAIT VALUES): fruit mass and seed mass
# taxa$est_SeedMass_g[is.na(taxa$est_SeedMass_g)] = exp(coef(mod)[1] + coef(mod)[2]*log(taxa$FruitMass_g[is.na(taxa$est_SeedMass_g)]))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$FruitMass_g)] =
# taxa$est_SeedMass_g[is.na(taxa$SeedMass_g)&!is.na(taxa$FruitMass_g)]
# notas = c(notas,"Missing information of Seed Mass was also obtained from studies providing values of number of seeds per kilogram. In additin, for some monospermic species was based on a conversion formula using Fruit_mass as an input")
#
# #### MERGING TRAIT AT GENUS LEVEL ####
# gen = as.character(trait.gen$TAX[trait.gen$TAX %in% taxa$genus])
# trait = generaliza[[1]]
# for(j in 1:length(gen)) {
# tmp = taxa[taxa$genus %in% gen[j],]
# for(i in 1:length(trait)) {
# tmp[is.na(tmp[,trait[i]]),trait[i]] = as.character(trait.gen[as.character(trait.gen$TAX) %in% gen[j],trait[i]])
# }
# taxa[taxa$genus %in% gen[j],trait] = tmp[,trait]
# }
# notas = c(notas,paste("Missing info at species level was replaced by genus-level averages for the following traits: ",paste(generaliza[[1]], collapse=","),".",sep=""))
#
# #### MERGING TRAIT AT FAMILY LEVEL ####
# fam = as.character(trait.fam$TAX[trait.fam$TAX %in% taxa$family])
# trait = generaliza[[2]]
# for(j in 1:length(fam)) {
# tmp = taxa[taxa$family %in% fam[j],]
# for(i in 1:length(trait)) {
# tmp[is.na(tmp[,trait[i]]),trait[i]] = as.character(trait.fam[as.character(trait.fam$TAX) %in% fam[j],trait[i]])
# }
# taxa[taxa$family %in% fam[j],trait] = tmp[,trait]
# }
# notas = c(notas,paste("Missing info at species level was replaced by family-level averages for the following traits: ",paste(generaliza[[2]], collapse=","),".",sep=""))
#
# #### EDITING MISSING TRAIT DATA FOR ABUNDANT OR FREQUENT SPECIES IN TREECO ###
# ## Maximum Height (m) ##
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Vellozia variabilis"] = 2
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Vellozia tubiflora"] = 2
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Ipomoea carnea"] = 2.5
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Erythroxylum nummularium"] = 4
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Cratylia mollis"] = 4
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Hyptis pachyphylla"] = 3
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Croton adenodontus"] = 3
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Eriope exaltata"] = 6
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Simaba ferruginea"] = 13
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Homalolepis ferruginea"] = 13
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Erythroxylum pauferrense"] = 6
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Ephedranthus dimerus"] = 20
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Myrcia costeira"] = 9
# taxa$MaxHeight_m[!is.na(taxa$Name_submitted) & taxa$Name_submitted == "Psychotria pubigera"] = 4
#
# ## Getting leaf Length and Width from the speciesLink measurements ##
# # tmp = read.csv("C://Users//renat//Documents//raflima//Pos Doc//Databases//Species traits//Atributos das espécies//leaf_size_speciesLink.csv",as.is=T)
# tmp = read.csv("E:/WD Backup.swstor/renato/NmQwODhiMTFiOWQ3NDcxOW/Volume{258b8dde-ad01-4a49-b95b-eb77d73987c4}//Users//renat//Documents//raflima//Pos Doc//Databases//Species traits//Atributos das especies//leaf_size_speciesLink.csv",as.is=T)
#
#
# tmp = tmp[!is.na(tmp$Length),]
# tmp1 = cbind.data.frame(aggregate(tmp$Length,list(tmp$species),mean),
# W=aggregate(tmp$Width,list(tmp$species),mean)$x)
# names(tmp1)[1:2] = c("species","L")
# tmp1$LA = pi*tmp1$L*tmp1$W/4
# notas = c(notas,"Missing information of Leaf Area was obtained from Leaf_length and Leaf_width using the formula of an ellipse: pi*L*W/4")
#
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Astrocaryum aculeatissimum"] = tmp1$LA[tmp1$species == "Astrocaryum aculeatissimum"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Euterpe edulis"] = tmp1$LA[tmp1$species == "Euterpe edulis"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Marlierea racemosa"] = tmp1$LA[tmp1$species == "Marlierea racemosa"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Myrcia aethusa"] = tmp1$LA[tmp1$species == "Myrcia aethusa"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Myrcia pubipetala"] = tmp1$LA[tmp1$species == "Myrcia pubipetala"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Pachystroma longifolium"] = tmp1$LA[tmp1$species == "Pachystroma longifolium"]
# taxa$LeafArea[!is.na(taxa$Name_submitted)&taxa$Name_submitted == "Astrocaryum aculeatissimum"] = tmp1$LA[tmp1$species == "Astrocaryum aculeatissimum"]
#
# ## Editing LeafType data ##
# taxa$LeafType[grepl("compostas",taxa$LeafType)&!grepl("simples",taxa$LeafType)] = "compostas"
# taxa$LeafType[!grepl("compostas",taxa$LeafType)&grepl("simples",taxa$LeafType)] = "simples"
# taxa$LeafType[!grepl("compostas",taxa$LeafType)&!grepl("simples",taxa$LeafType)] = NA
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Annona",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Bauhinia rufa",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Cheiloclinium",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus fontanesianus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus gaudichaudianus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Conchocarpus pentandrus",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Esenbeckia grandiflora",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Matayba",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Pseudobombax simplicifolium",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Roupala montana",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Swartzia simplex",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Tabebuia insignis",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Vitex mexiae",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Weinmannia humilis",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Aralia warmingiana",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Eriotheca pubescens",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Malouetia cestroides",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Joannesia princeps",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Malouetia cestroides",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Piptocarpha axillaris|Piptocarpha macropoda|Piptocarpha regnellii",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Protium heptaphyllum|Protium spruceanum|Protium widgrenii",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Schefflera calva|Schefflera macrocarpa",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Tabebuia roseoalba|Tabebuia aurea",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Vitex cymosa|Vitex megapotamica|Vitex polygama",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("Zeyheria montana|Zeyheria tuberculosa",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Actinostemon",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Allophylus",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Callisthene",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Celtis",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Dendropanax",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Faramea",taxa$Name_submitted)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Jacaranda",taxa$Name_submitted)] = "compostas"
# taxa$LeafType[!is.na(taxa$Name_submitted)&grepl("\\|",taxa$LeafType)&grepl("Sebastiania",taxa$Name_submitted)] = "simples"
# taxa$LeafType[grepl("compostas",taxa$LeafType)&grepl("simples",taxa$LeafType)] = NA
# taxa$LeafArea[is.infinite(taxa$LeafArea)] = NA
#
# #some final edits at genus or family level
# taxa$LeafType[!is.na(taxa$family)&is.na(taxa$LeafType)&grepl("Annonaceae|Melastomataceae|Myrtaceae",taxa$family)] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted)&is.na(taxa$LeafType)&grepl("Beilschmiedia|Mezilaurus",taxa$Name_submitted)] = "simples"
#
# #some final edits at species level (looked up in herbarium vouchers)
# taxa$LeafType[!is.na(taxa$Name_submitted) & is.na(taxa$LeafType) & taxa$Name_submitted %in%
# c("Bauhinia_longifolia","Cavanillesia_umbellata","Guapira_areolata","Pogonophora_schomburgkiana"
# )] = "simples"
# taxa$LeafType[!is.na(taxa$Name_submitted) & is.na(taxa$LeafType) & taxa$Name_submitted %in%
# c("Caryocar_brasiliense","Cenostigma_bracteosum","Connarus_suberosus","Esenbeckia_febrifuga","Pachira_endecaphylla",
# "Galipea_jasminiflora","Protium_atlanticum","Protium_icicariba","Sparattosperma_leucanthum"
# )] = "compostas"
# notas = c(notas,"Missing information of Leaf Type was obtained at genus-level for some taxa. Species with both compound and simple leafs along their onthogeny (e.g. Matayba, Roupala) were treated as having compound leaves")
#
# ### Final edits: Seed size
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Actinostemon")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Sebastiania")])))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Athenaea")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Capsicum")])))
# taxa$SeedMass_g[is.na(taxa$SeedMass_g) & taxa$genus %in% c("Anaxagorea")] = mean(as.double(unique(taxa$SeedMass_g[taxa$genus %in% c("Xylopia")])))
#
# ### Edits for very species rich genera without habit
# ##VERIFICAR A PROPORÇÃO DE ÁRVORES E ARBUSTOS POR FAMILIA E GENERO PARA FECHAR AS LISTAGEMS ABAIXO, PRINCIPALMENTE GENEROS
# #By family
# taxa$habito[!is.na(taxa$family) & is.na(taxa$habito) & taxa$family%in%
# c("Annonaceae","Burseraceae","Chrysobalanaceae","Lauraceae","Lecythidaceae","Moraceae","Myristicaceae","Myrtaceae","Proteaceae","Sapotaceae"
# )] = 1
# taxa$habito[!is.na(taxa$family) & is.na(taxa$habito) & taxa$family%in%
# c("Lacistemataceae","Loganiaceae","Pipeaceae","Siparunaceae","Violaceae"
# )] = 0.5
# #By genus
# taxa$habito[!is.na(taxa$genus) & is.na(taxa$habito) & taxa$genus%in%
# c("Alchornea","Anadenanthera"
# )] = 1
# taxa$habito[!is.na(taxa$genus) & is.na(taxa$habito) & taxa$genus%in%
# c("Athenaea","Brunfelsia","Capsicum","Piper","Eumachia","Chiococca","Stachytarpheta","Schweiggeria"
# )] = 0.5
#
# #### CHECKING COMMON SPECIES STILL WITHOUT TRAIT INFO ####
# tmp = c("establishment.AF","habito","extinction","endemism","ecological.group","dispersal.syndrome",
# "wsg_gcm3","MaxHeight_m","MaxDbh_cm",
# "SeedLength_cm","SeedWidth_cm","SeedDiameter_cm","SeedMass_g","FruitMass_g",
# "LeafArea","LeafType","SuccesionalGroup",
# "Deciduousness","LT","PericarpConsistency","SexualSystem","PollinationSyndrome","SLA_cm2_g.1")
# tmp1= NULL
# for(i in 1:length(tmp)) {
# vrvl = tmp[i]
# if(is.numeric(taxa[,vrvl])) { tmp2 = taxa$Name_submitted[is.na(taxa[,vrvl])]
# } else { tmp2 = taxa$Name_submitted[is.na(taxa[,vrvl])|(grepl("NA:",taxa[,vrvl])&!grepl("\\|",taxa[,vrvl]))]
# }
# tmp2 = tmp2[!grepl(" sp\\.",tmp2)&!is.na(tmp2)]
# tmp2 = tmp2[grepl(" ",tmp2)]
# if(is.null(tmp1)) { tmp1 = c(length(table(tmp2)),100*sum(table(tmp2))/dim(taxa)[1])
# } else { tmp1 = rbind.data.frame(tmp1,c(length(table(tmp2)),100*sum(table(tmp2))/dim(taxa)[1])) }
# }
# names(tmp1) =c("Nsp_without","prop.sp.without")
# rownames(tmp1) = tmp
# print("Check the number and proportion of species (not genera or families) without trait information.")
# print("Proportion below 40% generally results in good coverage for all individuals at the community level.")
# print(tmp1[order(tmp1$prop.sp.without),])
#
# #### FILTERING THE SELECTED METADATA (COLUMNS) ####
# colunas = c("X","species.original","Habit","Bark","LeafMargin","LeafTip","AcumenLength_cm","LeafSubtype","Leaflets",
# "LeafHairiness_upper","LeafHairiness_lower","FruitLipids","FruitWater","FruitProtein","FruitCarbo",
# "PollinationSubsyndrome","Anthesis","FlowerType","CorollaType","CorollaColour","SepalColour","CorollaLength_cm","CorollaWidth_cm",
# "ChemicalCompounds","PhysicalCompounds","Allelopathy","sem.kg","Flowers","Fruits","Seeds","LeafN","obs1","obs2","obs3",
# "GeogDist","Domain","Vegetation","TaxNotes","MinLeafLength_cm","MaxLeafLength_cm","MinLeafWidth_cm","MaxLeafWidth_cm",
# "LeafThickness_micro","FruitLength_cm","FruitWidth_cm","FruitDiameter_cm","LeafChlorophyllAB","LeafCarbon","LeafWater",
# "dry_mass_fraction","WoodCarbon_gkg.1","LeafDryMatter_mg.g","ChlorophyllContent_FCI","LeafTough_N.mm","PithProp","XylProp","BarkProp",
# "BarkProp","VesselDensity_n.mm2","VesselDiameter_microm","StomataDensity_n.mm2","StomataLength_microm","Kpot_kg.m.s.Mpa",
# "SuccesionalGroup","wsg")
# if(is.null(rm.colunas)) {colunas1 = colunas} else { colunas1 = c(colunas,rm.colunas) }
# if(is.null(inc.colunas)) {colunas1 = colunas1} else { colunas1 = colunas1[!colunas1 %in% inc.colunas] }
# if(!is.null(colunas1)) taxa = taxa[,!names(taxa) %in% colunas1]
#
# #### PREPARING AND RETURNING THE FINAL RESULTS ####
# notas = gsub("\\\n","",notas)
# notas1 = paste(">>>NOTE ",1:length(notas),": ",notas,sep="")
# resulta = list(taxa, notas1)
# names(resulta) = c("data_frame","editing_notes")
# return(resulta)
#
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.