all try data run

TRY.R

@@ -142,54 +142,54 @@ species.tab2$Latin_name_syn<- trim.trailing(species.tab2$Latin_name_syn)
 
 ## lapply(unique(species.tab2$Latin_name_syn)[1:10],FUN=tnrs)
 
-### find synonyme
-getsynonymnamesfromtsn(tsn = 502590)  
+## ### find synonyme
+## getsynonymnamesfromtsn(tsn = 502590)  
 
-### find synonyme
-tp_synonyms(id =502590 )
+## ### find synonyme
+## tp_synonyms(id =502590 )
 
-# Example R script which calls the TNRS in the context of adding names to a phylogeny
-## FROM Boyle et al. 2013 BMC Bioinformatics 
-library(ape)
-library(rjson)	
-library(RCurl) 
+## # Example R script which calls the TNRS in the context of adding names to a phylogeny
+## ## FROM Boyle et al. 2013 BMC Bioinformatics 
+## library(ape)
+## library(rjson)	
+## library(RCurl) 
 
-tnrs.api<-'http://tnrs.iplantc.org/tnrsm-svc'
+## tnrs.api<-'http://tnrs.iplantc.org/tnrsm-svc'
 
-#Tree topology from Ackerly, D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. PNAS 106:19699--19706.
-lobelioids.string<-'((((((Lobelia_kauaensis,Lobelia_villosa),Lobelia_gloria-montis),(Trematolobelia_kauaiensis,Trematolobelia_macrostachys)),((Lobelia_hypoleuca,Lobelia_yuccoides),Lobelia_niihauensis)),((Brighamia_insignis,Brighamia_rockii),(Delissea_rhytidosperma,Delissea_subcordata))),((((Cyanea_pilosa,Cyanea_acuminata),Cyanea_hirtella),(Cyanea_coriacea,Cyanea_leptostegia)),(((Clermontia_kakeana,Clermontia_parviflora),Clermontia_arborescens),Clermontia_fauriei)));'
+## #Tree topology from Ackerly, D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. PNAS 106:19699--19706.
+## lobelioids.string<-'((((((Lobelia_kauaensis,Lobelia_villosa),Lobelia_gloria-montis),(Trematolobelia_kauaiensis,Trematolobelia_macrostachys)),((Lobelia_hypoleuca,Lobelia_yuccoides),Lobelia_niihauensis)),((Brighamia_insignis,Brighamia_rockii),(Delissea_rhytidosperma,Delissea_subcordata))),((((Cyanea_pilosa,Cyanea_acuminata),Cyanea_hirtella),(Cyanea_coriacea,Cyanea_leptostegia)),(((Clermontia_kakeana,Clermontia_parviflora),Clermontia_arborescens),Clermontia_fauriei)));'
 
-#Transform the newick sting into an ape phylo object
-tree<-read.tree(text=lobelioids.string)
+## #Transform the newick sting into an ape phylo object
+## tree<-read.tree(text=lobelioids.string)
 
-#Obtain the taxa names
-old.names<-tree$tip.label
+## #Obtain the taxa names
+## old.names<-tree$tip.label
 
 
-#Change the underscore characters into blank spaces
-old.names<-gsub('_',' ',old.names)
-old.names <-  species.tab2$Latin_name_syn
-#Transporms the vector into a string
-old.names<-paste(old.names,collapse=',')
+## #Change the underscore characters into blank spaces
+## old.names<-gsub('_',' ',old.names)
+## old.names <-  species.tab2$Latin_name_syn
+## #Transporms the vector into a string
+## old.names<-paste(old.names,collapse=',')
 
-#The string needs to be URL-encoded
-old.names<-curlEscape(old.names)
+## #The string needs to be URL-encoded
+## old.names<-curlEscape(old.names)
 
-#Send a request to the TNRS service
-url<-paste(tnrs.api,'/matchNames?retrieve=best&names=',old.names,sep='')
-tnrs.json<-getURL(url) 
+## #Send a request to the TNRS service
+## url<-paste(tnrs.api,'/matchNames?retrieve=best&names=',old.names,sep='')
+## tnrs.json<-getURL(url) 
 
-#The response needs to be converted from JSON
-tnrs.results<-fromJSON(tnrs.json)
+## #The response needs to be converted from JSON
+## tnrs.results<-fromJSON(tnrs.json)
 
-#The corrected names are extracted from the response
-names<-sapply(tnrs.results[[1]], function(x) c(x$nameSubmitted,x$acceptedName))
-names<-as.data.frame(t(names),stringsAsFactors=FALSE)
+## #The corrected names are extracted from the response
+## names<-sapply(tnrs.results[[1]], function(x) c(x$nameSubmitted,x$acceptedName))
+## names<-as.data.frame(t(names),stringsAsFactors=FALSE)
 
-#If TNRS did not return any accepted name (no match, or name is already accepted), the submitted name is retained
-names[names[,2]=="",2]<-names[names[,2]=="",1] 
+## #If TNRS did not return any accepted name (no match, or name is already accepted), the submitted name is retained
+## names[names[,2]=="",2]<-names[names[,2]=="",1] 
 
-### SAME ERROR FOR FAGUS SYLVATICA TEH WEB SITE GIVE A GOOD RESULTS BUT NOT THE CALL FROM R ?
+## ### SAME ERROR FOR FAGUS SYLVATICA TEH WEB SITE GIVE A GOOD RESULTS BUT NOT THE CALL FROM R ?
 
 ### change format try species names
 TRY.DATA.FORMATED$AccSpeciesName <- as.character(TRY.DATA.FORMATED$AccSpeciesName)