R/Hodgson.R

## retrieve_Hodgson<-function(species,TRAITS,rest,data_csr){

##     url<-"http://people.exeter.ac.uk/rh203/plant-scientist-recent-science-functional-types-allocating-csr-csr-lookup-table.xls"

##     temp_dest<-tempfile(fileext=".xls")
##     download.file(url,temp_dest,mode="wb")

##     catminat_df<-read_excel(temp_dest,sheet=1,col_names=T,col_types=rep("text",2))
    
##     catminat_df<-catminat_df[grep("[0-9]+",catminat_df$rang_taxinomiqu,invert=T),]


##     ##### TODO correggere nomi delle specie\


##     ## remove entries for which CHOROLOGIE=="?"
##     catminat_df<-catminat_df[catminat_df$CHOROLOGIE!="?",]
    
##     ## change columns' name in order to
##     ## avoid possible conflicts with non-
##     ## ascii
##     ## french chars
##     recode_catminat_values<-c("Lumi.{1}re"="ell_L_fr",
##                               "Temp.{1}rature"="elle_T_fr",
##                               "Continentalit.{1}"="ell_C_fr",
##                               "Humidit.{1}_.{1}daphique"="ell_U_fr",
##                               "R.{1}action_du_sol_.pH."="ell_R_fr",
##                               "Niveau_trophique"="ell_N_fr",
##                               "Salinit.*"="ell_S_fr",
##                               "Texture"="Soil_texture_fr",
##                               "Mati.*re_organique"="organic_matter_fr",
##                               "Humidit.*_atmosph.*rique"="ell_U_atm_fr",
##                               "pollinisation"="poll_vect_fr",
##                               "diss.*mination"="dissemination_fr",
##                               "couleur_fleur"="flower_colour_fr",
##                               "fruit"="fruit_type_fr",
##                               "sexualit.*"="sex_reprod_fr",
##                               "ordre_maturation"="order_of_maturation",
##                               "inflorescence"="inflorescence_fr",
##                               "Nom.Phytobase"="species_name",
##                               "TYPE_BIOLOGIQUE"="li_form_fr"
##                               )

##     for(i in names(recode_catminat_values)){
##         names(catminat_df)<-gsub(i,recode_catminat_values[i],names(catminat_df))
##     }

##     catminat_df$species_name<-as.character(catminat_df$species_name)
##     catminat_df<-catminat_df[!is.na(catminat_df$species_name),]


    
##     catminat_df$species_name<-gsub("&amp","&",catminat_df$species_name,perl=TRUE)
##     catminat_df$species_name<-gsub(";","",catminat_df$species_name,perl=TRUE)
##     catminat_df$species_name<-gsub("\\s+\\*$","",catminat_df$species_name,perl=TRUE)
##     catminat_df$species_name<-gsub("\\s+A$","",catminat_df$species_name,perl=TRUE)
##     catminat_df$species_name<-gsub("\\s+B$","",catminat_df$species_name,perl=TRUE)


    

##     ## I split flowering dates into 2 columns,
##     ## flower begin and end
##     flowering<-as.character(catminat_df$floraison)
##     beg_flow_fr<-as.numeric(gsub("^([0-9]+)+\\-([0-9])+$","\\1",flowering))
##     end_flow_fr<-as.numeric(gsub("^([0-9]+)+\\-([0-9])+$","\\2",flowering))
##     catminat_df<-data.frame(catminat_df,beg_flow_fr,end_flow_fr)

    
##     ## I choose only a subset of the available columns in baseflor dataset
##     selected_columns_catminat<-c(
##         "species_name",
##         "CHOROLOGIE",
##         "inflorescence_fr",
##         "sex_reprod_fr",
##         "order_of_maturation",
##         "poll_vect_fr",
##         "fruit_type_fr",
##         "dissemination_fr",
##         "flower_colour_fr",
##         "macule",
##         "type_ligneux",
##         "li_form_fr",
##         "ell_L_fr",
##         "elle_T_fr",
##         "ell_C_fr",
##         "ell_U_atm_fr",
##         "ell_U_fr",
##         "ell_R_fr",
##         "ell_N_fr",
##         "ell_S_fr",
##         "Soil_texture_fr",
##         "organic_matter_fr",
##         "beg_flow_fr",
##         "end_flow_fr",
##         "PhytobaseID"
##         )

##     catminat_df<-catminat_df[,selected_columns_catminat]


##     ## recode inflorescenses types
##     inflorescences<-c(
##         "capitule de capitules$"="Compound capitulum",
##         "capitule simple$"="Capitulum",
##         "c.*ne$"="Cone",                                
##         "corymbe$"="Corymb",
##         "corymbe de capitules$"="Corymb of capitula",
##         "cyathe$"="Cyathium",
##         "cyme bipare$"="Dichasia cyme",                         
##         "cyme biscorpio.*de$"="Scorpioid cyme",
##         "cyme capituliforme$"="Capituliform cyme ",
##         "cyme d'.+pis$"="Cyme of spikes",
##         "cyme d'ombelles$"="Cyme of umbels",                     
##         "cyme de capitules$"="Cyme of capitula",
##         "cyme de glom.+rules$"="Cyme of glomerula",
##         "cyme multipare$"="Pleiochasium",
##         "cyme unipare h.*lico.*de$"="Helicoid cyme",              
##         "cyme unipare scorpio.*de$"="Scorpioid cyme",
##         ".*pi d'.+pillets$"="Spike of spikelets",
##         ".*pi de capitules$"="Spike of capitula",
##         ".+pi de cymes triflores$"="Spike of three-flowers cymes",              
##         ".+pi simple$"="Simple spike",
##         "fleur solitaire lat.+rale$"="Solitary lateral flower",
##         "fleur solitaire terminale$"="Solitary terminal flower",
##         "glom.+rules$"="Glomerula",                          
##         "glom.*rules spiciformes$"="Spike-like glomerula",
##         "ombelle d'ombellules$"="Umbel of umbels",
##         "ombelle simple$"="Simple umbel",
##         "ombelle simple d'.+pis$"="Simple umbel of spikes",               
##         "ombelle simple de capitules$"="Simple umbel of capitula",
##         "panicule d'.+pillets$"="Panicle of spikelets",
##         "panicule spiciforme$"="Spike-like panicle",
##         "rac.{1}me capituliforme$"="Capitulum-like raceme",                 
##         "rac.{1}me d'.+pis$"="Raceme of spikes",
##         "rac.{1}me d'ombelles$"="Raceme of umbels",
##         "rac.{1}me de capitules$"="Raceme of capitula",
##         "ra.{1}me de cymes bipares$"="Raceme of dichasia cymes",             
##         "rac.{1}me de cymes unipares h.{1}lico.{1}des$"="Raceme of helicoid cymes",
##         "rac.{1}me de cymes unipares scorpio.{1}des$"="Raceme of scorpioid cymes",
##         "rac.{1}me de rac.{1}mes$"="Raceme of racemes",
##         "rac.{1}me simple$"="Simple raceme",                       
##         "rac.{1}me de cymes bipares$"="Raceme of dichasia cymes", 
##         "spadice$"="Spadix",
##         "verticille d'ombelles$"="Verticil of umbels"               
##         )
##     catminat_df$inflorescence_fr<-catminat_replace(catminat_df$inflorescence_fr,inflorescences)

##     ## recode fruit types
##     fruit_types=c("ak.{1}ne$"="achene",
##         "baie$"="berry",
##         "capsule$"="capsule",
##         "caryopse$"="caryopsis",
##         "c.{1}ne$"="cone",
##         "drupe$"="drupe",
##         "follicule$"="follicle",
##         "catminat_dfusse$"="legume",
##         "pyxide$"="pyxid",
##         "samare$"="samara",
##         "silique$"="silique"  
##         )
##     catminat_df$fruit_type_fr<-catminat_replace(catminat_df$fruit_type_fr,fruit_types)

##     ## recode flower colours
##     flower_colours<-c("blanc$"="white",
##                       "jaune$"="yellow",
##                       "vert$"="green",
##                       "marron$"="brown",
##                       "bleu$"="blue",
##                       "jaune$"="yellow",
##                       "jauna$"="yellow",
##                       "noir$"="black"
##                       )
##     catminat_df$flower_colour_fr<-catminat_replace(catminat_df$flower_colour_fr,flower_colours)

##     ## recode dissemination types
##     dissemination<-c(
##         "an.*mochore$"="anemochores",
##         "myrm.*cochore$"="myrmecochores",
##         "myrm.*cochore$"="myrmecochores",
##         "autochore$"="autochores",
##         "barochore$"="barochores",
##         "endozoochore$"="endozoochores",
##         "endozoochorie$"="endozoochores",
##         ".+pizoochore$"="epizoochores",              
##         "dyszoochore$"="dyszoochores", 
##         "hydrochore$"="hydrochores"                             
##         )
##     catminat_df$dissemination_fr<-catminat_replace(catminat_df$dissemination_fr,dissemination)

##     ## recode sexual reproduction types
##     sex_reprod<-c(
##         "androdio.{1}que$"="Androdioecy",
##         "gynomono.{1}que" ="Gynomonoecious",
##         "gynodio.{1}que$"="Gynodioecious",
##         "polygame$"="Polygamous",
##         "mono.{1}que$"="Monoecious",
##         "dio.{1}que$"="Dioecious",
##         "hermaphrodite$"="Hermaphroditic",
##         "polygame$"="Polygamous"
##         )
##     catminat_df$sex_reprod_fr<-catminat_replace(catminat_df$sex_reprod_fr,sex_reprod)

##     ## remove species names where the phrase
##     ## "sans nom" is found
##     catminat_df<-catminat_df[grep("sans nom",catminat_df$species_name,invert=TRUE),]

##     ## recode pollen vector
##     poll_vec<-c(
##         "an.{1}mogame"="wind",
##         "autogame"="self",
##         "apogame"="apogamy",
##         "entomogame"="insect",
##         "hydrogame"="water"
##         )
##     catminat_df$poll_vect_fr<-catminat_replace(as.character(catminat_df$poll_vect_fr),poll_vec)

##     ## recode life_form_fr

##     ## -- for the moment leave the original values
    
    
##     ## remove entries without species names
##     catminat_df<-catminat_df[catminat_df$species_name!="",]


##     ## Remove double entries

##     ## beware: catminat is now read with readxl package and empty cells are coded as <NA>. not as empty strings
##     ##    catminat_df<-catminat_df[!(catminat_df$species_name=="Juncus articulatus" & catminat_df$sex_reprod_fr==""),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Juncus articulatus" & is.na(catminat_df$sex_reprod_fr)),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Capparis spinosa" & catminat_df$PhytobaseID=="13450"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Centaurium ery. erythraea" & catminat_df$PhytobaseID=="2361"),]
## ##    catminat_df<-catminat_df[!(catminat_df$species_name=="Centaurium ery. erythraea" & catminat_df$PhytobaseID=="2361"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Chenopodium ambrosioides" & is.na(catminat_df$flower_colour_fr)),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Chenopodium opulifolium" & catminat_df$CHOROLOGIE=="cosmopolite"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Cornus sanguinea" & catminat_df$PhytobaseID=="2258"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Crataegus mon. monogyna" & catminat_df$PhytobaseID=="1657"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Daphne laureola" & catminat_df$PhytobaseID=="2084"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Eryngium bourgatii" & catminat_df$PhytobaseID=="11913"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Festuca ovi. ovina" & catminat_df$PhytobaseID=="352"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Gaudinia fragilis" & catminat_df$li_form_fr=="test(hbis)"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Genista salzmannii" & catminat_df$PhytobaseID=="12481"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Medicago turbinata" & catminat_df$PhytobaseID=="12456"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Ophrys bertolonii" & catminat_df$PhytobaseID=="725"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Populus nigra" & catminat_df$PhytobaseID=="7038"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Rhamnus saxatilis" & catminat_df$PhytobaseID=="16181"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Rosmarinus officinalis" & catminat_df$PhytobaseID=="16080"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Salix rosmarinifolia" & catminat_df$PhytobaseID=="795"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Salvia officinalis" & catminat_df$PhytobaseID=="14526"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Taraxacum sagittilobum" & catminat_df$PhytobaseID=="15326"),]
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Thlaspi rot. rotundifolium" & catminat_df$PhytobaseID=="1274"),]
    
##     catminat_df<-catminat_df[!(catminat_df$species_name=="Linum bienne" & catminat_df$li_form_fr=="test(hbis)"),]

##     ## remove double entries
##     catminat_df<-catminat_df[!(duplicated(catminat_df)),]

##     ## fix flowering dates for Medicago turbinata
##     catminat_df[catminat_df$PhytobaseID==12456,c("beg_flow_fr","end_flow_fr")]<-c(4,6)
##     ## and remove double entry
##     catminat_df<-catminat_df[catminat_df$PhytobaseID!=11083,]

##     ## fix CHOROLOGIE for Rubus cinerascens and  Rubus conspicuus and then remove double entries
##     catminat_df<-catminat_df[(1:nrow(catminat_df))!=which(catminat_df$species_name=="Rubus cinerascens")[1],]
##     catminat_df<-catminat_df[(1:nrow(catminat_df))!=which(catminat_df$species_name=="Rubus conspicuus")[1],]

##     ##catminat_df<-catminat_df[row.names(catminat_df)!=(which(catminat_df$species_name=="Erodium glandulosum")[1]),]
##     ##catminat_df<-catminat_df[row.names(catminat_df)!=(which(catminat_df$species_name=="Erodium rupicola")[1]),]
##     ##catminat_df<-catminat_df[row.names(catminat_df)!=(which(catminat_df$species_name=="Onosma echioides")[1]),]

##     ## remove CHOROLOGIE column
##     catminat_df<-catminat_df[,names(catminat_df)!="CHOROLOGIE"]
    
##     save(file=file.path(directory,"catminat.Rda"),catminat_df)
## }
GioBo/TR8 documentation built on June 9, 2019, 8:32 a.m.