R/Hodgson.R
In GioBo/TR8: A Tool for Downloading Functional Traits Data for Plant Species
## 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("&","&",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 16, 2022, 9:10 p.m.
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## 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("&","&",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)
## }
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