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Last active December 16, 2015 03:09
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Getting data for a genus from GBIF.
Raw
gbif_genus.md 
install.packages("rgbif")
library(rgbif)

Getting all occurrences for a genus

The best way to approach this right now is to use the scientificname argument in the occurrencelist function. For example, use an asterisk "*" after "Abies", which will get you everything in the genus "Abies". Then you can clean up afterwards if you want. See below

Lets see how many records there are in the genus with lat/long data in Spain

There are only 2975, so we can just set maxresults below to this number

occurrencecount("Abies*", coordinatestatus=TRUE, originisocountrycode="ES")

[1] 2975

Lets get data using the asterisk

dataout <- occurrencelist(scientificname="Abies*",coordinatestatus=TRUE, 
                          originisocountrycode="ES", removeZeros=TRUE, maxresults=2975)
                          
head(dataout[,1:4])

         taxonName country decimalLatitude decimalLongitude
1 Abies alba Mill.      ES        42.92568       -0.8569100
2 Abies alba Mill.      ES        42.92568       -0.8569100
3 Abies alba Mill.      ES        43.02382       -1.3444000
4 Abies alba Mill.      ES        42.92568       -0.8569100
5 Abies alba Mill.      ES        42.92013       -0.8019660
6 Abies alba Mill.      ES        42.75954       -0.8809775

In the dataout data.frame there are 31 unique names

length(unique(dataout$taxonName))

[1] 31

but some are duplicates

unique(dataout$taxonName)

 [1] "Abies alba Mill."                                                    
 [2] "Abies alba L."                                                       
 [3] "Abies sp."                                                           
 [4] "Abies"                                                               
 [5] "Abies  alba"                                                         
 [6] "Abies  alba Mill."                                                   
 [7] "Abies  alba                                                 M Miller"
 [8] "Abies pinsapo Boiss."                                                
 [9] "Abies excelsa Poir."                                                 
[10] "Abies pectinata DC."                                                 
[11] "Abies balsamea (L.) Mill."                                           
[12] "Abies nordmanniana (Steven) Spach"                                   
[13] "Abies numidica De Lannoy ex Carriere"                                
[14] "Abies concolor Hildebr."                                             
[15] "Abies alba Miller"                                                   
[16] "Abies koreana"                                                       
[17] "Abies pinsapo var. \"Kelleris\""                                     
[18] "Abies pinsapo Boiss"                                                 
[19] "Abies  pinsapo Boiss."                                               
[20] "Abies  pinsapo"                                                      
[21] "Abies  excelsa DC."                                                  
[22] "Abies  pectinata DC."                                                
[23] "Abies  nordmanniana"                                                 
[24] "Abies  pectinata"                                                    
[25] "Abies  alba Miller"                                                  
[26] "Abies marocana Trab."                                                
[27] "Abies concolor (Gord.) Lindl. & Hildebr."                            
[28] "Abies pinsapo"                                                       
[29] "Abies cephalonica Loudon"                                            
[30] "Abies concolor (Gord.) Lindl.ex Hildebr."                            
[31] "Abies pinsapo Boiss. var. pinsapo"

So you can exlude ones you don't want or change names using regex, for example (notice one name replaced)

library(stringr)
unique(gsub("Abies pinsapo Boiss","Abies pinsapo", dataout$taxonName, fixed=TRUE))

 [1] "Abies alba Mill."                                                    
 [2] "Abies alba L."                                                       
 [3] "Abies sp."                                                           
 [4] "Abies"                                                               
 [5] "Abies  alba"                                                         
 [6] "Abies  alba Mill."                                                   
 [7] "Abies  alba                                                 M Miller"
 [8] "Abies pinsapo."                                                      
 [9] "Abies excelsa Poir."                                                 
[10] "Abies pectinata DC."                                                 
[11] "Abies balsamea (L.) Mill."                                           
[12] "Abies nordmanniana (Steven) Spach"                                   
[13] "Abies numidica De Lannoy ex Carriere"                                
[14] "Abies concolor Hildebr."                                             
[15] "Abies alba Miller"                                                   
[16] "Abies koreana"                                                       
[17] "Abies pinsapo var. \"Kelleris\""                                     
[18] "Abies pinsapo"                                                       
[19] "Abies  pinsapo Boiss."                                               
[20] "Abies  pinsapo"                                                      
[21] "Abies  excelsa DC."                                                  
[22] "Abies  pectinata DC."                                                
[23] "Abies  nordmanniana"                                                 
[24] "Abies  pectinata"                                                    
[25] "Abies  alba Miller"                                                  
[26] "Abies marocana Trab."                                                
[27] "Abies concolor (Gord.) Lindl. & Hildebr."                            
[28] "Abies cephalonica Loudon"                                            
[29] "Abies concolor (Gord.) Lindl.ex Hildebr."                            
[30] "Abies pinsapo. var. pinsapo"

Getting all occurrences for a genus using taxonconceptkey in occurrencelist

I can't wrap my head around the GBIF taxonconceptkeys - I thought I got it, but using a taxononcept key from a search of Abies keys, you get back non-Abies results

abies.keys <- taxonsearch("Abies", rank="genus", maxresults=1000)
data <- occurrencelist(taxonconceptKey=abies.keys[[1]], coordinatestatus=TRUE, originisocountrycode="ES", removeZeros=TRUE, maxresults=200)
head(data[,1:4])

          taxonName country decimalLatitude decimalLongitude
1      Megaspilidae   Spain        38.91060           1.2725
2         Telenomus   Spain        38.83330           1.3667
3         Telenomus   Spain        38.91670           1.3500
4             Idris   Spain        38.91670           1.3500
5 Conchoecia obtusa    <NA>        44.04585         -12.7067
6   Diaphus garmani    <NA>        28.04500         -14.0767

I will work on fixing this...

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