April 12, 2013
Real use cases from people using our software are awesome. They are important for many reasons: 1) They make the code more useable because we may change code to make the interace and output easier to understand; 2) They may highlight bugs in our code; and 3) They show us what functions users care the most about (if we can assume number of questions equates to use).
If someone has a question, others are likely to have the same, or a similar question. Thus, we are sharing use cases on our blog.
The use case: How do I get GBIF occurrences for all species in 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.
# install_github('rgbif', 'ropensci') # uncomment if you don't have it
# installed yet
library(rgbif)
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
Get some data
dataout <- occurrencelist(scientificname = "Abies*", coordinatestatus = TRUE,
originisocountrycode = "ES", removeZeros = TRUE, maxresults = 3000)
# take a quick peek
head(dataout[, 1:4])
## taxonName country decimalLatitude decimalLongitude
## 1 Abies alba Mill. ES 37.84 -4.8200
## 2 Abies alba Mill. ES 43.02 -1.3444
## 3 Abies alba Mill. ES 42.93 -0.8569
## 4 Abies alba Mill. ES 42.93 -0.8569
## 5 Abies alba Mill. ES 42.93 -0.8569
## 6 Abies alba Mill. ES 42.76 -0.8810
In the dataout data.frame there are 31 unique names
length(unique(dataout$taxonName))
## [1] 31
But some are duplicates just spelled in different ways, or with whitespace
unique(dataout$taxonName)
## [1] "Abies alba Mill."
## [2] "Abies alba L."
## [3] "Abies sp."
## [4] "Abies alba"
## [5] "Abies alba M Miller"
## [6] "Abies alba Mill."
## [7] "Abies"
## [8] "Abies pinsapo Boiss."
## [9] "Abies alba Miller"
## [10] "Abies pinsapo Boiss"
## [11] "Abies marocana Trab."
## [12] "Abies nordmanniana (Steven) Spach"
## [13] "Abies concolor (Gord.) Lindl. & Hildebr."
## [14] "Abies pinsapo"
## [15] "Abies koreana"
## [16] "Abies pinsapo var. \"Kelleris\""
## [17] "Abies excelsa DC."
## [18] "Abies nordmanniana"
## [19] "Abies pinsapo Boiss."
## [20] "Abies pinsapo"
## [21] "Abies alba Miller"
## [22] "Abies pectinata DC."
## [23] "Abies pectinata"
## [24] "Abies pectinata DC."
## [25] "Abies excelsa Poir."
## [26] "Abies balsamea (L.) Mill."
## [27] "Abies concolor Hildebr."
## [28] "Abies numidica De Lannoy ex Carriere"
## [29] "Abies pinsapo Boiss. var. pinsapo"
## [30] "Abies concolor (Gord.) Lindl.ex Hildebr."
## [31] "Abies cephalonica Loudon"
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 alba"
## [5] "Abies alba M Miller"
## [6] "Abies alba Mill."
## [7] "Abies"
## [8] "Abies pinsapo."
## [9] "Abies alba Miller"
## [10] "Abies pinsapo"
## [11] "Abies marocana Trab."
## [12] "Abies nordmanniana (Steven) Spach"
## [13] "Abies concolor (Gord.) Lindl. & Hildebr."
## [14] "Abies koreana"
## [15] "Abies pinsapo var. \"Kelleris\""
## [16] "Abies excelsa DC."
## [17] "Abies nordmanniana"
## [18] "Abies pinsapo Boiss."
## [19] "Abies pinsapo"
## [20] "Abies alba Miller"
## [21] "Abies pectinata DC."
## [22] "Abies pectinata"
## [23] "Abies pectinata DC."
## [24] "Abies excelsa Poir."
## [25] "Abies balsamea (L.) Mill."
## [26] "Abies concolor Hildebr."
## [27] "Abies numidica De Lannoy ex Carriere"
## [28] "Abies pinsapo. var. pinsapo"
## [29] "Abies concolor (Gord.) Lindl.ex Hildebr."
## [30] "Abies cephalonica Loudon"
Let us know if you have any questions on this tutorial.
And keep those use cases/questions coming!