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sckott / error.md
Created August 28, 2015 05:58 
[1] pry(main)> require 'alan'
LoadError: cannot load such file -- alan
from /Users/sacmac/.rbenv/versions/2.2.0-dev/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:54:in `require'
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sckott / taxize_classification.md
Last active August 29, 2015 13:56
Taxize

Using taxize to get a classification

Install taxize

install.packages("taxize")

Load taxize

@sckott
sckott / parse_error_messages.md
Last active August 29, 2015 13:56
Is there a general solution for parsing server error messages that aren't returned in the header in httr so that we can print error message for users in a package?

This is a call to the GBIF API. There is an intential error in the call that gives an error message from the server

com.spatial4j.core.exception.InvalidShapeException: Invalid latitude: latitudes are range -90 to 90: provided lat: [-125.0]

In R with httr:

library(httr)
call <- "http://api.gbif.org/v0.9/occurrence/search?geometry=POLYGON((38.4 -125, 40.9 -125, 40.9 -121.8, 38.4 -121.8, 38.4 -125))"
a &lt;- GET(call)
@sckott
sckott / spocc_via_ids.md
Created February 10, 2014 22:58

taxize integration: Pass in taxonomic identifiers

library(taxize)
library(spocc)

Via get_ids




  


  




    


          
    

      

        
        

          

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                sckott
                / my.geojson
            
            

              Created
              February 20, 2014 02:13
            

              
                Occurrences of three bird species mapped
              
          

        

      

        

  

    
    


          

    

      
      
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                sckott
                / crossref_alm.md
            
            

              Created
              February 24, 2014 17:15
            

              
                Get alm data for DOIs via Crossref using the alm R package
              
          

        

      

        

  

      

    
load alm


library(alm)


Define vector of DOIs, and search


Remember to get your api key, pass it in in the key parameter. Notice that we are passing the base url for the Crossref API, whereas the default is for the PLOS url http://alm.plos.org/api/v3/articles



  


  




    


          
    

      

        
        

          

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                sckott
                / rcharts_rsunlight.md
            
            

              Created
              February 24, 2014 21:51
            

          

        

      

        

  

      

    
install_github("ropengov/rsunlight")
library(rsunlight)
dream <- lapply(c('D','R'), function(x) cw_timeseries(phrase='i have a dream', party=x, start_date='1996-01-01', end_date='2013-01-01', granularity='month'))
df <- merge(dream[[1]], dream[[2]], by='month', all=TRUE)
df[is.na(df)] <- 0
names(df) <- c('date','D','R')
df$date <- as.character(df$date)
library(rCharts)
m1 &lt;- mPlot(x = "date", y = c("D", "R"), type = "Line", data = df)



  


  




    


          
    

      

        
        

          

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                sckott
                / abiesmagmap.geojson
            
            

              Created
              February 24, 2014 22:16
            

              
                Abies magnifica polygons
              
          

        

      

        

  

    
    


          

    

      
      
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                sckott
                / getncbidata.md
            
            

              Last active
              August 29, 2015 13:56
            

          

        

      

        

  

      

    
Install taxize


install.packages("taxize")


Load taxize


library(taxize)



  


  




    


          
    

      

        
        

          

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                sckott
                / mapgrammar.md
            
            

              Created
              March 1, 2014 00:00
            

              
                Possible map grammar workflow
              
          

        

      

        

  

      

    
Possible unified workflow for making maps with species names or identifiers as a starting point, with map as output.


species | speciesids %>%
	getdata %>% # occ(), occ_search()
	cleandata %>% # fixnames(), removeimposslatlongvals(), 
	datatransformation %>% # 
	baselayer %>% # "osmaps", "", etc.
	maptype %>% # "bubble", "choropleth", etc.
	annotations %&gt;% # tooltips(), symbols(), legend()