elevation function returns error (randomly?)

[dlebauer]

I am trying to extract elevation for different points around a boundary. I am sure there is a better way (e.g. using the raster package, and would love an example) but I think what I found may be a bug in the rgbif::elevation function:

If I try

library(ggplot2)
library(data.table)
library(rgbif)
d <- data.table(map_data("county"))
site <- d[region == "illinois"]
site[,elevation(latitude = lat, longitude = long)]

I get

Error in getdata(dat) : client error: (400) Bad Request

If I try this in a loop

  pts <- list()
  for(i in 1:nrow(site)){
    #elev[[i]] <- site[, GNgtopo30(lat = lat, lng = long)]
    pts[[i]] <- elevation(latitude = site$lat[i], longitude = site$long[i])
  }

I get the error

Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 0

But every time I run the loop, it fails on a different value of i.

Is this a bug?

[sckott]

hey @dlebauer Weird, b/c this just worked for me when I tried the first code block. I get

library(ggplot2)
library(data.table)
library(rgbif)
d <- data.table(map_data("county"))
site <- d[region == "illinois"]
out <- site[,elevation(latitude = lat, longitude = long)]
head(out)
#>   latitude longitude elevation
#> 1 40.21018 -91.49563  147.9956
#> 2 40.19299 -90.91121  209.8305
#> 3 40.10704 -90.91121  199.8696
#> 4 39.83775 -90.91121  222.0224
#> 5 39.75754 -90.91694  246.1425
#> 6 39.75754 -91.36385  142.0000

what does your session_info() say? I'll test this in some other contexts.

[dlebauer]

Here is session info - it happens on both Ubuntu 14.04 / R 3.1 / rgbif 0.8.11 (and previously w/ 0.5); and Windows 8.1 / R 3.1.1 / rgbif 0.5

Ubuntu

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] raster_2.3-12               RJSONIO_1.3-0               rgbif_0.8.0.99              geonames_0.998             
 [5] magrittr_1.5                RPostgreSQL_0.4             BioCro_0.93                 roxygen2_4.0.2             
 [9] knitr_1.8                   PEcAn.BIOCRO_1.4.1          RNCEP_1.0.7                 PEcAn.all_1.4.1            
[13] PEcAn.assim.batch_1.4.1     PEcAn.data.remote_1.4.1     PEcAn.data.land_1.4.1       rgdal_0.9-1                
[17] sp_1.0-16                   fields_7.1                  maps_2.3-9                  spam_1.0-1                 
[21] PEcAn.data.atmosphere_1.4.1 REddyProc_0.6-0             data.table_1.9.4            PEcAn.uncertainty_1.4.1    
[25] gridExtra_0.9.1             PEcAn.priors_1.4.1          PEcAn.MA_1.4.1              MASS_7.3-35                
[29] rjags_3-14                  coda_0.16-1                 lattice_0.20-29             PEcAn.settings_1.4.1       
[33] lubridate_1.3.3             PEcAn.DB_1.4.1              PEcAn.utils_1.4.1           udunits2_0.6               
[37] ncdf4_1.12                  randtoolbox_1.16            rngWELL_0.10-3              ggplot2_1.0.0              
[41] XML_3.98-1.1                plyr_1.8.1                  abind_1.4-3                 DBI_0.3.1                  
[45] testthat_0.9.1              devtools_1.7.0             

loaded via a namespace (and not attached):
 [1] assertthat_0.1     bitops_1.0-6       boot_1.3-13        chron_2.3-45       colorspace_1.2-4  
 [6] digest_0.6.4       evaluate_0.5.5     foreign_0.8-61     formatR_1.0        fossil_0.3.7      
[11] gtable_0.1.2       htmltools_0.2.6    httr_0.5           jsonlite_0.9.14    labeling_0.3      
[16] memoise_0.2.1      minpack.lm_1.1-8   munsell_0.4.2      proto_0.3-10       RColorBrewer_1.0-5
[21] Rcpp_0.11.3        RCurl_1.95-4.5     reshape2_1.4.1     rgeos_0.3-8        rjson_0.2.15      
[26] rmarkdown_0.5.1    rstudioapi_0.1     scales_0.2.4       shapefiles_0.7     stringr_0.6.2     
[31] tcltk_3.1.0        tgp_2.4-9          tools_3.1.0        whisker_0.3-2      yaml_2.1.13   

Windows 8.1

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plyr_1.8.1       devtools_1.6.1   maps_2.3-9       rgbif_0.8.0      data.table_1.9.2 ggplot2_1.0.0   

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4 digest_0.6.4     grid_3.1.1       gtable_0.1.2     httr_0.5         jsonlite_0.9.12 
 [7] labeling_0.3     lattice_0.20-29  magrittr_1.0.1   MASS_7.3-33      munsell_0.4.2    proto_0.3-10    
[13] Rcpp_0.11.2      RCurl_1.95-4.3   reshape2_1.4     rgeos_0.3-8      scales_0.2.4     sp_1.0-15       
[19] stringr_0.6.2    tools_3.1.1      whisker_0.3-2    XML_3.98-1.1     yaml_2.1.13     

[sckott]

hmm, now I'm getting errors, which suggests there's a usage limit problem, I'll see what can be done

[sckott]

@dlebauer Okay, try reinstalling latest from master, get a elevation API key, and try again. I wasn't requiring an API key before, and now it does, which although not idea having to get a key, each person can have their own rate limit - the rate limit for requests without keys wasn't really that clear, at least this is more clear. rates are:

2,500 requests per 24 hour period.
512 locations per request.
5 requests per second.

each batch request (e.g.,, request 50 points in one GET request) counts as one request, so 2500 isn't too bad if you use it smart

[dlebauer]

@sckott thanks for your help / quick fix!

my for loop works (requires nrow API requests). For this reason (my perspective), The bug could be closed.

  pts <- list()
  for(i in 1:nrow(site)){
    pts[[i]] <- site[i, elevation(latitude = lat, longitude = long, key = <key>)
  }

But not the vectorized version:

d <- data.table(map_data("county"))
site <- d[region == "illinois"]
site[,elevation(latitude = lat, longitude = long, key = "<key>")]

Error in getdata(dat) : client error: (400) Bad Request

---

2500 isn't too bad if you use it smart

Do you have suggestions for 'using it smart'?

[sckott]

Great, glad it works @dlebauer - I'm not too familiar with data.table, so perhaps there's something I'm missing here, but that last example works for me again.

In terms of using it smart, they count a batch request for lots of points as 1 request, so if you have 50 points, get all in one request instead of 50 separate requests for each point.

p.s.. i removed your api key 😄 from your comment

[sckott]

@dlebauer is this all good for you now?

[dlebauer]

Yes it is, and can be closed. Thanks for your help!

On Monday, March 23, 2015, Scott Chamberlain notifications@github.com
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@dlebauer https://github.com/dlebauer is this all good for you now?

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[sckott]

great