Problem with validate_names() #121

PMassicotte · 2017-05-12T12:59:27Z

Hi there.

I am trying to use this library to extract information from my collected species. I think I found a bug when validate_names() is not finding the requested species. As you can see in the second example, the valid name is not found, hence it is repeating the last valid name. One solution would be to always return a vector of the same size as the requested list. If the species is not found, simply return NA.

                                                       
library(dplyr)                                         
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(rfishbase)

This works

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo trutta")    
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning: FishBase says that 'Salmo trutta' can also be misapplied to other species
#>                     but is returning only the best match.  
#>                     See synonyms('Salmo trutta') for details
#> # A tibble: 2 × 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2          Salmo trutta          Salmo trutta

This crashes

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo truttaxxxx")
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning in check_and_parse(resp): Bad Request (HTTP 400).
#> Warning: no results found for query https://fishbase.ropensci.org/synonyms?
#> SynSpecies=truttaxxxx&SynGenus=Salmo&limit=50&fields=SynGenus%2CSynSpecies
#> %2CValid%2CMisspelling%2CStatus%2CSynonymy%2CCombination%2CSpecCode
#> %2CSynCode%2CCoL_ID%2CTSN%2CWoRMS_ID
#> Warning: Unknown or uninitialised column: 'SpecCode'.

#> Warning: Unknown or uninitialised column: 'SpecCode'.
#> Warning: No match found for species 'Salmo truttaxxxx'
#> # A tibble: 2 × 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2      Salmo truttaxxxx Oreochromis niloticus

cboettig · 2017-05-16T16:55:45Z

@sckott can you take a look at this when you get a chance?

sckott · 2017-05-16T17:02:01Z

@PMassicotte can you share your sessionInfo()

PMassicotte · 2017-05-16T17:53:40Z

@sckott

                                                       
library(dplyr)                                         
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(rfishbase)

This works

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo trutta")    
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning: FishBase says that 'Salmo trutta' can also be misapplied to other species
#>                     but is returning only the best match.  
#>                     See synonyms('Salmo trutta') for details
#> # A tibble: 2 × 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2          Salmo trutta          Salmo trutta

This crashes

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo truttaxxxx")
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning in check_and_parse(resp): Bad Request (HTTP 400).
#> Warning: no results found for query https://fishbase.ropensci.org/synonyms?
#> SynSpecies=truttaxxxx&SynGenus=Salmo&limit=50&fields=SynGenus%2CSynSpecies
#> %2CValid%2CMisspelling%2CStatus%2CSynonymy%2CCombination%2CSpecCode
#> %2CSynCode%2CCoL_ID%2CTSN%2CWoRMS_ID
#> Warning: Unknown or uninitialised column: 'SpecCode'.

#> Warning: Unknown or uninitialised column: 'SpecCode'.
#> Warning: No match found for species 'Salmo truttaxxxx'
#> # A tibble: 2 × 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2      Salmo truttaxxxx Oreochromis niloticus
                                                       
sessionInfo()                                          
#> R version 3.4.0 (2017-04-21)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Linux Mint 18.1
#> 
#> Matrix products: default
#> BLAS: /usr/lib/openblas-base/libblas.so.3
#> LAPACK: /usr/lib/libopenblasp-r0.2.18.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
#>  [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
#>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] rfishbase_2.1.2 dplyr_0.5.0    
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_0.12.10       tidyr_0.6.2        digest_0.6.12     
#>  [4] rprojroot_1.2      assertthat_0.2.0   R6_2.2.1          
#>  [7] jsonlite_1.4       DBI_0.6-1          backports_1.0.5   
#> [10] magrittr_1.5       evaluate_0.10      httr_1.2.1        
#> [13] stringi_1.1.5      curl_2.6           lazyeval_0.2.0    
#> [16] rmarkdown_1.5.9000 tools_3.4.0        stringr_1.2.0     
#> [19] yaml_2.1.14        compiler_3.4.0     htmltools_0.3.6   
#> [22] knitr_1.15.1       tibble_1.3.0

give back NA when no result found in query added utility fxn for defauling to NA when result is NULL or of length 0 bump dev version

sckott · 2017-05-18T22:20:13Z

@PMassicotte can you reinstall and try again. let me know if it works for you now.

PMassicotte · 2017-05-19T14:24:06Z

Looks like the problem is fixed.

                                                       
library(dplyr)                                         
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(rfishbase)

This works

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo trutta")    
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning: FishBase says that 'Salmo trutta' can also be misapplied to other species
#>                     but is returning only the best match.  
#>                     See synonyms('Salmo trutta') for details
#> # A tibble: 2 x 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2          Salmo trutta          Salmo trutta

This works now

df <- data_frame(                                      
myname = c("Oreochromis niloticus", "Salmo truttaxxxx")
)                                                      
                                                       
df %>%                                                 
mutate(valide_name = validate_names(myname))           
#> Warning in check_and_parse(resp): Bad Request (HTTP 400).
#> Warning: no results found for query https://fishbase.ropensci.org/synonyms?
#> SynSpecies=truttaxxxx&SynGenus=Salmo&limit=50&fields=SynGenus%2CSynSpecies
#> %2CValid%2CMisspelling%2CStatus%2CSynonymy%2CCombination%2CSpecCode
#> %2CSynCode%2CCoL_ID%2CTSN%2CWoRMS_ID
#> Warning: No match found for species 'Salmo truttaxxxx'
#> # A tibble: 2 x 2
#>                  myname           valide_name
#>                   <chr>                 <chr>
#> 1 Oreochromis niloticus Oreochromis niloticus
#> 2      Salmo truttaxxxx                  <NA>
                                                       
sessionInfo()                                          
#> R version 3.4.0 (2017-04-21)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Linux Mint 18.1
#> 
#> Matrix products: default
#> BLAS: /usr/lib/openblas-base/libblas.so.3
#> LAPACK: /usr/lib/libopenblasp-r0.2.18.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
#>  [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
#>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] rfishbase_2.1.2.1 dplyr_0.5.0      
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_0.12.10       tidyr_0.6.3        digest_0.6.12     
#>  [4] rprojroot_1.2      assertthat_0.2.0   R6_2.2.1          
#>  [7] jsonlite_1.4       DBI_0.6-1          backports_1.0.5   
#> [10] magrittr_1.5       evaluate_0.10      httr_1.2.1        
#> [13] rlang_0.1.1        stringi_1.1.5      curl_2.6          
#> [16] lazyeval_0.2.0     rmarkdown_1.5.9000 tools_3.4.0       
#> [19] stringr_1.2.0      yaml_2.1.14        compiler_3.4.0    
#> [22] htmltools_0.3.6    knitr_1.16         tibble_1.3.1

Thank you!

sckott · 2017-05-19T17:33:06Z

great, glad it works 👍

sckott added a commit that referenced this issue May 18, 2017

#121 fix for validate_names() via synonyms()

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f3eccc6

give back NA when no result found in query added utility fxn for defauling to NA when result is NULL or of length 0 bump dev version

sckott added the bug label May 19, 2017

sckott closed this May 19, 2017

cboettig modified the milestone: 2.2.0 Jul 12, 2017

ropensci / rfishbase

Problem with validate_names() #121

Problem with validate_names() #121

PMassicotte commented May 12, 2017

cboettig commented May 16, 2017

sckott commented May 16, 2017

PMassicotte commented May 16, 2017 •

edited

sckott commented May 18, 2017

PMassicotte commented May 19, 2017

sckott commented May 19, 2017

ropensci / rfishbase

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Problem with validate_names() #121

Problem with validate_names() #121

Comments

PMassicotte commented May 12, 2017

This works

This crashes

cboettig commented May 16, 2017

sckott commented May 16, 2017

PMassicotte commented May 16, 2017 • edited

This works

This crashes

sckott commented May 18, 2017

PMassicotte commented May 19, 2017

This works

This works now

sckott commented May 19, 2017

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PMassicotte commented May 16, 2017 •

edited