request consistent var names in value from downstream(...,intermediate=TRUE)

[philippi]

A call to downstream() with intermediate=TRUE returns a list for each submitted tsn, with "target" a data.frame, and "intermediate" a list of 1 or more data.frames.
The variables in target are
tsn, parentname, parenttsn, taxonname, rankid, rankname.
The variables in an intermediate data.frame are
tsn, parentname, parenttsn, taxonname, rankId, rankName.

The last 2 variables have slightly different names.
I'm trying to expand a name/tsn to all possible downstream names that might have been used for species occurrences, which should be a mainstream usage. If the variable names were consistent, I could use rbindlist. But "rankid" v "rankId" and "rankname" v "rankName" require several more steps.

[philippi]

library(taxize)
testTSN <- get_tsn("Corynorhinus",accepted=TRUE)
testdown <- downstream(testTSN,db='itis',downto='Subspecies',intermediate=TRUE)
str(testdown)

[philippi]

note that this is no biggie, just a request for consistency. As far as I can tell, the last listed data.frame within each intermediate list appears to be the same as the corresponding target data.frame, so I can just discard target and parse intermediate.

[eduardszoecs]

Thanks phillipi for reporting this.
Should be fixed now.

> library(taxize)
> library(taxize)
> testTSN <- get_tsn("Corynorhinus",accepted=TRUE)

Retrieving data for taxon 'Corynorhinus'

> testdown <- downstream(testTSN,db='itis',downto='Subspecies',intermediate=TRUE)
> testdown
$`555652`
$`555652`$target
     tsn               parentname parenttsn                            taxonname rankid   rankname
1 203453  Corynorhinus townsendii    203452   Corynorhinus townsendii townsendii    230 Subspecies
2 203454  Corynorhinus townsendii    203452  Corynorhinus townsendii virginianus    230 Subspecies
3 203458  Corynorhinus townsendii    203452   Corynorhinus townsendii pallescens    230 Subspecies
4 632276  Corynorhinus townsendii    203452       Corynorhinus townsendii ingens    230 Subspecies
5 632279  Corynorhinus townsendii    203452    Corynorhinus townsendii australis    230 Subspecies
6 947679 Corynorhinus rafinesquii    555664 Corynorhinus rafinesquii rafinesquii    230 Subspecies
7 948486 Corynorhinus rafinesquii    555664    Corynorhinus rafinesquii macrotis    230 Subspecies

$`555652`$intermediate
$`555652`$intermediate[[1]]
     tsn   parentname parenttsn                taxonname rankid rankname
1 203452 Corynorhinus    555652  Corynorhinus townsendii    220  Species
2 555655 Corynorhinus    555652   Corynorhinus mexicanus    220  Species
3 555664 Corynorhinus    555652 Corynorhinus rafinesquii    220  Species

$`555652`$intermediate[[2]]
     tsn               parentname parenttsn                            taxonname rankid   rankname
1 203453  Corynorhinus townsendii    203452   Corynorhinus townsendii townsendii    230 Subspecies
2 203454  Corynorhinus townsendii    203452  Corynorhinus townsendii virginianus    230 Subspecies
3 203458  Corynorhinus townsendii    203452   Corynorhinus townsendii pallescens    230 Subspecies
4 632276  Corynorhinus townsendii    203452       Corynorhinus townsendii ingens    230 Subspecies
5 632279  Corynorhinus townsendii    203452    Corynorhinus townsendii australis    230 Subspecies
6 947679 Corynorhinus rafinesquii    555664 Corynorhinus rafinesquii rafinesquii    230 Subspecies
7 948486 Corynorhinus rafinesquii    555664    Corynorhinus rafinesquii macrotis    230 Subspecies



attr(,"class")
[1] "downstream"
attr(,"db")
[1] "itis"

@sckott Shouldn't we make all thorughout taxize lowercase? Then we don't have to care...
I am not a fan of camelCase. This means a lot of changes and may be a midterm goal?
What do you think is it worth the time? It will be only an internal change and not user visible...

[eduardszoecs]

Closing this and opened a new issue #462 .

[sckott]

Sorry. On vacation now. Back to computer in a few days