the function `downstream` I started doesn't work

[ropensci]

the function `downstream` I started doesn't work

[sckott]

Hey @Edild, let me know if the function I just added downstream2 works for you? I am attempting to grab all taxonomic names downstream from an TSN, but it's been a bit challenging.

[sckott]

@Edild - akk, downstream2 doesn't work, trying to fix it now.

[eduardszoecs]

Seems to work like a charm :) Nice!

downstream2(114989)
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=114989
http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=114989
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665931
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665932
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665931
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665932
http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=665931
http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=665932
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=114990
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665935
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=114991
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=114992
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=114993
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665933
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665934
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665936
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=665937
$not
     parentName parentTsn rankName         taxonName    tsn
1 Mengenillidia    665931   Family         Mengeidae 114990
2 Mengenillidia    665931   Family     Mengenillidae 665935
3    Stylopidia    665932   Family        Stylopidae 114991
4    Stylopidia    665932   Family        Elenchidae 114992
5    Stylopidia    665932   Family   Halictophagidae 114993
6    Stylopidia    665932   Family    Myrmecolacidae 665933
7    Stylopidia    665932   Family      Corioxenidae 665934
8    Stylopidia    665932   Family     Bohartillidae 665936
9    Stylopidia    665932   Family Callipharixenidae 665937

I think this could be also easily done from the NCBI taxonomy-browser(http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=30261)... Using rentrez und get_uid()... I`ll make up a function/method these days...

Are there any restrictions with the usage of the ITIS-Api (eg like the NCBI-API. only 3 requests per second)? Not that they block any IP...

[sckott]

Cool. So it does work sometimes, but sometimes not. Working on it now.

[eduardszoecs]

Returns all Families: For me all queries worked yet...

> check <- downstream2(101594)
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=101594
http://www.itis.gov/ITISWebService/services/ITISService/getHierarchyDownFromTSN?tsn=101594
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=101596
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=101659
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=101664
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=101797
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=102020
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=102026
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=591725
http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=591726
> check
$not
  parentName parentTsn rankName        taxonName    tsn
1 Anisoptera    101594   Family        Aeshnidae 101596
2 Anisoptera    101594   Family      Petaluridae 101659
3 Anisoptera    101594   Family        Gomphidae 101664
4 Anisoptera    101594   Family     Libellulidae 101797
5 Anisoptera    101594   Family      Corduliidae 102020
6 Anisoptera    101594   Family Cordulegastridae 102026
7 Anisoptera    101594   Family Austropetaliidae 591725
8 Anisoptera    101594   Family    Neopetaliidae 591726

> str(check)
List of 1
 $ not:'data.frame':    8 obs. of  5 variables:
  ..$ parentName: Factor w/ 1 level "Anisoptera": 1 1 1 1 1 1 1 1
  ..$ parentTsn : Factor w/ 1 level "101594": 1 1 1 1 1 1 1 1
  ..$ rankName  : chr [1:8] "Family" "Family" "Family" "Family" ...
  ..$ taxonName : Factor w/ 8 levels "Aeshnidae","Austropetaliidae",..: 1 8 5 6 4 3 2 7
  ..$ tsn       : Factor w/ 8 levels "101596","101659",..: 1 2 3 4 5 6 7 8

So you want in the long run all families in a list-entry, all sub-families in a list entry etc...
Good idea...

[eduardszoecs]

When is see this:

Wouldn`t it be better when the data.frames are returned with 'stringsAsFactors = FALSE'?
What do you think?

[sckott]

Yeah, that would probably be better

[sckott]

works now., closed