ibartomeus / traitbase

This repo manages the dynamic individual trait database www.traitbase.info via traitbaseR (https://github.com/metadevpro/traitbaser)
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**small package issues** #19

Closed ibartomeus closed 4 years ago

ibartomeus commented 5 years ago
[X] load taxize with package
[X] `parseErrors` paradoxialy gives an error when there are no errors (Nacho will fix this)
[X] Add to `privateImport` an if statement to show a 404 error or the 505 when this occurs.
[x] cleanSpecies gives error -> Nacho (Update from elsewhere with verbose = TRUE)
[X] Modify ParseError to target unrecognized or ambigous species for you (Nacho)
eapm commented 5 years ago

Does loading taxize = working to access non ITIS sources? (for the wish list :))

KevCaz commented 5 years ago

In the upcoming PR:

KevCaz commented 5 years ago

see https://github.com/metadevpro/traitbaser/pull/7

KevCaz commented 5 years ago

When I retrieve the data base, all entries but a few have 12 columns, the few other have 11. Is that normal?

R> names(responseNA[[1]])
 [1] "_links"      "_id"         "species"     "order"       "superfamily" "family"      "subfamily"   "tribe"       "genus"

[10] "subgenus"    "__v"         "_createdAt"
R> names(responseNA[[19699]])
 [1] "_links"      "_id"         "genus"       "species"     "order"       "superfamily" "family"      "tribe"       "subgenu
s"
[10] "__v"         "_createdAt"
# subfamily missing
R> table(val)
val
   11    12
  344 19387

Regarding the to_dataframe() function, I think what we should do is: ensure all columns exist, sort all elements of the list and then use a do.call(rbind, list), that will be the output and if the user wants to remove metadata, it's up to him! Also, I think this function should also be part of auxiliar.R.

And I will remove the _links column and create a function that parse it. I cannot see how users can use it, but it may be useful for the development of the package.

ibartomeus commented 4 years ago

parseErrors paradoxialy gives an error when there are no errors (Nacho will fix this) FIXED.

ibartomeus commented 4 years ago

[] Modify ParseError to target unrecognized or ambigous species for you (Nacho) FIXED

ibartomeus commented 4 years ago

All fixed