Agfdhyk

I have this list l

l



    $`5216014`

    $`5216014`[[1]]

                name     key    rank

    1       Animalia       1 kingdom

    2       Chordata      44  phylum

    3 Elasmobranchii     121   class

    4     Rajiformes     884   order

    5        Rajidae    5877  family

    6           Raja 2342057   genus

    7  Raja montagui 5216014 species





    $`5216208`

    $`5216208`[[1]]

                   name     key    rank

    1          Animalia       1 kingdom

    2          Chordata      44  phylum

    3    Elasmobranchii     121   class

    4        Rajiformes     884   order

    5           Rajidae    5877  family

    6         Amblyraja 2420436   genus

    7 Amblyraja radiata 2420446 species

I would like to extract only row number 7 for column name and key and to create a database like this:

df



name                key

Raja montagui       5216014

Amblyraja radiata   2420446

I tried with lapply function:

lapply(l,function(x) x[7])

but the result is this:

$`5216014`

$`5216014`[[1]]

NULL





$`5216208`

$`5216208`[[1]]

NULL

I tried to transform l in a data frame:

data.frame(matrix(unlist(l)))

but I obtained one big column with all data as:

kingdom

phylum

class

order

family

genus

species

Animalia

Chordata

Elasmobranchii

4943

Rajiformes

Rajidae

Raja

Raja montagui

1

44

121

884

5877

2342057

5216014

4954

kingdom

phylum

class

order

family

genus

species

Animalia

Chordata

Elasmobranchii

Rajiformes

4965

Rajidae

Amblyraja

Amblyraja radiata

1

44

121

884

5877

2420436

2420446

kingdom

phylum

class

order

family

genus

species 

Where am I wrong?

P.S: this kind of list l is an output of packages rgbif, with code:

    keySpecies <- c(5216014,2420446)

    l.1 <- occ_search(taxonKey=keySpecies,

      limit=1, return='hier',

      curlopts=list(verbose=F))

l <- l.1[c(1:length(unique(keySpecies)))] #cut all element of list that are not useful

lapply(l,function(x) x[7]) is close, but you need to index [row, column], not just [row]. Instead do this:

res = lapply(l,function(x) x[7, c("name", "key")])

# or more simply

res = lapply(l, "[", 7, c("name", "key"))

This will still give you a list, which you'll need to combine together into a single data frame:

do.call(rbind, res)

Edit: I installed your package and ran your code, and apparently l is a list of lists of data frames, not a list of data frames. So we need to extract that as well:

res = lapply(lapply(l, "[[", 1), "[", 7, c("name", "key"))

res = do.call(rbind, res)

res

#                      name     key

# 5216014     Raja montagui 5216014

# 2420446 Amblyraja radiata 2420446