Retrieving column names in R

Question

I am trying to retrieve the column names of the data set model$data using the following formula:

sample(colnames(model$data),1)

When I run it I receive the following error message:

Error in sample.int(length(x), size, replace, prob) : 
  invalid first argument

Appreciate any help!

str(model) looks like this:

> str(model)
    List of 13
     $ data            :List of 1
      ..$ : num [1:1000, 1:56] 1 1 1 1 0 1 1 0 1 1 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : chr [1:1000] "7530" "5975" "552" "815" ...
      .. .. ..$ : chr [1:56] "Agriculture_and_Hunting" "Baking" "Biochemistry" "Braiding" ...
     $ unit.classif    : num [1:1000] 3 5 5 5 16 3 5 1 3 3 ...
     $ distances       : num [1:1000] 0.000806 0.000239 0.000239 0.000239 0.001953 ...
     $ grid            :List of 6
      ..$ pts              : num [1:25, 1:2] 1.5 2.5 3.5 4.5 5.5 1 2 3 4 5 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : NULL
      .. .. ..$ : chr [1:2] "x" "y"
      ..$ xdim             : num 5
      ..$ ydim             : num 5
      ..$ topo             : chr "hexagonal"
      ..$ neighbourhood.fct: Factor w/ 2 levels "bubble","gaussian": 1
      ..$ toroidal         : logi FALSE
      ..- attr(*, "class")= chr "somgrid"
     $ codes           :List of 1
      ..$ : num [1:25, 1:56] 0.000388 0.99996 1 1 1 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : chr [1:25] "V1" "V2" "V3" "V4" ...
      .. .. ..$ : chr [1:56] "Agriculture_and_Hunting" "Baking" "Biochemistry" "Braiding" ...
     $ changes         : num [1:100, 1] 0.00261 0.00263 0.00262 0.00254 0.00254 ...
     $ alpha           : num [1:2] 0.05 0.01
     $ radius          : Named num [1:2] 3 0
      ..- attr(*, "names")= chr [1:2] "67%" ""
     $ user.weights    : num 1
     $ distance.weights: num 1
     $ whatmap         : int 1
     $ maxNA.fraction  : int 0
     $ dist.fcts       : chr "sumofsquares"
     - attr(*, "class")= chr "kohonen"

Answer 1

Your data boils down to something like this structure:

> str(model)
List of 2
 $ data:List of 1
  ..$ : int [1:3, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:4] "a" "b" "c" "d"
 $ foo : num 1

but you have some other components that we don't need to bother with, and my data doesn't have row names and is a lot smaller.

model is a list of 2 (for me) and 13 (for you) parts.

The $data component is also a "List of 1" component.

So colnames(model$data) is trying to get the colnames of a list, and failing:

> colnames(model$data)
NULL

Which you would have spotted if you'd tried running colnames(model$data) yourself.

You want the colnames of the first element of the list model$data:

> colnames(model$data[[1]])
[1] "a" "b" "c" "d"

and hence:

> sample(colnames(model$data[[1]]),1)
[1] "b"

Its possible that because this is a "kohonen" class object that there are functions that get these data matrices for you. You'll need to read the documentation to figure this out. What I've shown above is digging in the structure to find the data you want.

Answer 2

$ is not valid as part of the data set (or frame) name since R uses it to denote column name (:)) so R actually tried to get the column name 'data' from the data frame named 'model' Try:

names(model)

And rename model$data to model

str(model)

> str(model)
List of 13
 $ data            :List of 1
  ..$ : num [1:1000, 1:56] 1 1 1 1 0 1 1 0 1 1 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:1000] "7530" "5975" "552" "815" ...
  .. .. ..$ : chr [1:56] "Agriculture_and_Hunting" "Baking" "Biochemistry" "Braiding" ...
 $ unit.classif    : num [1:1000] 3 5 5 5 16 3 5 1 3 3 ...
 $ distances       : num [1:1000] 0.000806 0.000239 0.000239 0.000239 0.001953 ...
 $ grid            :List of 6
  ..$ pts              : num [1:25, 1:2] 1.5 2.5 3.5 4.5 5.5 1 2 3 4 5 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "x" "y"
  ..$ xdim             : num 5
  ..$ ydim             : num 5
  ..$ topo             : chr "hexagonal"
  ..$ neighbourhood.fct: Factor w/ 2 levels "bubble","gaussian": 1
  ..$ toroidal         : logi FALSE
  ..- attr(*, "class")= chr "somgrid"
 $ codes           :List of 1
  ..$ : num [1:25, 1:56] 0.000388 0.99996 1 1 1 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:25] "V1" "V2" "V3" "V4" ...
  .. .. ..$ : chr [1:56] "Agriculture_and_Hunting" "Baking" "Biochemistry" "Braiding" ...
 $ changes         : num [1:100, 1] 0.00261 0.00263 0.00262 0.00254 0.00254 ...
 $ alpha           : num [1:2] 0.05 0.01
 $ radius          : Named num [1:2] 3 0
  ..- attr(*, "names")= chr [1:2] "67%" ""
 $ user.weights    : num 1
 $ distance.weights: num 1
 $ whatmap         : int 1
 $ maxNA.fraction  : int 0
 $ dist.fcts       : chr "sumofsquares"
 - attr(*, "class")= chr "kohonen"