Subscript out of bounds - general definition and solution

Question

When working with R I frequently get the error message  subscript out of bounds   For example     Load necessary libraries and data library igraph  library NetData  data kracknets  package    NetData      Reduce dataset to nonzero edges krack full nonzero edges  lt - subset krack full data frame   advice tie  gt  0   friendship tie  gt  0   reports to tie  gt  0      convert to graph data farme  krack full  lt - graph data frame krack full nonzero edges      Set vertex attributes for  i in V krack full         for  j in names attributes             krack full  lt - set vertex attribute krack full  j  index i  attributes i 1 j              Calculate reachability for each vertix reachability  lt - function g  m        reach mat   matrix nrow   vcount g                           ncol   vcount g       for  i in 1 vcount g             reach mat i     0         this node reach  lt - subcomponent g   i - 1   mode   m           for  j in 1  length this node reach                  alter   this node reach j    1             reach mat i  alter    1                     return reach mat     reach full in  lt - reachability krack full   in   reach full in   This generates the following error Error in reach mat i  alter    1   subscript out of bounds   However  my question is not about this particular piece of code  even though it would be helpful to solve that too   but my question is more general    What is the definition of a subscript-out-of-bounds error  What causes it  Are there any generic ways of approaching this kind of error

User · Answer

I sometimes encounter the same issue  I can only answer your second bullet  because I am not as expert in R as I am with other languages  I have found that the standard for loop has some unexpected results  Say x   0  for  i in 1 x      print i      The output is    1  1  1  0   Whereas with python  for example  for i in range x     print i   does nothing  The loop is not entered    I expected that if x   0 that in R  the loop would not be entered  However  1 0 is a valid range of numbers  I have not yet found a good workaround besides having an if statement wrapping the for loop

User · Answer

This is because you try to access an array out of its boundary    I will show you how you can debug such errors    I set options error recover  I run reach full in  lt - reachability krack full   in    I get    reach full in  lt - reachability krack full   in   Error in reach mat i  alter    1   subscript out of bounds Enter a frame number  or 0 to exit    1  reachability krack full   in    I enter 1  and I get    Called from  top level   I type ls   to see my current variables    1    tmp              alter             g                       i                 j                       m                     reach mat         this node reach     Now  I will see the dimensions of my variables     Browse 1  gt  i  1  1 Browse 1  gt  j  1  21 Browse 1  gt  alter  1  22 Browse 1  gt  dim reach mat   1  21 21   You see that alter is out of bounds  22   21    in the line      reach mat i  alter    1   To avoid such error  personally I do this     Try to use applyxx function  They are safer than for I use seq along and not 1 n  1 0  Try to think in a vectorized solution if you can to avoid mat i j  index access    EDIT vectorize the solution  For example  here I see that you don t use the fact that set vertex attribute is vectorized   You can replace     Set vertex attributes for  i in V krack full         for  j in names attributes             krack full  lt - set vertex attribute krack full  j  index i  attributes i 1 j             by this       set vertex attribute is vectorized      no need to loop over vertex  for  attr in names attributes         krack full  lt  lt - set vertex attribute krack full                                                attr  value   attributes  attr

User · Answer

Only an addition to the above responses  A possibility in such cases is that you are calling an object  that for some reason is not available to your query  For example you may subset by row names or column names  and you will receive this error message when your requested row or column is not part of the data matrix or data frame anymore   Solution  As a short version of the responses above  you need to find the last working row name or column name  and the next called object should be the one that could not be found   If you run parallel codes like  foreach   then you need to convert your code to a for loop to be able to troubleshoot it

User · Answer

It just means that either alter  gt  ncol  reach mat   or i  gt  nrow  reach mat    in other words  your indices exceed the array boundary  i is greater than the number of rows  or alter is greater than the number of columns    Just run the above tests to see what and when is happening

User · Answer

If this helps anybody  I encountered this while using purr  map   with a function I wrote which was something like this   find nearby shops  lt - function base account       states table   gt            filter state    base account state    gt            left join target locations  by   c  border states     state      gt            mutate x latitude   base account latitude                 x longitude   base account longitude    gt            mutate dist miles   geosphere  distHaversine p1   cbind longitude  latitude                                                         p2   cbind x longitude  x latitude   1609 344     nearby shop numbers  lt - base locations   gt        split f   base locations id    gt        purrr  map df find nearby shops     I would get this error sometimes with samples  but most times I wouldn t   The root of the problem is that some of the states in the base locations table  PR  did not exist in the states table  so essentially I had filtered out everything  and passed an empty table on to mutate   The moral of the story is that you may have a data issue and not  just  a code problem  so you may need to clean your data    Thanks for agstudy and zx8754 s answers above for helping with the debug

User · Answer

This came from standford s sna free tutorial and it states that        Reachability can only be computed on one vertex at a time  To   get graph-wide statistics  change the value of  vertex    manually or write a for loop   Remember that  unlike R objects    igraph objects are numbered from 0    ok  so when ever using igraph  the first roll column is 0 other than 1  but matrix starts at 1  thus for any calculation under igraph  you would need x-1  shown at   this node reach  lt - subcomponent g   i - 1   mode   m   but for the alter calculation  there is a typo here  alter   this node reach j    1  delete  1 and it will work alright

[r] Subscript out of bounds - general definition and solution?

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