R error sum not meaningful for factors

Question

I have a file called rRna RDP taxonomy phylum with the following data     364   Firmicutes             39 31 244   Proteobacteria         26 35 218   Actinobacteria         23 54 65    Bacteroidetes          7 02 22    Fusobacteria           2 38 6     Thermotogae            0 65 3     unclassified Bacteria  0 32 2     Spirochaetes           0 22 1     Tenericutes            0 11 1     Cyanobacteria          0 11   And I m using this code for creating a pie chart in R    if file exists  rRna RDP taxonomy phylum         family  lt - read table   rRna RDP taxonomy phylum   sep   t       piedat  lt - rbind family 1 7                     as data frame t c sum family 8 nrow family  1                                     Others                                   sum family 8 nrow family  3           png file     graph RDP phylum low png   width 600  height 550  res 75      pie as numeric piedat V3   labels piedat V3  clockwise TRUE  col graph col  main  More representative Phyliums       legend  topright   legend piedat V2  cex 0 8  fill graph col      dev off       png file     graph RDP phylm high png   width 1300  height 850  res 75      pie as numeric piedat V3   labels piedat V3  clockwise TRUE  col graph col  main  More representative Phyliums       legend  topright   legend piedat V2  cex 0 8  fill graph col      dev off       I ve been using this code for different datafiles and it works fine  but with the file presented adobe it crash returning the following message    Error in Summary factor c 6L  2L  1L   na rm   FALSE       sum not meaningful for factors Calls  rbind - gt  as data frame - gt  t - gt  Summary factor Execution halted   I need to understand why it crash with this file and if there s any way to prevent this kind of errors    Thanks

User · Accepted Answer

The error comes when you try to call sum x  and x is a factor    What that means is that one of your columns  though they look like numbers are actually factors  what you are seeing is the text representation   simple fix  convert to numeric   However  it needs an intermeidate step of converting to character first   Use the following     family   1   lt - as numeric as character  family   1     family   3   lt - as numeric as character  family   3       For a detailed explanation of why the intermediate as character step is needed  take a look at this question  How to convert a factor to integer numeric without loss of information

[r] R error "sum not meaningful for factors"

Examples related to r

Examples related to r-factor

Examples related to categorical-data