Vector of logicals based on row membership - r

Question

thank you for your patience.
I am dealing with a large dataset detailing patients and medications.
Medications are hard to code, as they are (usually) meaningless unless matched with doses.
I have a dataframe with vectors (Drug1, Drug2..... Drug 16) where individual patients are represented by rows.
The vectors are actually factors, with 100s of possible levels (all the drugs the patient could be on).
All I want to do is produce a vector of logicals (TTTTFFFFTTT......) that I could then cbind into a dataframe which will tell me whether a patient is or is not on a particular, drug.
I could then use particularly important drugs' presence or absence as categorical covariates in a model.
I've tried grep, to search along the rows, and I can generate a vector of identifiers, but I cannot seem to generate the vector of logicals.
I realise I'm doing something simply wrong.
names(drugindex)
[1] "book.MRN" "DRUG1" "DRUG2" "DRUG3" "DRUG4" "DRUG5"
[7] "DRUG6" "DRUG7" "DRUG8" "DRUG9" "DRUG10" "DRUG11"
[13] "DRUG12" "DRUG13" "DRUG14" "DRUG15" "DRUG16"
> truvec<-drugindex$book.MRN[as.vector(unlist(apply(drugindex[,2:17], 2, grep, pattern="Lamotrigine")))]
> truvec
truvec
[1] 0024633 0008291 0008469 0030599 0027667
37 Levels: 0008291 0008469 0010188 0014217 0014439 0015822 ... 0034262
> head(drugindex)
book.MRN DRUG1 DRUG2 DRUG3 DRUG4 DRUG5
4 0008291 Venlafaxine Procyclidine Flunitrazepam Amisulpiride Clozapine
31 0008469 Venlafaxine Mirtazapine Lithium Olanzapine Metoprolol
3 0010188 Flurazepam Valproate Olanzapine Mirtazapine Esomeprazole
13 0014217 Aspirin Ramipril Zuclopenthixol Lorazepam Haloperidol
15 0014439 Zopiclone Diazepam Haloperidol Paracetamol <NA>
5 0015822 Olanzapine Venlafaxine Lithium Haloperidol Alprazolam
DRUG6 DRUG7 DRUG8 DRUG9 DRUG10 DRUG11 DRUG12
4 Lamotrigine Alprazolam Lithium Alprazolam <NA> <NA> <NA>
31 Lamotrigine Ramipril Alprazolam Zolpidem Trifluoperazine <NA> <NA>
3 Paracetamol Alprazolam Citalopram <NA> <NA> <NA> <NA>
13 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
15 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
5 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
DRUG13 DRUG14 DRUG15 DRUG16
4 <NA> <NA> <NA> <NA>
31 <NA> <NA> <NA> <NA>
3 <NA> <NA> <NA> <NA>
13 <NA> <NA> <NA> <NA>
15 <NA> <NA> <NA> <NA>
5 <NA> <NA> <NA> <NA>
And what I want is a vector of logicals for each drug, saying whether that patient is on it
Thank you all for your time.
Ross Dunne MRCPsych
"Te occidere possunt sed te edere ne possunt, nefas est".

Answer 1

You were close with your apply attempt, but MARGIN=2 applies the function over columns, not rows. Also, grep returns the locations of the matches; you want grepl, which returns a logical vector. Try this:
apply(x[,-1], 1, function(x) any(grepl("Aspirin",x)))
You could also use %in%, which you may find more intuitive:
apply(x[,-1], 1, "%in%", x="Aspirin")

Answer 2

First, a comment on data structure. You have data in what some call a "wide" format, with a single row per patient and multiple columns for the drugs. It is usually the case that the "long" format, with reapeated rows per patient and a single column for drugs is more amenable to data manipulation. To reshape your data from wide to long and vice versa, take a look at the reshape package. In this case, you would have something like:
library(reshape)
dnow <- melt(drugindex, id.var='book.MRN')
subset(dnow, value=='Lamotrigine')
Much cleaner, and obvious, code, if I may say so ...
Edit: If you need the old structure back you can use cast:
cast(subset(dnow, value=='Lamotrigine'), book.MRN ~ value)
as suggested by #jonw in the comments.