I'm getting this error message:
nms<-names(data)[grep(vars,names(data))]
Warning message:
In grep(vars, names(data)) :
argument 'pattern' has length > 1 and only the first element will be used
Is there a way around this?
On Thu, Jul 19, 2012 at 6:17 PM, Rui Barradas <ruipbarra...@sapo.pt> wrote:
> Hello,
>
> I guess so, and I can save you some typing.
>
> vars <- sort(apply(expand.grid("L", 1:8, 1:2), 1, paste, collapse=""))
>
>
> Then use it and see the result.
>
> Rui Barradas
>
> Em 20-07-2012 00:00, Lib Gray escreveu:
>
>> The variables are actually L11, L12, L21, L22, ... , L81, L82. Would just
>> creating a vector c(L11,... ,L82) be fine? (I'm about to try it, but I
>> wanted to check to see if that was going to be a big issue).
>>
>> On Thu, Jul 19, 2012 at 3:27 PM, Rui Barradas <ruipbarra...@sapo.pt>
>> wrote:
>>
>> Hello,
>>>
>>> Try the following. The data is your example of Patient A through E, but
>>> from the output of dput().
>>>
>>> dat <- structure(list(Patient = structure(c(1L, 1L, 1L, 1L, 1L, 2L,
>>> 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L), .Label = c("A",
>>> "B", "C", "D", "E"), class = "factor"), Cycle = c(1L, 2L, 3L,
>>> 4L, 5L, 1L, 2L, 1L, 3L, 4L, 5L, 1L, 2L, 4L, 5L, 1L, 2L, 3L),
>>> V1 = c(0.4, 0.3, 0.3, 0.4, 0.5, 0.4, 0.4, 0.9, 0.3, NA, 0.4,
>>> 0.2, 0.5, 0.6, 0.5, 0.1, 0.5, 0.4), V2 = c(0.1, 0.2, NA,
>>> NA, 0.2, NA, NA, 0.9, 0.5, NA, NA, 0.5, 0.7, 0.4, 0.5, NA,
>>> 0.3, 0.3), V3 = c(0.5, 0.5, 0.6, 0.4, 0.5, NA, NA, 0.9, 0.6,
>>> NA, NA, NA, NA, NA, NA, NA, NA, NA), V4 = c(1.5, 1.6, 1.7,
>>> 1.8, 1.5, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
>>> NA), V5 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
>>> NA, NA, NA, NA, NA, NA)), .Names = c("Patient", "Cycle",
>>> "V1", "V2", "V3", "V4", "V5"), class = "data.frame", row.names = c(NA,
>>> -18L))
>>>
>>> dat
>>>
>>> nms <- names(dat)[grep("^V[1-9]$", names(dat))]
>>> dd <- split(dat, dat$Patient)
>>> fun <- function(x) any(is.na(x)) && any(!is.na(x))
>>> ix <- sapply(dd, function(x) Reduce(`|`, lapply(x[, nms], fun)))
>>>
>>> dd[ix]
>>> do.call(rbind, dd[ix])
>>>
>>>
>>> I'm assuming that the variables names are as posted, V followed by one
>>> single digit 1-9. To keep the Patients with complete cases just negate
>>> the
>>> index 'ix', it's a logical index.
>>> Note also that dput() is the best way of posting a data example.
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Em 19-07-2012 15:15, Lib Gray escreveu:
>>>
>>> Hello,
>>>>
>>>> I didn't give enough information when I sent an query before, so I'm
>>>> trying
>>>> again with a more detailed explanation:
>>>>
>>>> In this data set, each patient has a different number of measured
>>>> variables
>>>> (they represent tumors, so some people had 2 tumors, some had 5, etc).
>>>> The
>>>> problem I have is that often in later cycles for a patient, tumors that
>>>> were originally measured are now missing (or a "new" tumor showed up).
>>>> We
>>>> assume there are many different reasons for why a tumor would be
>>>> measured
>>>> in one cycle and not another, and so I want to subset OUT the "problem"
>>>> patients to better study these patterns.
>>>>
>>>> An example:
>>>>
>>>> Patient Cycle V1 V2 V3 V4 V5
>>>> A 1 0.4 0.1 0.5 1.5 NA
>>>> A 2 0.3 0.2 0.5 1.6 NA
>>>> A 3 0.3 NA 0.6 1.7 NA
>>>> A 4 0.4 NA 0.4 1.8 NA
>>>> A 5 0.5 0.2 0.5 1.5 NA
>>>>
>>>> I want to keep patient A; they have 4 measured tumors, but tumor 2 is
>>>> missing data for cycles 3 and 4
>>>>
>>>> B 1 0.4 NA NA NA NA
>>>> B 2 0.4 NA NA NA NA
>>>>
>>>> I do not want to keep patient B; they have 1 tumor that is measure
>>>> consistently in both cycles
>>>>
>>>> C 1 0.9 0.9 0.9 NA NA
>>>> C 3 0.3 0.5 0.6 NA NA
>>>> C 4 NA NA NA NA NA
>>>> C 5 0.4 NA NA NA NA
>>>>
>>>> I do want to keep patient C; all their data is missing for cycle 4 and
>>>> cycle 5 only measured one tumor
>>>>
>>>> D 1 0.2 0.5 NA NA NA
>>>> D 2 0.5 0.7 NA NA NA
>>>> D 4 0.6 0.4 NA NA NA
>>>> D 5 0.5 0.5 NA NA NA
>>>>
>>>> I do not want patient D, their two tumors were measured each cycle
>>>>
>>>> E 1 0.1 NA NA NA NA
>>>> E 2 0.5 0.3 NA NA NA
>>>> E 3 0.4 0.3 NA NA NA
>>>>
>>>> I DO want patient E; they only had one tumor register in Cycle 1, but
>>>> cycles 2 and 3 had two tumors.
>>>>
>>>>
>>>> Thanks for any help!
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________****________________
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>>>> <https://stat.**ethz.ch/mailman/listinfo/r-**help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>>> >
>>>> PLEASE do read the posting guide http://www.R-project.org/**
>>>> posting-guide.html
>>>> <http://www.R-project.org/**posting-guide.html<http://www.R-project.org/posting-guide.html>
>>>> >
>>>>
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>
>
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