[R] Subsetting problem data, 2
Chris Campbell
ccampbell at mango-solutions.com
Fri Jul 20 10:09:40 CEST 2012
Hi!
# toy data
toyData <- data.frame(x = 1:4, y = 5:8, xy = 9:12, z = 13:16)
vars <- c("x", "z")
# "pattern" is an argument of grep
args(grep)
# "pattern" must only consist of a single element
# otherwise only the first element is used
grep(pattern = vars, x = names(toyData))
# one way to do this - a loop
# create a vector to collect the output of each call
toyColIndexList <- vector(length = length(vars), mode = "list")
# grep each element in turn
for (i in seq_along(vars)) {
toyColIndexList[[i]] <- grep(pattern = vars[i], x = names(toyData))
}
# combine all of the answers
toyColIndex <- unlist(toyColIndexList)
# remove duplicated columns if present
toyColIndex <- toyColIndex[!duplicated(toyColIndex)]
# select the elements we want
toyData[, toyColIndex]
# alternatively we could use regular expressions
grep(pattern = ("x|z"), x = names(toyData))
# hope this helps
Best wishes
Chris
Chris Campbell
Mango Solutions
Data Analysis that Delivers
http://www.mango-solutions.com
+44 (0) 1249 705 450
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Lib Gray
Sent: 20 July 2012 01:17
To: Rui Barradas
Cc: r-help
Subject: Re: [R] Subsetting problem data, 2
I'm still getting the message (if this is what you were suggesting I try).
The data set I'm using has many more columns other than these variables; could that be a problem? I didn't think it would affect it.
>pattern <- "L[1-8][12]"
> 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
>
On Thu, Jul 19, 2012 at 6:55 PM, Rui Barradas <ruipbarradas at sapo.pt> wrote:
> Hello,
>
> Sorry, forgot about that. It's trickier to write code without a
> dataset to test it.
>
> Try
>
> pattern <- "L[1-8][12]"
>
> and after the grep print nms to see if it's right.
>
> Rui Barradas
>
> Em 20-07-2012 00:33, Lib Gray escreveu:
>
>> 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 <ruipbarradas at 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
>>>> <ruipbarradas at 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]]
>>>>>>
>>>>>> ______________________________******________________
>>>>>> R-help at r-project.org mailing list
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>>>>>> thz.ch/mailman/****listinfo/r-help>
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>>>>>> ethz.ch/mailman/**listinfo/r-help>
>>>>>> >
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>>>>>> h/mailman/listinfo/r-**help>
>>>>>> <http**s://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.et
>>>>>> hz.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-pro
>>>>>> ject.org/**posting-guide.html>
>>>>>> <http://www.**R-project.org/posting-guide.**html<http://www.R-pro
>>>>>> ject.org/posting-guide.html>
>>>>>> >
>>>>>>
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>
>>>>>>
>>>>>>
>
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