[R] range () does not remove NA's with complete.cases() for dates (dplyr/mutate)
William Dunlap
wdunlap at tibco.com
Mon Nov 10 19:30:15 CET 2014
> Would you like to bring to Hadley's attention that mutate does
> set the NA value for the new column?
This may not be mutate()'s problem.
The Date class is messed up with regard to NA's and Inf's. E.g., what gets
printed as NA does not correspond to what is.na() returns and its range()
method does not appear to pass the finite=TRUE argument to range.default:
> d <- as.Date(c("2014-10-31", c("2014-11-10")))
> d1 <- range(d[0], finite=TRUE)
Warning messages:
1: In min.default(numeric(0), na.rm = FALSE) :
no non-missing arguments to min; returning Inf
2: In max.default(numeric(0), na.rm = FALSE) :
no non-missing arguments to max; returning -Inf
> d1
[1] NA NA
> is.na(d1)
[1] FALSE FALSE
> dput(d1)
structure(c(Inf, -Inf), class = "Date")
> range(c(d1, d), finite=TRUE)
[1] NA NA
> range(c(d1, d), finite=TRUE, na.rm=TRUE)
[1] NA NA
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, Nov 10, 2014 at 10:09 AM, Muhuri, Pradip (SAMHSA/CBHSQ) <
Pradip.Muhuri at samhsa.hhs.gov> wrote:
> Mark,
>
> Thank you very much for further looking into this issue. So, the "ugly"
> solution is better! Would you like to bring to Hadley's attention that
> mutate does set the NA value for the new column?
>
> Regards,
>
> Pradip
>
> Pradip K. Muhuri, PhD
> SAMHSA/CBHSQ
> 1 Choke Cherry Road, Room 2-1071
> Rockville, MD 20857
> Tel: 240-276-1070
> Fax: 240-276-1260
>
>
> -----Original Message-----
> From: Mark Sharp [mailto:msharp at TxBiomed.org]
> Sent: Monday, November 10, 2014 12:23 PM
> To: Muhuri, Pradip (SAMHSA/CBHSQ)
> Cc: r-help at r-project.org
> Subject: Re: [R] range () does not remove NA's with complete.cases() for
> dates (dplyr/mutate)
>
> Pradip,
>
> For some reason mutate is not setting the is.NA value for the new column.
> Note the output below using your data structures.
>
> > ## It looks at first as if the second element of both columns are NA.
> > data2$mrjdate[2]
> [1] NA
> > data2$oiddate[2]
> [1] NA
> > ## for convenience
> > mrj <- data2$mrjdate[2]
> > oid <- data2$oiddate[2]
> > mode(mrj)
> [1] "numeric"
> > mode(oid)
> [1] "numeric"
> > str(mrj)
> Date[1:1], format: NA
> > str(oid)
> Date[1:1], format: NA
> > class(mrj)
> [1] "Date"
> > class(oid)
> [1] "Date"
> > ## But note:
> > identical(mrj, oid)
> [1] FALSE
> > all.equal(mrj, oid)
> [1] "'is.NA' value mismatch: 0 in current 1 in target"
> ## functioning code
> data2$mrjdate[2]
> data2$oiddate[2]
> mrj <- data2$mrjdate[2]
> oid <- data2$oiddate[2]
> mode(mrj)
> mode(oid)
> str(mrj)
> str(oid)
> class(mrj)
> class(oid)
> # But note:
> identical(mrj, oid)
> all.equal(mrj, oid)
>
> ## This ugly solution does not have the problem.
> > data3 <- data1
> > data3$oiddate <- as.Date(sapply(seq_along(data3$id), function(row) {
> + if (all(is.na(unlist(data1[row, -1])))) {
> + max_d <- NA
> + } else {
> + max_d <- max(unlist(data1[row, -1]), na.rm = TRUE)
> + }
> + max_d}),
> + origin = "1970-01-01")
> >
> > range(data3$mrjdate[complete.cases(data3$mrjdate)])
> [1] "2004-11-04" "2009-10-24"
> > range(data3$cocdate[complete.cases(data3$cocdate)])
> [1] "2005-08-10" "2011-10-05"
> > range(data3$inhdate[complete.cases(data3$inhdate)])
> [1] "2005-07-07" "2011-10-13"
> > range(data3$haldate[complete.cases(data3$haldate)])
> [1] "2007-11-07" "2011-11-04"
> > range(data3$oiddate[complete.cases(data3$oiddate)])
> [1] "2006-09-01" "2011-11-04"
> >
> Working code below.
>
> data3 <- data1
> data3$oiddate <- as.Date(sapply(seq_along(data3$id), function(row) {
> if (all(is.na(unlist(data1[row, -1])))) {
> max_d <- NA
> } else {
> max_d <- max(unlist(data1[row, -1]), na.rm = TRUE)
> }
> max_d}),
> origin = "1970-01-01")
>
> range(data3$mrjdate[complete.cases(data3$mrjdate)])
> range(data3$cocdate[complete.cases(data3$cocdate)])
> range(data3$inhdate[complete.cases(data3$inhdate)])
> range(data3$haldate[complete.cases(data3$haldate)])
> range(data3$oiddate[complete.cases(data3$oiddate)])
>
>
> On Nov 10, 2014, at 10:10 AM, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
>
> > Hello,
> >
> > The range() with complete.cases() removes NA's for the date variables
> that are read from a data frame. However, the issue is that the same
> function does not remove NA's for the other date variable that is created
> using the dplyr/mutate(). The console and the reproducible example are
> given below. Any advice how to resolve this issue would be appreciated.
> >
> > Thanks,
> >
> > Pradip Muhuri
> >
> >
> > ################# cut and pasted from the R console ####################
> >
> > id mrjdate cocdate inhdate haldate oiddate
> > 1 1 2004-11-04 2008-07-18 2005-07-07 2007-11-07 2008-07-18
> > 2 2 <NA> <NA> <NA> <NA> <NA>
> > 3 3 2009-10-24 <NA> 2011-10-13 <NA> 2011-10-13
> > 4 4 2007-10-10 <NA> <NA> <NA> 2007-10-10
> > 5 5 2006-09-01 2005-08-10 <NA> <NA> 2006-09-01
> > 6 6 2007-09-04 2011-10-05 <NA> <NA> 2011-10-05
> > 7 7 2005-10-25 <NA> <NA> 2011-11-04 2011-11-04
> >>
> >> # range of dates
> >>
> >> range(data2$mrjdate[complete.cases(data2$mrjdate)])
> > [1] "2004-11-04" "2009-10-24"
> >> range(data2$cocdate[complete.cases(data2$cocdate)])
> > [1] "2005-08-10" "2011-10-05"
> >> range(data2$inhdate[complete.cases(data2$inhdate)])
> > [1] "2005-07-07" "2011-10-13"
> >> range(data2$haldate[complete.cases(data2$haldate)])
> > [1] "2007-11-07" "2011-11-04"
> >> range(data2$oiddate[complete.cases(data2$oiddate)])
> > [1] NA "2011-11-04"
> >
> >
> > ################ reproducible code #############################
> >
> > library(dplyr)
> > library(lubridate)
> > library(zoo)
> > # data object - description of the
> >
> > temp <- "id mrjdate cocdate inhdate haldate
> > 1 2004-11-04 2008-07-18 2005-07-07 2007-11-07
> > 2 NA NA NA NA
> > 3 2009-10-24 NA 2011-10-13 NA
> > 4 2007-10-10 NA NA NA
> > 5 2006-09-01 2005-08-10 NA NA
> > 6 2007-09-04 2011-10-05 NA NA
> > 7 2005-10-25 NA NA 2011-11-04"
> >
> > # read the data object
> >
> > data1 <- read.table(textConnection(temp),
> > colClasses=c("character", "Date", "Date", "Date",
> "Date"),
> > header=TRUE, as.is=TRUE
> > )
> >
> >
> > # create a new column
> >
> > data2 <- data1 %>%
> > rowwise() %>%
> > mutate(oiddate=as.Date(max(mrjdate,cocdate, inhdate, haldate,
> >
> na.rm=TRUE), origin='1970-01-01'))
> >
> > # print records
> >
> > print (data2)
> >
> > # range of dates
> >
> > range(data2$mrjdate[complete.cases(data2$mrjdate)])
> > range(data2$cocdate[complete.cases(data2$cocdate)])
> > range(data2$inhdate[complete.cases(data2$inhdate)])
> > range(data2$haldate[complete.cases(data2$haldate)])
> > range(data2$oiddate[complete.cases(data2$oiddate)])
> >
> >
> >
> >
> >
> > Pradip K. Muhuri, PhD
> > SAMHSA/CBHSQ
> > 1 Choke Cherry Road, Room 2-1071
> > Rockville, MD 20857
> > Tel: 240-276-1070
> > Fax: 240-276-1260
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-help
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> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
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