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:msh...@txbiomed.org] Sent: Monday, November 10, 2014 12:23 PM To: Muhuri, Pradip (SAMHSA/CBHSQ) Cc: r-help@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]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. NOTICE: This E-Mail (including attachments) is confidential and may be legally privileged. It is covered by the Electronic Communications Privacy Act, 18 U.S.C.2510-2521. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution or copying of this communication is strictly prohibited. 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