[R] range () does not remove NA's with complete.cases() for dates (dplyr/mutate)

[Mark Sharp]

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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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