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)])

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

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

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