R help - Jun 2008 - data frame manipulation - splitting monitoring interval and assigning stage

Hello, everyone.

I'm hoping to prevent myself from doing a lot of pointing and clicking
in Excel. I have a dataframe of bird nest check observations, in which
I know the date of the first check, the date of the second check (both
currently in Julian date format), the status of the nest at the second
check (alive or failed), and the date that the nest hatched (i.e.
changed from Incubation stages to Brood-rearing stage). Many nests
have more than one record, as there were several nest checks
throughout the duration of the nesting attempt.

What I want to do is assign a nest Stage variable, either Incubation
or Brood-rearing. It's very easy to do so when the second nest check
was before the hatch date (incubation), or when the first nest check
was after the hatch date (brood-rearing). But I can't figure out a
quick way to split the interval when it contained both incubation and
brood-rearing activities.

I'd like to go from:

Check1     Check2     HatchDate
101           121           110

to:

Check1     Check2     HatchDate    Stage
101           109          110               I
110           121          110               B

because even though the nest wasn't actually checked on the day of
hatching, we know that it transitioned to the next stage on hatch day.

There's other covariates as well as the unique nest ID which need to
be carried along too, just like HatchDate.

If anyone who is good at dataframe manipulation could suggest some
code to perform these actions, I would really appreciate it. Thanks in
advance.


cheers, Jessi Brown
Ecology, Evolution, and Conservation Biology
University of Nevada, Reno

Is this what you want:
> x <- read.table(textConnection("Check1     Check2     HatchDate
+ 101           121           110
+ 130  150 140
+ 140  150  160"), header=TRUE)
> closeAllConnections()
> x
  Check1 Check2 HatchDate
1    101    121       110
2    130    150       140
3    140    150       160
> do.call(rbind, apply(x,1,function(.row){
+     if (.row[3] < .row[2]){
+         # split out the data
+         data.frame(Check1=c(.row[1], .row[3]),
+                    Check2=c(.row[3] - 1, .row[2]),
+                    Check3=c(.row[3], .row[3]),
+                    Stage=c("I", "B"))
+     }
+     else {
+         # normal; just copy over
+         data.frame(Check1=.row[1], Check2=.row[2], Check3=.row[3],
Stage="X")
+     }
+ }))
           Check1 Check2 Check3 Stage
Check1        101    109    110     I
HatchDate     110    121    110     B
Check11       130    139    140     I
HatchDate1    140    150    140     B
Check12       140    150    160     X


On Wed, Jun 25, 2008 at 1:29 PM, Jessi Brown <jessilbrown at gmail.com>
wrote:
> Hello, everyone.
>
> I'm hoping to prevent myself from doing a lot of pointing and clicking
> in Excel. I have a dataframe of bird nest check observations, in which
> I know the date of the first check, the date of the second check (both
> currently in Julian date format), the status of the nest at the second
> check (alive or failed), and the date that the nest hatched (i.e.
> changed from Incubation stages to Brood-rearing stage). Many nests
> have more than one record, as there were several nest checks
> throughout the duration of the nesting attempt.
>
> What I want to do is assign a nest Stage variable, either Incubation
> or Brood-rearing. It's very easy to do so when the second nest check
> was before the hatch date (incubation), or when the first nest check
> was after the hatch date (brood-rearing). But I can't figure out a
> quick way to split the interval when it contained both incubation and
> brood-rearing activities.
>
> I'd like to go from:
>
> Check1     Check2     HatchDate
> 101           121           110
>
> to:
>
> Check1     Check2     HatchDate    Stage
> 101           109          110               I
> 110           121          110               B
>
> because even though the nest wasn't actually checked on the day of
> hatching, we know that it transitioned to the next stage on hatch day.
>
> There's other covariates as well as the unique nest ID which need to
> be carried along too, just like HatchDate.
>
> If anyone who is good at dataframe manipulation could suggest some
> code to perform these actions, I would really appreciate it. Thanks in
> advance.
>
>
> cheers, Jessi Brown
> Ecology, Evolution, and Conservation Biology
> University of Nevada, Reno
>
> ______________________________________________
> R-help at 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.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?