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Muhuri, Pradip (SAMHSA/CBHSQ)

2015-Jan-03 13:20 UTC

[R] R function to convert person-level observations to person-period observations

Hello,

I was trying to convert person-level observations to person-period observations
using an R custom function obtained from the UCLA web site
(http://www.ats.ucla.edu/stat/r/faq/person_period.htm).  Please see my
reproducible example below.  The function (PLPP) in the R script takes five
arguments.


1)  data (i.e., the data set to be converted)

2)  id (i.e., the identifier for each observation)

3)  period (i.e., number pf periods the person or observation was followed-up)

4)  event (i.e., the variable that indicates whether the event occurred or not
or whether the observation was censored (depending on which direction you are
converting).

5)  direction which "indicates whether the function should go from
person-level to person-period or from person-period to person-level".
On my example data set, the R script ran successfully.  Based on 3 person-level
observations (A died in year 2, B is censored in year 5, C died in year 3), I
get 10 period-level observations - correct results.   But the issue is that the
value of the "dead" indicator variable is incorrect.  I have a gut
feeling that the function needs to tweaked a bit to get desired results.


Correct results
  ID dead   studyyrs
1  A    1        2
2  B    0        5
3  C    1        3

Incorrect results - the "dead" column

   ID dead    studyyrs

1   A    0        1

2   A    0        2

3   B    0        1

4   B    0        2

5   B    0        3

6   B    0        4

7   B    1        5

8   C    0        1

9   C    0        2

10  C    0        3




Desired results

   ID dead    studyyrs

1   A    0        1

2   A    1        2

3   B    0        1

4   B    0        2

5   B    0        3

6   B    0        4

7   B    0        5

8   C    0        1

9   C    0        2

10  C    1        3


I would appreciate receiving your help or hints for resolving the issue. 
Thanks,



##  Below is my reproducible code is shown below)

## Below is my data frame (3 observations)
df <- data.frame( ID=LETTERS[1:3], dead=c(1,0,1), studyyrs=c(2,5,3) )
df

## Person-Level Person-Period Converter Function - Source:
http://www.ats.ucla.edu/stat/r/faq/person_period.htm
PLPP <- function(data, id, period, event, direction = c("period",
"level")) {
  ## Data Checking and Verification Steps
  stopifnot(is.matrix(data) || is.data.frame(data))
  stopifnot(c(id, period, event) %in% c(colnames(data), 1:ncol(data)))

  if (any(is.na(data[, c(id, period, event)]))) {
    stop("PLPP cannot currently handle missing data in the id, period, or
event variables")
  }

  ## Do the conversion - Source:
http://www.ats.ucla.edu/stat/r/faq/person_period.htm
  switch(match.arg(direction),
         period = {
           index <- rep(1:nrow(data), data[, period])
           idmax <- cumsum(data[, period])
           reve <- !data[, event]
           dat <- data[index, ]
           dat[, period] <- ave(dat[, period], dat[, id], FUN = seq_along)
           dat[, event] <- 0
           dat[idmax, event] <- reve},
         level = {
           tmp <- cbind(data[, c(period, id)], i = 1:nrow(data))
           index <- as.vector(by(tmp, tmp[, id],
                                 FUN = function(x) x[which.max(x[, period]),
"i"]))
           dat <- data[index, ]
           dat[, event] <- as.integer(!dat[, event])
         })

  rownames(dat) <- NULL
  return(dat)
}

tpp <- PLPP(data = df, id = "ID", period = "studyyrs",
            event = "dead", direction = "period")
tpp



Pradip K. Muhuri,
SAMHSA/CBHSQ


	[[alternative HTML version deleted]]

David Barron

2015-Jan-03 15:18 UTC

head link

[R] R function to convert person-level observations to person-period observations

Your data are wrong. The 'event' variable (dead in your example) needs
to be 1 for cases that end in an event and 0 for spells that are
censored: yours is the other way around.  If you change the 'dead'
variable to c(1,0,1) you will get the desired result.

If you really need to reverse the behaviour of the function, change the line
reve <- !data[, event]
to
reve <- data[, event]

David

On 3 January 2015 at 13:20, Muhuri, Pradip (SAMHSA/CBHSQ)
<Pradip.Muhuri at samhsa.hhs.gov> wrote:> Hello,
>
> I was trying to convert person-level observations to person-period
observations using an R custom function obtained from the UCLA web site
(http://www.ats.ucla.edu/stat/r/faq/person_period.htm).  Please see my
reproducible example below.  The function (PLPP) in the R script takes five
arguments.
>
>
> 1)  data (i.e., the data set to be converted)
>
> 2)  id (i.e., the identifier for each observation)
>
> 3)  period (i.e., number pf periods the person or observation was
followed-up)
>
> 4)  event (i.e., the variable that indicates whether the event occurred or
not or whether the observation was censored (depending on which direction you
are converting).
>
> 5)  direction which "indicates whether the function should go from
person-level to person-period or from person-period to person-level".
> On my example data set, the R script ran successfully.  Based on 3
person-level observations (A died in year 2, B is censored in year 5, C died in
year 3), I get 10 period-level observations - correct results.   But the issue
is that the value of the "dead" indicator variable is incorrect.  I
have a gut feeling that the function needs to tweaked a bit to get desired
results.
>
>
> Correct results
>   ID dead   studyyrs
> 1  A    1        2
> 2  B    0        5
> 3  C    1        3
>
> Incorrect results - the "dead" column
>
>    ID dead    studyyrs
>
> 1   A    0        1
>
> 2   A    0        2
>
> 3   B    0        1
>
> 4   B    0        2
>
> 5   B    0        3
>
> 6   B    0        4
>
> 7   B    1        5
>
> 8   C    0        1
>
> 9   C    0        2
>
> 10  C    0        3
>
>
>
>
> Desired results
>
>    ID dead    studyyrs
>
> 1   A    0        1
>
> 2   A    1        2
>
> 3   B    0        1
>
> 4   B    0        2
>
> 5   B    0        3
>
> 6   B    0        4
>
> 7   B    0        5
>
> 8   C    0        1
>
> 9   C    0        2
>
> 10  C    1        3
>
>
> I would appreciate receiving your help or hints for resolving the issue. 
Thanks,
>
>
>
> ##  Below is my reproducible code is shown below)
>
> ## Below is my data frame (3 observations)
> df <- data.frame( ID=LETTERS[1:3], dead=c(1,0,1), studyyrs=c(2,5,3) )
> df
>
> ## Person-Level Person-Period Converter Function - Source:
http://www.ats.ucla.edu/stat/r/faq/person_period.htm
> PLPP <- function(data, id, period, event, direction =
c("period", "level")) {
>   ## Data Checking and Verification Steps
>   stopifnot(is.matrix(data) || is.data.frame(data))
>   stopifnot(c(id, period, event) %in% c(colnames(data), 1:ncol(data)))
>
>   if (any(is.na(data[, c(id, period, event)]))) {
>     stop("PLPP cannot currently handle missing data in the id, period,
or event variables")
>   }
>
>   ## Do the conversion - Source:
http://www.ats.ucla.edu/stat/r/faq/person_period.htm
>   switch(match.arg(direction),
>          period = {
>            index <- rep(1:nrow(data), data[, period])
>            idmax <- cumsum(data[, period])
>            reve <- !data[, event]
>            dat <- data[index, ]
>            dat[, period] <- ave(dat[, period], dat[, id], FUN =
seq_along)
>            dat[, event] <- 0
>            dat[idmax, event] <- reve},
>          level = {
>            tmp <- cbind(data[, c(period, id)], i = 1:nrow(data))
>            index <- as.vector(by(tmp, tmp[, id],
>                                  FUN = function(x) x[which.max(x[,
period]), "i"]))
>            dat <- data[index, ]
>            dat[, event] <- as.integer(!dat[, event])
>          })
>
>   rownames(dat) <- NULL
>   return(dat)
> }
>
> tpp <- PLPP(data = df, id = "ID", period =
"studyyrs",
>             event = "dead", direction = "period")
> tpp
>
>
>
> Pradip K. Muhuri,
> SAMHSA/CBHSQ
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

Muhuri, Pradip (SAMHSA/CBHSQ)

2015-Jan-03 18:22 UTC

head link

[R] R function to convert person-level observations to person-period observations

Hello David,

Thank you so much for your advice.    The revision of the code as "reve
<- data[, event]" in the function (but with no changing of the example
data) seems to provide the desired results (shown below).   These 3 subjects are
followed for 5 years.  Subject A experienced the event in year 2, and subject C
experienced the event in year 3 while subject B were censored at the end
follow-up period (i.e., year 5).  The person-period observations now seem to be
consistent with the person-level observations.  Do you see any issues?

Regards,

Pradip

###########################################################################################
## person-level observations                                                   
 ID dead studyyrs
1  A    1        2
2  B    0        5
3  C    1        3

## person-period observation
   ID dead studyyrs
1   A    0        1
2   A    1        2
3   B    0        1
4   B    0        2
5   B    0        3
6   B    0        4
7   B    0        5
8   C    0        1
9   C    0        2
10  C    1        3

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: David Barron [mailto:dnbarron at gmail.com] 
Sent: Saturday, January 03, 2015 10:19 AM
To: Muhuri, Pradip (SAMHSA/CBHSQ)
Cc: r-help at r-project.org
Subject: Re: [R] R function to convert person-level observations to
person-period observations

Your data are wrong. The 'event' variable (dead in your example) needs
to be 1 for cases that end in an event and 0 for spells that are
censored: yours is the other way around.  If you change the 'dead'
variable to c(1,0,1) you will get the desired result.

If you really need to reverse the behaviour of the function, change the line
reve <- !data[, event] to reve <- data[, event]

David

On 3 January 2015 at 13:20, Muhuri, Pradip (SAMHSA/CBHSQ) <Pradip.Muhuri at
samhsa.hhs.gov> wrote:> Hello,
>
> I was trying to convert person-level observations to person-period
observations using an R custom function obtained from the UCLA web site
(http://www.ats.ucla.edu/stat/r/faq/person_period.htm).  Please see my
reproducible example below.  The function (PLPP) in the R script takes five
arguments.
>
>
> 1)  data (i.e., the data set to be converted)
>
> 2)  id (i.e., the identifier for each observation)
>
> 3)  period (i.e., number pf periods the person or observation was 
> followed-up)
>
> 4)  event (i.e., the variable that indicates whether the event occurred or
not or whether the observation was censored (depending on which direction you
are converting).
>
> 5)  direction which "indicates whether the function should go from
person-level to person-period or from person-period to person-level".
> On my example data set, the R script ran successfully.  Based on 3
person-level observations (A died in year 2, B is censored in year 5, C died in
year 3), I get 10 period-level observations - correct results.   But the issue
is that the value of the "dead" indicator variable is incorrect.  I
have a gut feeling that the function needs to tweaked a bit to get desired
results.
>
>
> Correct results
>   ID dead   studyyrs
> 1  A    1        2
> 2  B    0        5
> 3  C    1        3
>
> Incorrect results - the "dead" column
>
>    ID dead    studyyrs
>
> 1   A    0        1
>
> 2   A    0        2
>
> 3   B    0        1
>
> 4   B    0        2
>
> 5   B    0        3
>
> 6   B    0        4
>
> 7   B    1        5
>
> 8   C    0        1
>
> 9   C    0        2
>
> 10  C    0        3
>
>
>
>
> Desired results
>
>    ID dead    studyyrs
>
> 1   A    0        1
>
> 2   A    1        2
>
> 3   B    0        1
>
> 4   B    0        2
>
> 5   B    0        3
>
> 6   B    0        4
>
> 7   B    0        5
>
> 8   C    0        1
>
> 9   C    0        2
>
> 10  C    1        3
>
>
> I would appreciate receiving your help or hints for resolving the 
> issue.  Thanks,
>
>
>
> ##  Below is my reproducible code is shown below)
>
> ## Below is my data frame (3 observations) df <- data.frame( 
> ID=LETTERS[1:3], dead=c(1,0,1), studyyrs=c(2,5,3) ) df
>
> ## Person-Level Person-Period Converter Function - Source: 
> http://www.ats.ucla.edu/stat/r/faq/person_period.htm
> PLPP <- function(data, id, period, event, direction =
c("period", "level")) {
>   ## Data Checking and Verification Steps
>   stopifnot(is.matrix(data) || is.data.frame(data))
>   stopifnot(c(id, period, event) %in% c(colnames(data), 1:ncol(data)))
>
>   if (any(is.na(data[, c(id, period, event)]))) {
>     stop("PLPP cannot currently handle missing data in the id, period,
or event variables")
>   }
>
>   ## Do the conversion - Source:
http://www.ats.ucla.edu/stat/r/faq/person_period.htm
>   switch(match.arg(direction),
>          period = {
>            index <- rep(1:nrow(data), data[, period])
>            idmax <- cumsum(data[, period])
>            reve <- !data[, event]
>            dat <- data[index, ]
>            dat[, period] <- ave(dat[, period], dat[, id], FUN =
seq_along)
>            dat[, event] <- 0
>            dat[idmax, event] <- reve},
>          level = {
>            tmp <- cbind(data[, c(period, id)], i = 1:nrow(data))
>            index <- as.vector(by(tmp, tmp[, id],
>                                  FUN = function(x) x[which.max(x[,
period]), "i"]))
>            dat <- data[index, ]
>            dat[, event] <- as.integer(!dat[, event])
>          })
>
>   rownames(dat) <- NULL
>   return(dat)
> }
>
> tpp <- PLPP(data = df, id = "ID", period =
"studyyrs",
>             event = "dead", direction = "period") tpp
>
>
>
> Pradip K. Muhuri,
> SAMHSA/CBHSQ
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

R help - Jan 2015 - R function to convert person-level observations to person-period observations

[R] R function to convert person-level observations to person-period observations

[R] R function to convert person-level observations to person-period observations

[R] R function to convert person-level observations to person-period observations