How to modify a S4 function (in the package NADA)

I want to get access to the code of an S4 method in order to possibly modify
a function to accomplish my particular needs: in my case the function in is
cenfit() from the package NADA

Now, given my reproducible example:

my.ex<-structure(list(TEC = c(0.21, 0.077, 0.06, 0.033, 0.014, 0.0072), LR =
c(0L, 0L, 1L, 0L, 1L, 0L)), .Names = c("TEC", "LR"), class = "data.frame",
row.names = c(NA, -6L))

and the following few lines of code:

library(?NADA)

attach(my.ex)

cenfit(TEC,LR)

giving this output:

  n      n.cen         median       mean      sd
6.00     2.00              0.033           0.058       0.083

I would like to add one more result to the above, namely ?sum?, very simply
computed as the product of ?n? times ?mean?

Do you think that is possible or convenient?

I?ve been reading that editing a S4 methods needs particular attention as by
using showMethods("cenfit") and then getMethod("cenfit"); in fact, I?ve been
trying that but without much success (i.e. understanding of the cumbersome
output)

can anyone give me some help on how is probably better to proceed in order
to get my new result?

different alternative solutions or hints or advices are also more than
welcomed
(I?m pretty new on R and specially on the field of function handling and
customizing)

all the best

max

Hi,

Your reproducible example isn't reproducible for me, as I get an error message.

But regardless, the easiest thing to do is write your own wrapper,
something like:

mycenfit <- function(x, y) {
   result <- cenfit(x, y)
   c(result, sum = result$n * result$mean)
}

No need to change anything in the package itself. Incidentally, using
attach() is generally a really bad idea. with() is much safer.

Sarah

On Thu, Nov 15, 2012 at 7:00 AM, maxbre <mbressan at arpa.veneto.it> wrote:

I want to get access to the code of an S4 method in order to possibly modify
a function to accomplish my particular needs: in my case the function in is
cenfit() from the package NADA

Now, given my reproducible example:

my.ex<-structure(list(TEC = c(0.21, 0.077, 0.06, 0.033, 0.014, 0.0072), LR =
c(0L, 0L, 1L, 0L, 1L, 0L)), .Names = c("TEC", "LR"), class = "data.frame",
row.names = c(NA, -6L))

and the following few lines of code:

library(?NADA)

attach(my.ex)

cenfit(TEC,LR)

giving this output:

   n      n.cen         median       mean      sd
6.00     2.00              0.033           0.058       0.083

I would like to add one more result to the above, namely ?sum?, very simply
computed as the product of ?n? times ?mean?

Do you think that is possible or convenient?

I?ve been reading that editing a S4 methods needs particular attention as by
using showMethods("cenfit") and then getMethod("cenfit"); in fact, I?ve been
trying that but without much success (i.e. understanding of the cumbersome
output)

can anyone give me some help on how is probably better to proceed in order
to get my new result?

different alternative solutions or hints or advices are also more than
welcomed
(I?m pretty new on R and specially on the field of function handling and
customizing)

all the best

max

--
Sarah Goslee
http://www.functionaldiversity.org

library(NADA)
my.ex<-structure(list(TEC = c(0.21, 0.077, 0.06, 0.033, 0.014, 0.0072), LR =

with(my.ex, cenfit(TEC,LR))

On 11/15/2012 06:10 AM, Sarah Goslee wrote:

Hi,

Your reproducible example isn't reproducible for me, as I get an error
message.

But regardless, the easiest thing to do is write your own wrapper,
something like:

mycenfit <- function(x, y) {
   result <- cenfit(x, y)
   c(result, sum = result$n * result$mean)
}

No need to change anything in the package itself. Incidentally, using
attach() is generally a really bad idea. with() is much safer.

Sarah

On Thu, Nov 15, 2012 at 7:00 AM, maxbre <mbressan at arpa.veneto.it> wrote:

I want to get access to the code of an S4 method in order to possibly
modify
a function to accomplish my particular needs: in my case the function in
is
cenfit() from the package NADA

Now, given my reproducible example:

my.ex<-structure(list(TEC = c(0.21, 0.077, 0.06, 0.033, 0.014, 0.0072),
LR =
c(0L, 0L, 1L, 0L, 1L, 0L)), .Names = c("TEC", "LR"), class =
"data.frame",
row.names = c(NA, -6L))

and the following few lines of code:

library(?NADA)

attach(my.ex)

cenfit(TEC,LR)

giving this output:

   n      n.cen         median       mean      sd
6.00     2.00              0.033           0.058       0.083

actually, cenfit() returns an object

xx = cenfit(my.ex$TEC, as.logical(my.ex$LR))

and what you're seeing is the result of the object's 'show' method

xx

         n      n.cen     median       mean         sd
6.00000000 2.00000000 0.03300000 0.05836667 0.08350178

You can see the body of the show method with

    selectMethod(show, class(xx))

and methods that are available to work on xx with

    showMethods(class=class(xx), where=search())

Sarah is right that you'd likely want to write your own function, using a
combination of available methods, e.g.,

censtats <- function(x) {
    s = summary(x)
    c(n = nrow(s), n.cen = nrow(s) - sum(s$n.event), median = median(x),
      mean = mean(x)[["mean"]], sd = sd(x))
}

Martin

I would like to add one more result to the above, namely ?sum?, very
simply
computed as the product of ?n? times ?mean?

Do you think that is possible or convenient?

I?ve been reading that editing a S4 methods needs particular attention as
by
using showMethods("cenfit") and then getMethod("cenfit"); in fact, I?ve
been
trying that but without much success (i.e. understanding of the
cumbersome
output)

can anyone give me some help on how is probably better to proceed in
order
to get my new result?

different alternative solutions or hints or advices are also more than
welcomed
(I?m pretty new on R and specially on the field of function handling and
customizing)

all the best

max