xyplot: logarithmic y-axis

This should be simple but I am struggling. I like to easily switch in xyplot
between a linear or logarithmic y-axis by setting a logical flag logY to
False or True. This switch changes the scales argument of xyplot. I found
out that the original two-dimentional data (Conc vs Time in my case) are
converted to log10(Conc) if log=TRUE in scales, but it appears that
functions like panel.curve need to provide the y values in log10 form (if
there is an automatic method, I would like to know). I therefore like to
pass on the value logY to my custom panel.curve function. How do I do that?
I think that the value of logY should go into xyplot that should pass it on
to the panel function and then to the panel.curve function.

On 12/15/06, RMan54 <RMan54 at cox.net> wrote:

This should be simple but I am struggling. I like to easily switch in
xyplot
between a linear or logarithmic y-axis by setting a logical flag logY to
False or True. This switch changes the scales argument of xyplot. I found
out that the original two-dimentional data (Conc vs Time in my case) are
converted to log10(Conc) if log=TRUE in scales, but it appears that
functions like panel.curve need to provide the y values in log10 form (if
there is an automatic method, I would like to know). I therefore like to
pass on the value logY to my custom panel.curve function. How do I do
that?
I think that the value of logY should go into xyplot that should pass it
on
to the panel function and then to the panel.curve function.

It probably should, but doesn't.

-Deepayan

Please take no offence since none was intended. What I meant is that it
should be simple for me to know how to do this but it isn't because of my
inexperience. I  think that the lattice package is great.

However, how can I pass on my own varaibles through xyplot?

Thanks, -Rene


Deepayan Sarkar wrote:

On 12/15/06, RMan54 <RMan54 at cox.net> wrote:

This should be simple but I am struggling. I like to easily switch in
xyplot
between a linear or logarithmic y-axis by setting a logical flag logY to
False or True. This switch changes the scales argument of xyplot. I found
out that the original two-dimentional data (Conc vs Time in my case) are
converted to log10(Conc) if log=TRUE in scales, but it appears that
functions like panel.curve need to provide the y values in log10 form (if
there is an automatic method, I would like to know). I therefore like to
pass on the value logY to my custom panel.curve function. How do I do
that?
I think that the value of logY should go into xyplot that should pass it
on
to the panel function and then to the panel.curve function.

It probably should, but doesn't.

-Deepayan

On 12/15/06, RMan54 <RMan54 at cox.net> wrote:

Please take no offence since none was intended. What I meant is that it
should be simple for me to know how to do this but it isn't because of my
inexperience. I  think that the lattice package is great.

I didn't mean to suggest that I was offended. I only agreed with you
that it would be nice if there were a way of knowing inside the panel
function whether a log scale is being used, and informing you that
there isn't.

However, how can I pass on my own varaibles through xyplot?

Any arguments not recognized by xyplot will be passed to the panel
function.

-Deepayan

Thanks, -Rene


Deepayan Sarkar wrote:

On 12/15/06, RMan54 <RMan54 at cox.net> wrote:

This should be simple but I am struggling. I like to easily switch in
xyplot
between a linear or logarithmic y-axis by setting a logical flag logY

to

False or True. This switch changes the scales argument of xyplot. I

found

out that the original two-dimentional data (Conc vs Time in my case)

are

converted to log10(Conc) if log=TRUE in scales, but it appears that
functions like panel.curve need to provide the y values in log10 form

(if

there is an automatic method, I would like to know). I therefore like

to

pass on the value logY to my custom panel.curve function. How do I do
that?
I think that the value of logY should go into xyplot that should pass

it

on
to the panel function and then to the panel.curve function.

It probably should, but doesn't.

-Deepayan

I added logY as the last argument to xyplot and in my curve function. I got
the following error message:

Error in myCurve(x) : argument "log" is missing, with no default

myCurve <-function(x, log) {
    f <- ... # calculate curve here
    if (log==T) f <- log10(f)
    return(f)
}

logY=T
xyplot(Conc ~ Time | Subj,
       groups=Dose,
       data = mydata,
       scales=list(x=list(at=seq(0,96,24)), y=list(log=logY)),
       panel = function(...) {
           panel.abline(h=c(0, 50, 100, 150, 200, 250) ,
                      v=c(0,24,48,72,96), col.line="gray")
           panel.xyplot(...)
           panel.curve(myCurve, from=0, to=96, n=300, ..., log=logY)
           },
       logY
       )