R help - Oct 2009 - Modify the plot from countCDFxt

Hello,

I am running the plot from countCDFxt (popbio). I would like to report the
y-axis as a percent instead of the log scale (e^01...). I can add an axis
with axis(2, 0:1, line =2) but I'm having trouble understanding how to
assign
the tic marks (with 'at ='). I'd like to tell it to make tics with
the
percent value (or decimal if that's my only option) at the equivalent of
e^-1, e^-2, etc, but the values don't seem to line up correctly. I'd
also
like to replace the provided axis with my axis instead of just placing my
axis out a line but I'm unsure how to do that. 

library(popbio)
logNE <- log(erbr$NEast[-1]/erbr$NEast[-6])
countCDFxt(mean(logNE), var(logNE), nt=5, Nc=1317, Ne=200)
axis(2, 0:1, labels = c(0.018, 0.050, 0.135, 0.368, 1), at = c(0.018, 0.050,
0.135, 0.368, 1), line =1)

Year? ????? NEast NWest
2004? ????? 731?? 1732
2005? ????? 898?? 2004
2006? ????? 714?? 1130
2007? ????? 1748? 1722
2008? ????? 1901? 1661
2009? ????? 1317? 1563

1. How do I tell axis() to report as a percent?
2. Why don't my values in label and at match the given axis?
3. How do I replace the axis label in countCDFxt?

Thanks for any help,

Michelle

Michelle DePrenger-Levin wrote:
> Hello,
> 
> I am running the plot from countCDFxt (popbio). I would like to report the
> y-axis as a percent instead of the log scale (e^01...). I can add an axis
> with axis(2, 0:1, line =2) but I'm having trouble understanding how to
assign
> the tic marks (with 'at ='). I'd like to tell it to make tics
with the
> percent value (or decimal if that's my only option) at the equivalent
of
> e^-1, e^-2, etc, but the values don't seem to line up correctly.
I'd also
> like to replace the provided axis with my axis instead of just placing my
> axis out a line but I'm unsure how to do that. 
> 
> library(popbio)
> logNE <- log(erbr$NEast[-1]/erbr$NEast[-6])
> countCDFxt(mean(logNE), var(logNE), nt=5, Nc=1317, Ne=200)
> axis(2, 0:1, labels = c(0.018, 0.050, 0.135, 0.368, 1), at = c(0.018,
0.050,
> 0.135, 0.368, 1), line =1)
> 
> Year        NEast NWest
> 2004        731   1732
> 2005        898   2004
> 2006        714   1130
> 2007        1748  1722
> 2008        1901  1661
> 2009        1317  1563
> 
> 1. How do I tell axis() to report as a percent?
The function countCDFxt() is unfortunately quite inflexible.
The only way to change the axis is to modify the function.
Fortunately, it's a pretty simple function. Just modify the
plotting part.
> 2. Why don't my values in label and at match the given axis?
Because you don't provide the correct at=...? You should be
able to just set at=c(1e-2, 1e-1, ...) as displayed on the
plot.
> 3. How do I replace the axis label in countCDFxt?
Again, the only way is to rewrite the function, perhaps
to allow additional graphics parameters like yaxt="n".

What's that '0:1' doing in your axis() call?

[Please look up the definition of "reproducible". See
bottom of this post.]

  -Peter Ehlers
> 
> Thanks for any help,
> 
> Michelle
> 
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