R help - May 2010 - [Fwd: Re: Plotting log-axis with the exponential base to a plot with the default logarithm base 10]

Hello!
Thank you for answering!
What I am trying to do is to plot my raw values (biomass of different
species) on a logaritmic y-axis with the base of e. When I type
"log="y"",
the axis transforms into a logaritmic axis with the base of 10.

Best regards,
Elisabeth
> Dear Elisabeth,
>
>     I'm not sure if I have understood your question -- are you trying
> to use a different logarithmic base?
>
>                                                          Kind regards,
>
>                                                          Xianwen
>
> On Sun, May 9, 2010 at 8:05 PM, Elisabeth Bjerke Rastad
> <ebr024 at post.uit.no> wrote:
>> Hello!
>>
>> I have a problem which I have tried to solve for several days now..
>>
>> I have plottet a lineplot.CI in the library "sciplot", and I
am trying
>> to
>> plot it with a logaritmic y-axis (with exponential base).
>>
>> The problem is that; when I type "log "y"", the
axis transforms into the
>> logaritmic of base 10.
>>
>> I wonder if someeone could tell me how to specify that I would like to
>> use
>> the exponential logaritmic y-axis. I have tried a lot (but obviously
not
>> all, I guess this problem is possible to solve..)
>>
>> Hope you would like to help me! Thank you a lot in advance!!
>>
>> Greetings,
>>
>> Elisabeth B. R??stad
>> (Master's student, Norway)
>>
>> ______________________________________________
>> 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.
>>
>
>
>
> --
> Xianwen Chen, M.Sc.
> Scientific assistant, BFE, UiT (www.uit.no)
> Tel.: +47 776 46 112 | Fax: +47 776 46 020
>
>

Elisabeth, question to you: How is it that you recognise that it is
"a logaritmic axis with the base of 10", as opposed to any other base?
Ted.

On 10-May-10 17:15:04, Elisabeth Bjerke Rastad wrote:
> Hello!
> Thank you for answering!
> What I am trying to do is to plot my raw values (biomass of different
> species) on a logaritmic y-axis with the base of e. When I type
> "log="y"",
> the axis transforms into a logaritmic axis with the base of 10.
> 
> Best regards,
> Elisabeth
> 
>> Dear Elisabeth,
>>
>>     I'm not sure if I have understood your question -- are you
trying
>> to use a different logarithmic base?
>>
>>                                                          Kind regards,
>>
>>                                                          Xianwen
>>
>> On Sun, May 9, 2010 at 8:05 PM, Elisabeth Bjerke Rastad
>> <ebr024 at post.uit.no> wrote:
>>> Hello!
>>>
>>> I have a problem which I have tried to solve for several days now..
>>>
>>> I have plottet a lineplot.CI in the library "sciplot",
and I am
>>> trying
>>> to
>>> plot it with a logaritmic y-axis (with exponential base).
>>>
>>> The problem is that; when I type "log "y"", the
axis transforms into
>>> the
>>> logaritmic of base 10.
>>>
>>> I wonder if someeone could tell me how to specify that I would like
>>> to
>>> use
>>> the exponential logaritmic y-axis. I have tried a lot (but
obviously
>>> not
>>> all, I guess this problem is possible to solve..)
>>>
>>> Hope you would like to help me! Thank you a lot in advance!!
>>>
>>> Greetings,
>>>
>>> Elisabeth B. R??stad
>>> (Master's student, Norway)
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>>
>> --
>> Xianwen Chen, M.Sc.
>> Scientific assistant, BFE, UiT (www.uit.no)
>> Tel.: +47 776 46 112 | Fax: +47 776 46 020
>>
>>
> 
> ______________________________________________
> 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.
--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 10-May-10                                       Time: 22:48:35
------------------------------ XFMail ------------------------------

Elisabeth,

You should listen to Ted (Harding). He answered your question with:
>> the vertical axis is scaled logarithmically with the 
>> numerical annotations corresponding to the *raw* values of Y, 
>> not to their log-transformed values. Therefore it does not matter 
>> what base of logarithms is used...
And he has tried to help you further by asking you to answer the following
question:
>> How is it that you recognise that it is 
>> "a logaritmic axis with the base of 10", as opposed to any
other base?
Maybe a little graphic demonstration (run the script below) will help to
convince you. The top row of the figure re-poses Ted's question, viz
"How do
you know which logarithmic base was used to plot which sub-figure?" You
will
see from my script that the first is plotted using natural logs, whereas the
next two use logs to base 10. (The last of them uses R's log="y"
argument.)
What's the difference?

The first two sub-figures on the bottom row show the scales that were hidden
in the sub-figures above them (from the script you will see that all I did
was turn off the annotation/labelling of the scale).

The last sub-figure on the bottom row is identical in __appearance__ to that
above it. However, as you will see from my script, it plots data that have
been transformed to natural logarithms. For scale-annotation, however, I
have used raw data values. That was Ted's first point: it doesn't matter
which base of logarithm your data have been transformed to if you annotate
the scale using (backtransformed) raw values.

## Show that log="y" does the job you want done even if internally it
uses
logs to the base 10
## rather than natural logarithms
par(mfrow=c(2,3))
plot(log(1:10), yaxt="n", ylab="")
plot(log10(1:10), yaxt="n", ylab="")
plot((1:10), log="y")
plot(log(1:10))
plot(log10(1:10))
plot(log(1:10), yaxt="n")
axis(side=2, at=sapply(c(1,2,5,10), FUN=function(x) log(x)),
labels=c(1,2,5,10))

Regards, Mark
-- 
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