problem plotting PDF of detection probability in R
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ej...@st-andrews.ac.uk
May 12, 2016, 1:37:00 PM5/12/16
to distance-sampling
Good day,
Below are simple histograms of some simulated distance data from point transects.
> par(mfrow = c(1,2))
> hist(trunc.dat, main=NULL, probability=TRUE)
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = TRUE)
Note that when I specify "probability = FALSE", I get the following plot and error message.
>hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = FALSE)
Warning message:
In plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
When I plot the pdf of detection probability for a model fitted to these data, the histogram looks like the one where the areas are wrong, and the line does not match the data.
>plot(fit.hn, pdf = T)
The simple fix recommended for the histogram doesn't work with plot.ds().
> plot(fit.hn, pdf = T, freq=FALSE)
Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab = ylab, main = "", :
formal argument "freq" matched by multiple actual arguments
Any ideas why plot.ds is produces a histogram that is apparently wrong behind the line for the fitted pdf, or other ways to produce an accurate plot?
Thanks,
Eric
Below are simple histograms of some simulated distance data from point transects.
> par(mfrow = c(1,2))
> hist(trunc.dat, main=NULL, probability=TRUE)
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = TRUE)
Note that when I specify "probability = FALSE", I get the following plot and error message.
>hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = FALSE)
Warning message:
In plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
When I plot the pdf of detection probability for a model fitted to these data, the histogram looks like the one where the areas are wrong, and the line does not match the data.
>plot(fit.hn, pdf = T)
The simple fix recommended for the histogram doesn't work with plot.ds().
> plot(fit.hn, pdf = T, freq=FALSE)
Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab = ylab, main = "", :
formal argument "freq" matched by multiple actual arguments
Any ideas why plot.ds is produces a histogram that is apparently wrong behind the line for the fitted pdf, or other ways to produce an accurate plot?
Thanks,
Eric
David Lawrence Miller
May 16, 2016, 10:25:13 AM5/16/16
to ej...@st-andrews.ac.uk, distance-sampling
Hi Eric, hi listfolk,
I think there was a bug in how the histogram was rescaled for the point
transect pdf case (it was being rescaled when it didn't need to be).
Eric: can you try out the new version I've just pushed to github and see
whether you get something working? Else please send your example data to
me off-list and I'll take a look and we can report back to the list.
You can install the latest version of mrds using the devtools package:
library(devtools)
install_github("DistanceDevelopment/mrds")
cheers,
--dave
On 12/05/2016 13:37, ej...@st-andrews.ac.uk wrote:
> Good day,
> Below are simple histograms of some simulated distance data from point
> transects.
>> par(mfrow = c(1,2))
>> hist(trunc.dat, main=NULL, probability=TRUE)
>> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = TRUE)
>
>
>
> You received this message because you are subscribed to the Google
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> To post to this group, send email to distance...@googlegroups.com
> <mailto:distance...@googlegroups.com>.
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> <https://groups.google.com/d/msgid/distance-sampling/890a46f6-ff8e-42c9-b142-a9e297060799%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout.
I think there was a bug in how the histogram was rescaled for the point
transect pdf case (it was being rescaled when it didn't need to be).
Eric: can you try out the new version I've just pushed to github and see
whether you get something working? Else please send your example data to
me off-list and I'll take a look and we can report back to the list.
You can install the latest version of mrds using the devtools package:
library(devtools)
install_github("DistanceDevelopment/mrds")
cheers,
--dave
On 12/05/2016 13:37, ej...@st-andrews.ac.uk wrote:
> Good day,
> Below are simple histograms of some simulated distance data from point
> transects.
>> par(mfrow = c(1,2))
>> hist(trunc.dat, main=NULL, probability=TRUE)
>> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = TRUE)
>
>
>
> Note that when I specify "probability = FALSE", I get the following plot
> and error message.
>>hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = FALSE)
> Warning message:
> In plot.histogram(r, freq = freq1, col = col, border = border, angle =
> angle, :
> the AREAS in the plot are wrong -- rather use 'freq = FALSE'
>
>
>
>
> and error message.
>>hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL, probability = FALSE)
> Warning message:
> In plot.histogram(r, freq = freq1, col = col, border = border, angle =
> angle, :
> the AREAS in the plot are wrong -- rather use 'freq = FALSE'
>
>
>
>
> When I plot the pdf of detection probability for a model fitted to these
> data, the histogram looks like the one where the areas are wrong, and
> the line does not match the data.
>>plot(fit.hn, pdf = T)
>
> data, the histogram looks like the one where the areas are wrong, and
> the line does not match the data.
>>plot(fit.hn, pdf = T)
>
> The simple fix recommended for the histogram doesn't work with plot.ds().
>> plot(fit.hn, pdf = T, freq=FALSE)
> Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab = ylab, main
> = "", :
> formal argument "freq" matched by multiple actual arguments
>
> Any ideas why plot.ds is produces a histogram that is apparently wrong
> behind the line for the fitted pdf, or other ways to produce an accurate
> plot?
>
> Thanks,
> Eric
>
>
>
>
>
> --
>> plot(fit.hn, pdf = T, freq=FALSE)
> Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab = ylab, main
> = "", :
> formal argument "freq" matched by multiple actual arguments
>
> Any ideas why plot.ds is produces a histogram that is apparently wrong
> behind the line for the fitted pdf, or other ways to produce an accurate
> plot?
>
> Thanks,
> Eric
>
>
>
>
>
> You received this message because you are subscribed to the Google
> Groups "distance-sampling" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to distance-sampl...@googlegroups.com
> <mailto:distance-sampl...@googlegroups.com>.
> To post to this group, send email to distance...@googlegroups.com
> <mailto:distance...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/distance-sampling/890a46f6-ff8e-42c9-b142-a9e297060799%40googlegroups.com
> <https://groups.google.com/d/msgid/distance-sampling/890a46f6-ff8e-42c9-b142-a9e297060799%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout.
Eric Howe
May 16, 2016, 3:19:31 PM5/16/16
to David Lawrence Miller, distance-sampling
Good day list members,
Thank you very much David, that resolved the problem with the bar heights in the histogram. I haven't yet figured out a way to ensure that the line fits in the plot area, since plot.ds() doesn't seem to accept either "ylim" or "add" as arguments. Any ideas welcome!
David Lawrence Miller
May 16, 2016, 4:31:33 PM5/16/16
to Eric Howe, distance-sampling
Hi Eric, hi listfolk,
Glad to hear that worked. I've pushed another change to github fixing
default y axis limits for point transect PDF plotting and allowing you
to set your own values. Let me know if that works for you.
cheers,
--dave
On 16/05/2016 15:19, Eric Howe wrote:
> Good day list members,
> Thank you very much David, that resolved the problem with the bar
> heights in the histogram. I haven't yet figured out a way to ensure that
> the line fits in the plot area, since plot.ds() doesn't seem to accept
> either "ylim" or "add" as arguments. Any ideas welcome!
> Eric
>
>
>
> <mailto:distance-sampl...@googlegroups.com
> <mailto:distance-sampling%2Bunsu...@googlegroups.com>>.
Glad to hear that worked. I've pushed another change to github fixing
default y axis limits for point transect PDF plotting and allowing you
to set your own values. Let me know if that works for you.
cheers,
--dave
On 16/05/2016 15:19, Eric Howe wrote:
> Good day list members,
> Thank you very much David, that resolved the problem with the bar
> heights in the histogram. I haven't yet figured out a way to ensure that
> the line fits in the plot area, since plot.ds() doesn't seem to accept
> either "ylim" or "add" as arguments. Any ideas welcome!
> Eric
>
>
>
> Inline images 1
>
>
> On 16 May 2016 at 10:25, David Lawrence Miller
>
>
> On 16 May 2016 at 10:25, David Lawrence Miller
> <da...@ninepointeightone.net <mailto:da...@ninepointeightone.net>> wrote:
>
> Hi Eric, hi listfolk,
>
> I think there was a bug in how the histogram was rescaled for the
> point transect pdf case (it was being rescaled when it didn't need
> to be).
>
> Eric: can you try out the new version I've just pushed to github and
> see whether you get something working? Else please send your example
> data to me off-list and I'll take a look and we can report back to
> the list.
>
> You can install the latest version of mrds using the devtools package:
>
> library(devtools)
> install_github("DistanceDevelopment/mrds")
>
> cheers,
> --dave
>
>
> On 12/05/2016 13:37, ej...@st-andrews.ac.uk
>
> Hi Eric, hi listfolk,
>
> I think there was a bug in how the histogram was rescaled for the
> point transect pdf case (it was being rescaled when it didn't need
> to be).
>
> Eric: can you try out the new version I've just pushed to github and
> see whether you get something working? Else please send your example
> data to me off-list and I'll take a look and we can report back to
> the list.
>
> You can install the latest version of mrds using the devtools package:
>
> library(devtools)
> install_github("DistanceDevelopment/mrds")
>
> cheers,
> --dave
>
>
> On 12/05/2016 13:37, ej...@st-andrews.ac.uk
> <mailto:ej...@st-andrews.ac.uk> wrote:
>
> Good day,
> Below are simple histograms of some simulated distance data from
> point
> transects.
>
> par(mfrow = c(1,2))
> hist(trunc.dat, main=NULL, probability=TRUE)
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL,
> probability = TRUE)
>
>
>
>
> Note that when I specify "probability = FALSE", I get the
> following plot
> and error message.
>
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL,
> probability = FALSE)
>
> Warning message:
> In plot.histogram(r, freq = freq1, col = col, border = border,
> angle =
> angle, :
> the AREAS in the plot are wrong -- rather use 'freq = FALSE'
>
>
>
>
> When I plot the pdf of detection probability for a model fitted
> to these
> data, the histogram looks like the one where the areas are
> wrong, and
> the line does not match the data.
>
> plot(fit.hn <http://fit.hn>, pdf = T)
>
> Good day,
> Below are simple histograms of some simulated distance data from
> point
> transects.
>
> par(mfrow = c(1,2))
> hist(trunc.dat, main=NULL, probability=TRUE)
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL,
> probability = TRUE)
>
>
>
>
> Note that when I specify "probability = FALSE", I get the
> following plot
> and error message.
>
> hist(trunc.dat, breaks = c(1,4,7,10,15), main = NULL,
> probability = FALSE)
>
> Warning message:
> In plot.histogram(r, freq = freq1, col = col, border = border,
> angle =
> angle, :
> the AREAS in the plot are wrong -- rather use 'freq = FALSE'
>
>
>
>
> When I plot the pdf of detection probability for a model fitted
> to these
> data, the histogram looks like the one where the areas are
> wrong, and
> the line does not match the data.
>
>
>
> The simple fix recommended for the histogram doesn't work with
> plot.ds().
>
> plot(fit.hn <http://fit.hn>, pdf = T, freq=FALSE)
>
> The simple fix recommended for the histogram doesn't work with
> plot.ds().
>
>
> Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab =
> ylab, main
> = "", :
> formal argument "freq" matched by multiple actual arguments
>
> Any ideas why plot.ds is produces a histogram that is apparently
> wrong
> behind the line for the fitted pdf, or other ways to produce an
> accurate
> plot?
>
> Thanks,
> Eric
>
>
>
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "distance-sampling" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to distance-sampl...@googlegroups.com
> <mailto:distance-sampling%2Bunsu...@googlegroups.com>
> Error in plot.histogram(hh, ylim = ylim, xlab = xlab, ylab =
> ylab, main
> = "", :
> formal argument "freq" matched by multiple actual arguments
>
> Any ideas why plot.ds is produces a histogram that is apparently
> wrong
> behind the line for the fitted pdf, or other ways to produce an
> accurate
> plot?
>
> Thanks,
> Eric
>
>
>
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "distance-sampling" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to distance-sampl...@googlegroups.com
> <mailto:distance-sampl...@googlegroups.com
> <mailto:distance-sampling%2Bunsu...@googlegroups.com>>.
> To post to this group, send email to
> distance...@googlegroups.com
> <mailto:distance...@googlegroups.com>
> <mailto:distance...@googlegroups.com
> distance...@googlegroups.com
> <mailto:distance...@googlegroups.com>
Eric Howe
May 18, 2016, 1:32:43 PM5/18/16
to David Lawrence Miller, distance-sampling
Dear David and list members,
With the new default settings for ylim in plot.ds(), the probability density curve fit within the plot area. I also tried setting my own ylim values and that worked as well. Much appreciated!Reply all
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