Report abundance or total biomass | HTML results

[ejosymart]

1) Is there a way to show the population abundance (or total biomass) with confidence intervals?

2) I updated wham, but the html plot of results only shows the heading (diagnostic, results, etc). I tried with different R versions (3.6.3 to 4.1).

Regards.

[timjmiller]

Hi Josymar,

1. Currently, the only measure of stock size that is generated with plotted confidence intervals is spawning stock biomass.
2. Are you saying when you click on the results heading nothing shows up? If not, are there any error or warning messages when you fitted the wham model or when you use plot_wham_output()? Are there any png files of plots in a directory created in your working directory?

On Mon, Oct 11, 2021 at 6:51 AM Josymar Torrejón-Magallanes < @.***> wrote:

1.

Is there a way to show the population abundance (or total biomass) with confidence intervals? 2.

I updated wham, but the html plot of results only shows the heading (diagnostic, results, etc). I tried with different R versions (3.6.3 to 4.1).

Regards.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/timjmiller/wham/issues/50, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7FMI2SLGEFSGS3KYQLUGK6RBANCNFSM5FX53SJA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

[ejosymart]

Hi Tim,

There was a warning message when I use plot_wham_output().

Warning messages: 1: In min(x) : ningún argumento finito para min; retornando Inf 2: In max(x) : ningun argumento finito para max; retornando -Inf 3: In min(x) : ningún argumento finito para min; retornando Inf 4: In max(x) : ningun argumento finito para max; retornando -Inf

But, there was no problem with png files, I can see all of them inside the "plots_png" file.

The problem is when I use out.type = 'html'. The code runs (with the warning message previously mentioned), creates an "html" file with all the html subfiles (i.e. diagnostics, input_data, etc) but they were black. Also, my browser opens a new tab, displays the headings (home, diagnostics, etc.), but each sub-tab was blank too.

Thanks.

[brianstock-NOAA]

Hi Josymar,

What OS are you using? Can you please share the output of sessionInfo()? I'm guessing you are on Windows and this is a duplicate of https://github.com/timjmiller/wham/issues/42. It's hard for me to troubleshoot because I am on Linux and the html output works fine.

@timjmiller perhaps we should just change the default out.type of plot_wham_output()to be 'png' or 'pdf'?

[timjmiller]

Could you also provide an example script (with any necessary files) that produces the error? I can check on a windows machine.

On Thu, Oct 14, 2021 at 10:03 AM Brian Stock @.***> wrote:

Hi Josymar,

What OS are you using? Can you please share the output of sessionInfo()? I'm guessing you are on Windows and this is a duplicate of #42 https://github.com/timjmiller/wham/issues/42. It's hard for me to troubleshoot because I am on Linux and the html output works fine.

@timjmiller https://github.com/timjmiller perhaps we should just change the default out.type of plot_wham_output()to be 'png' or 'pdf'?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/timjmiller/wham/issues/50#issuecomment-943389176, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7DF3AWUPZR73NLT6FTUG3PKPANCNFSM5FX53SJA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

[timjmiller]

Josymar, see the recent posts to issue #42. Is Firefox your default browser? If so, try opening wham_output.html in Chrome or internet explorer.

[ejosymart]

Hi Tim and Brian,

I was using Firefox in Windows. Now, the html opens for me using Chrome.

Thanks!