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AndrewLJackson / SIBER

ellipse and convex hull fitting package for stable isotope data
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Clairification - SIBER works without SIAR?? #57

Closed naalipalo closed 4 years ago

naalipalo commented 4 years ago

Ive had an accident on my computer and had to reload all packages. I did not reload SIAR since your other site says DO NOT USE...except it seems now that SIBER functions do not work. Ive got SIMMR and SIBER on but no SIAR. When I run the script in SIBER, I get to the function standard.ellipse and it tells me:

Error in standard.ellipse(spx[[j]], spy[[j]], steps = 1) : could not find function "standard.ellipse"

?standard.ellipse No documentation for ‘standard.ellipse’ in specified packages and libraries: you could try ‘??standard.ellipse’ ??standard.ellipse

So I am going to load the SIAR package, and hopefully this will fix the issue, but you should note that even though you said SIAR is not being used SIBER is still dependent upon it (it seems). Would running the ellipse library fix this issue instead of SIAR?

AndrewLJackson commented 4 years ago

hi That is very odd. The only instance of code standard.ellipse that I see in the SIBER package is in a file in SIBER/tmp/StandardEllipseCalc.R which is not part of the package build so should never appear.

What version of SIBER have you got installed? Latest is 2.1.4

What function caused that error?

Best wishes Andrew

-- Dr Andrew Jackson, PhD, FTCD Associate Professor Irish Research Council Laureate School of Natural Sciences, Department of Zoology Trinity College Dublin, the University of Dublin Dublin 2, Ireland.

+353 1 896 2728 | a.jackson@tcd.iemailto:a.jackson@tcd.ie Twitter: @yodacomplexhttps://twitter.com/yodacomplex http://www.tcd.ie/Zoology/research/http://www.tcd.ie/Zoology/research/groups/jackson/groups/jackson/

From: naalipalo notifications@github.com Reply to: AndrewLJackson/SIBER reply@reply.github.com Date: Tuesday 14 January 2020 at 21:23 To: AndrewLJackson/SIBER SIBER@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [AndrewLJackson/SIBER] Clairification - SIBER works without SIAR?? (#57)

Ive had an accident on my computer and had to reload all packages. I did not reload SIAR since your other site says DO NOT USE...except it seems now that SIBER functions do not work. Ive got SIMMR and SIBER on but no SIAR. When I run the script in SIBER, I get to the function standard.ellipse and it tells me:

Error in standard.ellipse(spx[[j]], spy[[j]], steps = 1) : could not find function "standard.ellipse"

?standard.ellipse No documentation for ‘standard.ellipse’ in specified packages and libraries: you could try ‘??standard.ellipse’ ??standard.ellipse

So I am going to load the SIAR package, and hopefully this will fix the issue, but you should note that even though you said SIAR is not being used SIBER is still dependent upon it (it seems)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/AndrewLJackson/SIBER/issues/57?email_source=notifications&email_token=AAZLLMANCJPKBSYWXDIUQYDQ5YUMLA5CNFSM4KGZYW4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IGFV4NA, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAZLLMBB7S35TNUMBPO3W73Q5YUMLANCNFSM4KGZYW4A.

naalipalo commented 4 years ago

OK, so I have been working on trying to create a script to run my data through all of this and was given an older script. Also, Ive been watching your siber.elipse pod cast.  It has

for (j in unique(group)){    # Fit a standard ellipse to the data   SE <- standard.ellipse(spx[[j]],spy[[j]],steps=1)     # Extract the estimated SEA and SEAc from this object   SEA[j] <- SE$SEA   SEAc[j] <- SE$SEAc     # plot the standard ellipse with d.f. = 2 (i.e. SEAc)   # These are plotted here as thick solid lines   lines(SE$xSEAc,SE$ySEAc,col=j,lty=1,lwd=3) for coding instructions.  In trying to answer your reply, I just noticed that you loaded the package siar, though it was doing the siber ellipses in it....so that could explain a bunch.Apologize for the confusion. 

~K

On Wednesday, January 15, 2020, 12:26:37 AM AKST, Andrew Jackson <notifications@github.com> wrote:

hi That is very odd. The only instance of code standard.ellipse that I see in the SIBER package is in a file in SIBER/tmp/StandardEllipseCalc.R which is not part of the package build so should never appear.

What version of SIBER have you got installed? Latest is 2.1.4

What function caused that error?

Best wishes Andrew

-- Dr Andrew Jackson, PhD, FTCD Associate Professor Irish Research Council Laureate School of Natural Sciences, Department of Zoology Trinity College Dublin, the University of Dublin Dublin 2, Ireland.

+353 1 896 2728 | a.jackson@tcd.iemailto:a.jackson@tcd.ie Twitter: @yodacomplexhttps://twitter.com/yodacomplex http://www.tcd.ie/Zoology/research/http://www.tcd.ie/Zoology/research/groups/jackson/groups/jackson/

From: naalipalo notifications@github.com Reply to: AndrewLJackson/SIBER reply@reply.github.com Date: Tuesday 14 January 2020 at 21:23 To: AndrewLJackson/SIBER SIBER@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [AndrewLJackson/SIBER] Clairification - SIBER works without SIAR?? (#57)

Ive had an accident on my computer and had to reload all packages. I did not reload SIAR since your other site says DO NOT USE...except it seems now that SIBER functions do not work. Ive got SIMMR and SIBER on but no SIAR. When I run the script in SIBER, I get to the function standard.ellipse and it tells me:

Error in standard.ellipse(spx[[j]], spy[[j]], steps = 1) : could not find function "standard.ellipse"

?standard.ellipse No documentation for ‘standard.ellipse’ in specified packages and libraries: you could try ‘??standard.ellipse’ ??standard.ellipse

So I am going to load the SIAR package, and hopefully this will fix the issue, but you should note that even though you said SIAR is not being used SIBER is still dependent upon it (it seems)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/AndrewLJackson/SIBER/issues/57?email_source=notifications&email_token=AAZLLMANCJPKBSYWXDIUQYDQ5YUMLA5CNFSM4KGZYW4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IGFV4NA, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAZLLMBB7S35TNUMBPO3W73Q5YUMLANCNFSM4KGZYW4A.

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AndrewLJackson commented 4 years ago

Those podcasts and all old code from siar is a very long time out of date as per the github page for SIBER. You can use the podcasts for the concepts which are the same. There are extensive vignettes in SIBER explaining all the current functionality

––––––––––––

Dr Andrew Jackson, PhD, FTCD Associate Professor School of Natural Sciences, Department of Zoology Trinity College Dublin, the University of Dublin Dublin 2, Ireland.

+353 1 896 2728 | a.jackson@tcd.iemailto:a.jackson@tcd.ie

Twitter: @yodacomplexhttps://twitter.com/yodacomplex http://www.tcd.ie/Zoology/research/research/theoretical/AndrewJackson.php

Trinity College Dublin, the University of Dublin is ranked 1st in Ireland and in the top 100 world universities by the QS World University Rankings.

On 15 Jan 2020, at 20:43, naalipalo notifications@github.com wrote:

OK, so I have been working on trying to create a script to run my data through all of this and was given an older script. Also, Ive been watching your siber.elipse pod cast. It has

for (j in unique(group)){

Fit a standard ellipse to the data

SE <- standard.ellipse(spx[[j]],spy[[j]],steps=1)

Extract the estimated SEA and SEAc from this object

SEA[j] <- SE$SEA SEAc[j] <- SE$SEAc

plot the standard ellipse with d.f. = 2 (i.e. SEAc)

These are plotted here as thick solid lines

lines(SE$xSEAc,SE$ySEAc,col=j,lty=1,lwd=3) for coding instructions. In trying to answer your reply, I just noticed that you loaded the package siar, though it was doing the siber ellipses in it....so that could explain a bunch.Apologize for the confusion.

~K

On Wednesday, January 15, 2020, 12:26:37 AM AKST, Andrew Jackson notifications@github.com wrote:

hi That is very odd. The only instance of code standard.ellipse that I see in the SIBER package is in a file in SIBER/tmp/StandardEllipseCalc.R which is not part of the package build so should never appear.

What version of SIBER have you got installed? Latest is 2.1.4

What function caused that error?

Best wishes Andrew

-- Dr Andrew Jackson, PhD, FTCD Associate Professor Irish Research Council Laureate School of Natural Sciences, Department of Zoology Trinity College Dublin, the University of Dublin Dublin 2, Ireland.

+353 1 896 2728 | a.jackson@tcd.iemailto:a.jackson@tcd.ie Twitter: @yodacomplexhttps://twitter.com/yodacomplex http://www.tcd.ie/Zoology/research/http://www.tcd.ie/Zoology/research/groups/jackson/groups/jackson/

From: naalipalo notifications@github.com Reply to: AndrewLJackson/SIBER reply@reply.github.com Date: Tuesday 14 January 2020 at 21:23 To: AndrewLJackson/SIBER SIBER@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [AndrewLJackson/SIBER] Clairification - SIBER works without SIAR?? (#57)

Ive had an accident on my computer and had to reload all packages. I did not reload SIAR since your other site says DO NOT USE...except it seems now that SIBER functions do not work. Ive got SIMMR and SIBER on but no SIAR. When I run the script in SIBER, I get to the function standard.ellipse and it tells me:

Error in standard.ellipse(spx[[j]], spy[[j]], steps = 1) : could not find function "standard.ellipse"

?standard.ellipse No documentation for ‘standard.ellipse’ in specified packages and libraries: you could try ‘??standard.ellipse’ ??standard.ellipse

So I am going to load the SIAR package, and hopefully this will fix the issue, but you should note that even though you said SIAR is not being used SIBER is still dependent upon it (it seems)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/AndrewLJackson/SIBER/issues/57?email_source=notifications&email_token=AAZLLMANCJPKBSYWXDIUQYDQ5YUMLA5CNFSM4KGZYW4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IGFV4NA, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAZLLMBB7S35TNUMBPO3W73Q5YUMLANCNFSM4KGZYW4A.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

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