Calibfit

[BEN JEMAA HSAN]

Good evening Alexandre,
I still have problems in the calibfit command, as I am working on feather samples from migratory gateways that are passing through the sample site so I cannot have their isotopic signatures in this site so I cannot calibrate my data.

[Alexandre Courtiol]

Well, this is indeed problematic.

How do you expect to assign birds without information on sedentary individuals?

This is not an IsoriX issue, but I think a general requirement to perform any assignments using any method (isotope based or not).

Some people do use calibration published by others, so your way out would be to have access to such datasets.

You need, ideally, isotopic data from the same species, in the same physiological state, with the same ages, sampled at the same time as when you bird took off, and from the same areas than your candidate areas.

You also need several data point per locations.

Those data should also have been measured in the same fashion in the lab (same protocol, same isotopes, same standard...).

The more you depart from this ideal situation, the further from the truth your assignment will be.

It is difficult to collect or get such data, but calibration is the bread and butter of assignments.

[BEN JEMAA HSAN]

Hello, it's not isorix's fault . Maybe I'll use other calibration curves . thank you Alexandre

[BEN JEMAA HSAN]

Hi , Alex

sorry about my multiple questions, I want to talk about getelev () because I couldn't download the gmted2010_30mn.tif file

> getelev(path = Users/hssan/Desktop/Thése/isorix, overwrite = FALSE, verbose = TRUE)
[1] the function attempts to download gmted2010_30mn.tif from internet
Error in downloadfile(address = address_elev, filename = filename_elev,  :
  object 'Users' not found

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[Alexandre Courtiol]

Hi,

Your path must be wrong. If you are using Windows, I would recommend to use:

getelev(path = choose.dir(), overwrite = FALSE, verbose = TRUE)

That should let you define the path using menus instead of typing it.

++

[BEN JEMAA HSAN]

  Hi, i m having the same problem with getelev () , despite i use raster lattice sp isorix packages and i defined my path with menu..

getelev(path = choose.dir(), overwrite = FALSE, verbose = TRUE)

1] the function attempts to download gmted2010_30mn.tif from internet

trying URL 'http://62.141.164.7/donload/gmted2010_30mn.tif'

Error in  utils :: download.file(address , destfile = complete_path, mode = "wb")

cannot open URL 'http://62.141.164.7/donload/gmted2010_30mn.tif'

IN addition;warning message

Error in  utils :: download.file(address , destfile = complete_path, mode = "wb")

internet0pnUrl failed: 'Impossible d'établir une connexion avec le serveur'

[Alexandre Courtiol]

Not the same problem at all, now the function is trying to download, so you got the path thingy right!

This time the issue does not seem to be on your side, it seems that the server hosting the file is down...

Try to download the file from here instead: https://www.dropbox.com/s/5rpzqv55hq61ust/gmted2010_30mn.tif?dl=0

Do it directly outside R.

Let me know how this goes! (I will email the people managing the server hosting the file!)

[BEN JEMAA HSAN]

Thank you for your answer i will try this tomorrow

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[BEN JEMAA HSAN]

Hi Alex , it s good for raster (), then i run the command for building isoscape , after 7 hours :

> preyscape <- isoscape(raster = Elevprey, isofit = preysfit)
[1] Building the isoscapes...
[1] (this may take a while)
  |==========================================================================| 100%
[1] predictions for all 22206744 locations have been computed in 17351 sec.
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning messages:
1: In .warn_pw(object) :
  Prior weights are not taken in account in residVar computation.
2: In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'C:/Users/hssan/AppData/Local/Temp/RtmpEn0s8t/rs-graphics-af3469a5-5529-47f1-8f6b-da627a80715e/bebbca73-9cc3-41b9-a378-c04f22c5f024.snapshot', probable reason 'No such file or directory'
Graphics error: Plot rendering error

[Alexandre Courtiol]

Hi again,

Here the golden rule is too always start with a low resolution isoscape so that if something is not right you notice after 30 seconds and not 17351.

Once you make it work, then increase the resolution.

I think the issue here as nothing to do with IsoriX.

I am afraid that this discussion is not getting interested for all the people in this group.

The mailing list is for general issues and discussions, but you seem to bump into a wall at each step (which can happen, no judgement).

So before people pull out from this list, I propose to continue directly in private: please email me at cour...@izw-berlin.de

So please email me there and I'll do my best to sort you out!

++