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BAStag & FLightR Mac OSX

Geolocator R FLightR BAStag

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#1 emilymck

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Posted 06 April 2016 - 12:43 PM

Hello!

 

I would like to try FLightR (i.e. template fit) method on some of my Intigeo data. I have previously analyzed these tags with GeoLight. 

 

I am following the example posted on GitHub for the Godwits but I run into a problem getting the 'twilight events' file. This actually uses the BAStag package not the FLightR package, but I don't know another way to have my data formatted properly for FLightR. 

 

It seems to be an issue with the interactive plots called by the 'twl' function. Here is the code from the Godwit example as well as the error. 

 

> twl<-preprocessLight(d.lux, threshold, offset = offset,lmax=12)
 
Error in setGraphicsEventEnv(which, as.environment(list(...))) : 
  this graphics device does not support event handling
 
I am using Mac OS X 10.11.3 El Capitan, R version 3.2.4 Very Secure Dishes
 
I have not had any trouble looking at the transitions with GeoLight but it doesn't seem to produce files in the correct format for FlightR. 
 
Thanks for any help!
Emily
 


#2 Eldar

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Posted 07 April 2016 - 04:59 AM

  Hi Emily,

To me you have two separate issues:

  1. BAStag does not work on your machine
  2. You have already used GeoLight to define twilights, so you would like to plug them to FLightR.

First issue is for Mike Sumner (hope he will reply you shortly).

 

For the second I have added a new function to FLightR, try:

# update FLightR
library(devtools)
install_github("eldarrak/FLightR") # note the version
library(FLightR)

# and if you have e.g. raw data as 'd' and GeoLight twilights as gl_twl 
TAGS.twilights<-GeoLight2TAGS<-function (d, gl_twl)
write.csv(TAGS.twilights, file="tmp.csv", quote=FALSE, row.names=FALSE)
Now you should be able to read this file with FLightR
 
PS. I hope you follow fresh FLightR routine from here
  Cheers,
     Eldar


#3 mdsumner

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Posted 07 April 2016 - 08:40 AM

Please try opening the graphics window first with

X11(type = "Xlib")

We have seem this a few times, but not explored in detail.

Cheers, Mike

#4 mdsumner

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Posted 21 April 2016 - 12:37 AM

Also, if you have issues with BAStag (or SGAT) please consider posting direct to the Issues tab on the relevant Github repo

 

i.e. https://github.com/S...n/BAStag/issues

 

I've put this in as something to check out.

 

https://github.com/S...BAStag/issues/4

 

Ultimately we'd like all this to go on in the browser, but that's a year or two away at least. 



#5 emilymck

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Posted 14 July 2016 - 09:09 AM

Unfortunately I am even more stuck than before. 

 

Basically there are 3 ways to edit twilight events: GeoLight, BAStag, and TAGS. None of these are working for me at the moment. 

 

GeoLight's twilightCalc function either won't delete false sunrises (if you open in regular plotting window), or, if I open the graphics window first (i.e., "X11(type = "Xlib")", it  will delete the false transitions when clicked, but it won't advance to the next set of dates, so it's functionally  useless. 

 

I then tried to download BAStag to edit transitions and I run into errors even downloading the package: 

> install_github("SWotherspoon/BAStag")
Downloading GitHub repo SWotherspoon/BAStag@master
Installing BAStag
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD  \
  INSTALL  \
  '/private/var/folders/6v/0c0gs62x0w3brzc073t3r4m40000gn/T/Rtmpsv7jze/devtools57721bc196df/SWotherspoon-BAStag-6348427'  \
  --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests 
 
* installing *source* package ‘BAStag’ ...
** R
** byte-compile and prepare package for lazy loading
Error : object ‘bringToTop’ is not exported by 'namespace:grDevices'
ERROR: lazy loading failed for package ‘BAStag’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BAStag’
Error: Command failed (1)
 
Finally TAGS does not recognize my lux files at all so they cannot be edited there. 
 
Any suggestions would be appreciated. I have the latest version of R, running R studio. 
 
So far my only thoughts are to dig up my old versions of TransEdit and MigrateTech's Intiproc software and try to get that working... 
 
Emily


#6 emilymck

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Posted 14 July 2016 - 09:18 AM

Update, 

 

I've got GeoLight working again. You have to open the quartz window first, by running the line

X11(type = "Xlib")

then you can use the regular click to delete transitions and use a two-finger click on the track-pad to advance (on MacBook Pro). 

 

Still would like to be able to use or at least compare BAStag as this GeoLight function is not very user friendly. 

 

Emily







Also tagged with one or more of these keywords: Geolocator, R, FLightR, BAStag

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