The flywatch from jefferislab

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Code to analyse movies of flies – principally based on Yoshi Aso's (Janelia) behaviour rig

License: GNU General Public License v3.0

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Integrate Mike's PI_Extractor code

Hi @michaeljohndolan

I added your code to the demo folder – this seemed the most natural place to put what is essentially a script for the moment. Some change was necessary because if the code is placed in the R subdirectory it breaks package load/install (see #1).

However we it might be good to pull out some of the code into separate functions.

Remind me also to show you how to do package development in Rstudio – it's easy to run package Check.

Error during installation

> devtools::install_github(c("jefferislab/flywatch"))
Downloading github repo jefferislab/flywatch@master
Installing flywatch
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  '/private/var/folders/c1/1739134j5xzftpgg3j7h74h80000gw/T/Rtmp4VNZh1/devtools58a533cc7c2/jefferislab-flywatch-1d1f332'  \
  --library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library' --install-tests 

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
* installing *source* package 'flywatch' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'ggplot2' was built under R version 3.2.3
[1] "These are the genotypes to be analysed. Please check for naming errors:"
[1] "ST"
Warning in readTIFF(source = files[j], all = TRUE, as.is = FALSE) :
  TIFFReadDirectory: Unknown field with tag 50838 (0xc696) encountered
Warning in readTIFF(source = files[j], all = TRUE, as.is = FALSE) :
  TIFFReadDirectory: Unknown field with tag 50839 (0xc697) encountered
Error in FUN(X[[i]], ...) : 
  'x' must be an array of at least two dimensions
Error : unable to load R code in package 'flywatch'
ERROR: lazy loading failed for package 'flywatch'
* removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/flywatch'
Error: Command failed (1)

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