30-Oct-2010,  version 1.6-10
Improved [ and [<- methods. Removed [[ methods

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29-Oct-2010,  version 1.6-9
Introduced sub-setting of Raster* objects with Spatial* objects

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27-Oct-2010,  version 1.6-7
Additional options to linesToRaster (to match polygonsToRaster)
as.matrix implemented for Raster* objects (suggested by Michael Sumner)

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26-Oct-2010,  version 1.6-6
writeRaster now takes optional arguments varname, varunit, longname, xname, yname, zname, zunit, for writing netcdf files (requested by Mario Frasca). 

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25-Oct-2010,  version 1.6-5
Merged 'focalValues' into 'extract' 
Removed 'getValuesExtent', it was a synonym to 'extract(x=Raster, y=extent)' 
Temporary files are now only deleted (at startup of raster) if they are at least 24 hrs old
Generic function 'cut' implemented for Raster objects (suggested by Steven Mosher)
Bug fix in addLayer with RasterBrick (reported by Steven Mosher)

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23-Oct-2010,  version 1.6-4
Fixed bug in reading values from a 2-dimensional netcdf file (no 'time') (reported by Steven Mosher)

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22-Oct-2010,  version 1.6-3
Fixed bug in reading cell values from netcdf file that can not be read into memory (reported by Steven Mosher)

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19-Oct-2010,  version 1.6-2
New generic function 'extract', to replace xyValues, cellValues, lineValues, polygonValues
Improvements to rasterFromXYZ (thanks to Thiago Veloso).

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15-Oct-2010,  version 1.6-1
writeHdr can now write VRT (GDAL virtual raster) header files to accompany .gri files such that these can be viewed in e.g. ArcGIS and QGIS.
Adjustments to calc to allow it to return any number of layers from a computation on a multiple layer object

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6-Oct-2010,  version 1.5-15
netcdf files writing in chunks. 
netcdf create a RasterLayer from a RasterBrick no longer goes to disk (copy parameters in memory)

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4-Oct-2010,  version 1.5-14
raster() now also takes an "image" (a list with x, y and z) argument and coerces it to a RasterLayer

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2-Oct-2010,  version 1.5-13
bug fixes in .readRowsAscii (reported by Manuel Spnola), setMinMax
filenames in Raster objects from working directory now get the full path appended (no errors when the workdir changes)
new functions (under development): morph, morphMerge

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30-Sep-2010,  version 1.5-12
New function lineValues (extract values from Raster* by lines, like polygonValues)
bug fixes: 
projectRaster now works for RasterStack objects
focalFilter now works with a 'filename' argument (bug reported by Bill McCoy)

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25-Sep-2010,  version 1.5-11
Added argument NAvalue to writeRaster to allow to manually set the NA value (flag) when writing to file.

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23-Sep-2010,  version 1.5-10
Added a RasterStackBrick version of 'count'

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21-Sep-2010,  version 1.5-9
Added a RasterStackBrick version of 'flip'

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20-Sep-2010,  version 1.5-8
added functions gain, gain<-, offs, and offs<- to get or set the gain (scale) and offset parameters of a Raster object
fixed bug when creating a RasterLayer from a BIL file that has the coordinates in a world file rather than in the hdr file (reported by Steven Mosher)

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16-Sep-2010,  version 1.5-7
fixed bug when creating a RasterLayer from a SAGA grid file with non-integer resolution (reported by Matthew Landis)

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14-Sep-2010,  version 1.5-6

reclass can now also process a multi-layer Raster object
cover and overlay can now also process mulitple multi-layer Raster objects to return another multi-layer object

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2-Sep-2010,  version 1.5-2

improved speed of gridDistance (JvE)
rasterToPoints can now take a matrix of values and return a brick with layer for each column (suggested by Steven Mosher)
writeRaser (internal saveAs function) takes more care as not to overwrite its own source file, even if overwrite=TRUE

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30-Aug-2010, version 1.5-0

calc now uses rowSums and rowMeans where appropriate, and automatically detects whether these functions are appropriate (suggested by Matteo Mattiuzzi). This is also implemented in stackApply, and improved (automatic detection) in aggregate.
removed functions: 'filename<-', values, copryRasterFile, renameRasterFile, removeRasterFile.
bug fix: RasterBricks sometimes had a link to the filename of the object it was created from in a computation. 

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27-Aug-2010, version 1.4-8

Minor bug fixes in ncdf/brick handling

Bug fixes in dropLayer for a RasterBrick (reported by Steven Mosher)

Added option 'setfileext' (default TRUE) to turn off the automatic setting of the file extension when writing raster files (based on the format). (requested by Jonathan Greenberg)

ext(filename) <- 'x'  now only removes the old extension if it has less than 5 characters (including the dot).

Added arguments to all xyValues methods such that both of the below functions work (before only test1 would work; bug reported by Roman Lustrik)
test1 = function(r, xy, ...) {  return( xyValues(r, xy, ...) ) }
test2 = function(r, xy, buffer, fun) { return( xyValues(r, xy, buffer=buffer, fun=fun) )}

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25-Aug-2010, version 1.4-7

bug fixes: 
writing via gdal did not respond to the 'options' argument (reported by Tom Kurkowski and  Jorrel Aunario)
cellValues (and getValues) bug in ncdf brick fixed. (reported by Steven Mosher)

new function:
stackApply applies a function over sets of layers of a RasterStack/Brick
'hasValues' while 'dataContent' has now been removed. 

improvements:
area now takes na.rm=TRUE and weights=TRUE arguments, and returns a Brick if input is Stack/Brick and na.rm=T (suggested by Steven Mosher). 
as.logical now works for a multi-layer object (suggested by Steven Mosher)

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23-Aug-2010, version 1.4-5

Setting the nodata value with NAvalues now also affects reading of values from netcdf files (suggested by Steven Mosher)
cellStats now returns values per layer (rather than all combined) (suggested by Steven Mosher)
Minor bug fix in rasterToPoints with multi-layer objects (reported by Jon Olav Skoien).
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20-Aug-2010, version 1.4-4

Minor bug fixes in crop (reported by Jon Olav Skoien) and in focalNA (reported by Matteo Mattiuzzi)
Changes in gridDistance to avoid it (igraph) from crashing when using very complex grids.
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14-Aug-2010, version 1.4-2

Added @data@gain and @data@offset slots to Raster* objects and use these when reading values from file
v = v * r@gain + r@offset  (suggestion by Jonathan Greenberg)

It is now possible to do Arith (e.g. addition, multiplication) with a RasterStack or Brick using a vector argument of lenght that equals nlayers(object).
E.g. you can mutliply a RasterStack with 5 layers with vector c(1,3,5,3,1), where indices are matched to layers.

It is also possible to do Arith & Math with mutliple RasterStackBrick objects (as long as nlayers is the same) and with a RasterStack/Brick and a RasterLayer objects.

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4-Aug-2010, version 1.3-10

Expanded sampleRandom by adding a 'cells' and 'extent' argument; 

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3-Aug-2010, version 1.3-9

Switched from RNetCDF to ncdf package for netcdf file support

Added three slots to class BasicRaster
unit='vector' ; to store the unit of the layer(s), e.g. "kg m-2 s-1"
zname='character' ; to store the name of the z (layers) variable, e.g. "time"
zvalue='vector' ; to store the values of the z variable, e.g. the dates corresponding to each later
These slots are now filled for values from netcdf files with "CF" type convention (e.g. cmip), with an attempt to covert "days since" to a Date (coverted to string).
Not yet used in writing, or with other formats

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2-Aug-2010, version 1.3-8

New clump function, now always using igraph (also for large rasters) & minor bug fix

Fixes to subs function (needs more checking)

To allow for better behaviour when using objects derived from Raster* objects (perhaps in other packages), replaced code like
  if (class(x) == 'RasterLayer') 
with
  if (inherits(x, 'RasterLayer'))

Bug fix: error when indexing a RasterStack as in s[1]  (as reported by Kevin Ummel)

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27-July-2010, version 1.3-3
Starting this log