PBSmapping Changes
==================
2.59  2008-10-07  Rowan
  - Standardised 'ChangeLog.txt' of PBS packages for viewing in HTML.
	Header lines comprise:  version  date  builder
  - Standardised references section in '*.Rd' files.
  - POSTED ON CRAN.
2.58  2008-08-25  Rowan
  - Modified function '.addLabels()' to NOT allow values in '...' to flow through to 'title()'.
	Conflicts with formal arguments like 'xlab'.
2.57  2008-07-24  Rowan
  - Modified function '.addLabels()' to allow values in '...' to flow through to 'title()'.
  - POSTED ON CRAN.
2.56a  2008-07-23  Jon
  - Modified the vignette and changed the file name to 'PBSmappingIntro'.
2.56  2008-07-16  Rowan
  - Revised 'importShapefile()' and fixed bug when 0-vertex polygons occur.
  - Added '00ReadMe' vignette.
  - Moved User's Guide and 'ChangeLog.txt' to '../inst/doc'.
  - Removed 'gamma' fom 'legalNames' in '.plotMaps'.
2.55  2008-01-22  Rowan
  - Revised 'calcConvexHull()' in PBSmapping.r to use 'chull()' in package grDevices
  - Removed 'calcConvexHull' from PBSmapping.c
  - Removed 'conveHull', 'sortPointList', and 'rightTurn' from polygons.c (and polygons.h).
  - Substituted 'findCells()' for 'findPolys()' in '.PBSfig09()'.
  - Built with R-2.6.1.
  - POSTED ON CRAN.
2.54  2007-10-03  Rowan
  - Updated User's Guide
  - Built with R-2.6.0.
  - POSTED ON CRAN.
2.53  2007-10-01  Nick
  - src/convGSHHS.c: Modified 'importGSHHS (...)' to remove the local variable 's' 
	involved in the call to 'extracGSHHS (...)' in hopes of eliminating a compiler warning.
  - Modified the 'inFileName' argument of  'extracGSHHS (...)' so that the argument is 
	now 'const char *' to elimiate a warning message from the C compiler.
  - R/PBSmapping.R: Modified 'combineEvents (...)' to remove code that supported S-PLUS.
	The code caused a warning message in the R build because R doesn't support the 'unpaste' function.
  - Modified 'importPolys (...)', 'importEvents (...)', and 'importLocs (...)' 
	to change 'T' to 'TRUE' and '=' to '<-'.
  - R/PBSfigs.R: Modified '.initPBS (...)', '.PBSfig05 (...)', and
	'.PBSfig10 (...)' to replace 'T'/'F' with 'TRUE'/'FALSE'.
  - Modified '.initPBS (...)' to replace vectorized (|) with non-vectorized (||) operator.
2.52a  2007-09-30  Nick
  - src/PBSmapping.c: Modified 'void pnpoly (...)' to address a warning message
	about 'limits' being used without initialization.
  - src/convGSHHS.c: Modified 'convGSHHS (...)' to address a warning
	message about C++ style comments and correct a spelling mistake.
  - Modified in various other places to change C++ style comments to C style.
2.52  2007-08-28  Rowan
  - Revised 'makeTopography()' to allow combinations z[x,y] to be NA or duplicated.
	If the latter, values of Z for z[x,y] are summarised using the new argument 'func'.
2.51  2007-07-11  Rowan
  - Revised example code in .\man\makeTopography.Rd (changed "extra" to "Extra" for UNIX compatibility).
  - Changed name of "VERSION.TXT" to "GPChistory.txt" and moved from .\src\ to .\R\inst\Extra.
  - POSTED ON CRAN.
2.50  2007-06-29  Rowan
  - Revised the User's Guide & Rd files. Bumped up version for release.
2.17  2007-06-06  Rowan
  - Changed code for '.PBSfig08()' in .\R\PBSfigs.r to account for new PIDs in revised nepacLLhigh.
  - Removed references to S-PLUS from .\R\PBSfigs.r
  - Revised the UG.
2.16  2007-06-06  Rowan
  - Revised the User's Guide.
  - Checked and revised 'aleutian' bathymetry example for Appendix B.
  - Revised Rd files.
  - Removed the function 'outputGSHHS()' from .\R\PBSmapping.r
2.15  2007-06-04  Rowan
  - Recoded '.fixGSHHSWorld()'
  - Added R code to 'importGSHHS()' to activate argument n (in C, SEXP minVerts is not used).
  - Rebuilt data objects: 'nepacLL', 'nepacLLhigh', 'worldLL', 'worldLLhigh' using DB gshhs_1.5.zip
  - Extracted and removed figure functions from .\R\PBSmapping.r and placed them into file: .\R\PBSfigs.r 
  - Updated the user guide PBSmapping-UG.pdf
  - Removed directory .../inst/GSHHS.
  - Changed the name of 'checkClipLimits()' to '.checkClipLimits()'.
  - Changed names ('polySet', 'polyData', 'eventData', 'locationSet') to
	('PolySet', 'PolyData', 'EventData', 'LocationSet') in .\R\PBSmapping.r.
2.14  2007-05-29  Alex
  - Updated GSHHS C code to read new database format:
	url: gshhs_1.8_src.zip DB: gshhs_1.5.zip from ftp://ftp.soest.hawaii.edu/pwessel/gshhs
2.13  2007-02-14  Alex
  - R/PBSmapping.r: Added 'outputGSHHS()', 'importPolys()', 'importEvents()', 'importLocs()'.
  - src/convGSHHS.c: handles .Call interface
  - man/importGSHHS.Rd: Created documentation
  - man/outputGSHHS.Rd: Created documentation
2.12  2007-02-08  Alex
  - R/PBSmapping.r: Added 'importGSHHS()'.
  - src/convGSHHS.c: Created underlying C code for 'importGSHHS'.
  - man/importGSHHS.Rd: Created documentation
2.11  2007-01-23  Rowan
  - Added two directories under '.../inst':
	GSHHS
	 - Steps to convert GSHHS to PBSmapping format.
	 - Wessel's C-code for converting binary to ASCII.
	 - Boers' code to convert ASCII to PBSmapping.
	 - Boers' code (& Couture-Beil) to clip polygons
	Utils
	 - C-code by Boers and Couture-Beil for 'clipPolys()', 'convUL()', and 'findPolys()'.
  - Changed 'convUL.Rd' to specify that UTM coordinates are in kilometres.
  - Resaved the data files using 'save("data",file="data.rda")'.Compresses binary files more than earlier saves.
2.10b  2007-01-03  Jon
   - Built for R only, with first attempts to remove traces of S-PLUS.
2.10a  2006-11-14  Nick
  - R/PBSmapping.R 'importShapefile()': Eliminated a bug that caused some 
	"reef" shapefiles not to load.  It occurred when no POS entries needed reversing.
2.10  2006-10-02  Nick
  - R/PBSmapping.R: Added argument 'PACKAGE = "PBSmapping"' to all .C() calls.
  - man/contourLines.Rd: Removed (only necessary for S-PLUS).
  - src/gpc.c: Removed "../common/" from #include's.
  - src/PBSmapping.c: Removed "../common/", "../gpc/", and "../mcd" from #include's.
2.09  2006-09-04  Nick
  - RS_Docs/calcArea.Rd: Fixed typo.
  - RS_Docs/dividePolys.Rd: Fixed typo.
  - RS_Docs/calcSummary.Rd: Fixed typo.
  - RS_Docs/importShapefile.Rd: Fixed typo.
  - RS_Docs/pythagoras.Rd: Fixed typo.
  - RS_Docs/calcVoronoi.Rd: Fixed typo.
  - RS_Docs/importShapefile.Rd: Updated to reflect new argument in function.
  - RS_Source/PBSmapping importShapefile(): Added arguments "projection" and "zone".
  - RS_Docs/calcVoronoi.Rd: Updated to reflect the new behaviour where it returns a PolySet matching the limits.
  - RS_Source/PBSmapping '.expandEdges()': Added function to address an issue in 'calcVoronoi()'.
	when points appeared outside of the polygons.
  - 'calcVoronoi()': Updated to use the new function '.expandEdges()' and create a PolySet with the proper extents.
  - POSTED ON CRAN.
2.08g  2006-08-25  Nick
  - RS_Docs/calcVoronoi.Rd: Added comments about setting the "projection" and "zone" attributes.
  - RS_Source/PBSmapping 'calcVoronoi()': No longer uses the attributes "projection" and "zone"
	from the input data set.  Instead, sets "projection" to 1 and "zone" to NULL; these
	values are more appropriate for the result.
2.08f  2006-08-15  Nick
  - RS_Source/PBSmapping '.addCorners()': Cleaned up the code. 
  - 'calcVoronoi()': Cleaned up the code.
2.08e  2006-08-10  Nick
  - C/common/polygons.c 'convexHull()': Fixed a (trivial) bug in 'calcConvexHull()'
	that caused it to produce incorrect (bizarre) results.
  - RS_Source/PBSmapping '.addCorners()': Added function.
2.08d  2006-08-04  Nick
  - RS_Docs/calcVoronoi.Rd: Updated to reflect the removed "close" argument.
  - RS_Source/PBSmapping 'calcVoronoi()': Removed 'close' argument.
2.08c  2006-07-20  Nick
  - RS_Docs/dividePolys.Rd: Minor updates.
  - RS_Docs/combinePolys.Rd: Minor updates.
  - RS_Source/PBSmapping 'addPolys()': Identified and corrected two bugs that caused errors 
	in S-PLUS re: the "colHoles" argument.  One bug involved a difference between R/S-PLUS
	polygon commands, where the S-PLUS version fails when given less than 3 points.
	The other involved the code 'pProps$colHoles[is.na(pProps$colHoles)] <- "transparent"';
	which would convert the 'colHoles' element to a character vector even if it made no replacements.
  - '.insertNAs()': Created function with a similar _purpose_ as the old 'insertNAs()' function 
	in 'addLines()' and 'addPolys()'.  This function replaces it, operates drastically different, and 
	is faster (in one test in R, ~11 seconds for 'plotMap(nepacLLhigh)' compared to ~77 seconds previously).
2.08b  2006-07-19  Nick
  - RS_Docs/calcVoronoi.Rd: Created a better example based on Rowan's code/suggestion.
  - RS_Source/PBSmapping 'calcVoronoi()': Corrected bug where the function would fail 
	when a polygon contained more than two points on a boundary.
2.08a  2006-07-18  Nick
  - RS_Source/PBSmapping '.checkProjection()': Updated error message since it can compare 
	the projection of non-PolySet with that of a plot region.
  - 'addLabels()': Identified and fixed bug where EventData containing a PID/SID column 
	would incorrectly be recognized as PolyData.
  - Removed message when 'fullValidation' == T : (is.EventData, is.LocationSet, is.PolyData, is.PolySet)
  - Added a check for "data frames" to better support conversions between PBS Mapping data types:
	('as.EventData()', 'as.LocationSet()', 'as.PolyData()', 'as.PolySet()').
  - RS_Docs/importShapefile.Rd: Cleaned up documentation and expanded it for clarity.
2.08  2006-07-17  Nick
  - R_Other/DESCRIPTION (Suggests): Removed suggests for 'sp' since not (yet) suggested.
  - RS_Source/PBSmapping '.pbsproj()': Commented out to make release 2.08.
2.07c  2006-07-16  Nick
  - RS_Docs/importShapefile.Rd: Updated to reflect additional argument and ability to import DBFs.
  - RS_Source/PBSmapping (importShapefileDBF): Removed function.
  - 'importShapefile()': Updated function to import DBFs.
2.07b  2006-07-13  Nick
  - RS_Source/PBSmapping 'calcVoronoi()': Added warning for data of an "LL" projection.
  - RS_Docs/calcVoronoi.Rd: Added "close" argument to match code.
  - RS_Source/PBSmapping 'calcVoronoi()': Added argument "close = TRUE".
	When TRUE, calls "closePolys" to close the polygons (i.e., corners).
2.07a  2006-07-10  Nick
  - RS_Source/PBSmapping 'dividePolys()': Created new function.
  - RS_Docs/combinePolys.Rd: Created documentation for new function.
  - RS_Source/PBSmapping 'calcVoronoi()': Added code to add attributes to the result as well as close the polygons.
  - 'combinePolys()': Created new function.
2.07  2006-07-07  Nick
  - RS_Source/PBSmapping 'SpatialPolygons2PolySet()': Commented out to make release 2.07.
  - 'SpatialLines2PolySet()': Commented out to make release 2.07.
  - 'SpatialPoints2EventData()': Commented out to make release 2.07.
  - RS_Docs/importShapefileDBF.Rd: Created.
  - RS_Docs/importShapefile.Rd: Created.
  - RS_Source/PBSmapping '.checkRDeps()': Made hidden by renaming from 'checkRDeps()'; 
	updated other functions to reflect the change.
  - 'importShapefile()': Rewrote so that it depends only on the C code included with  "maptools" and nothing else.
	It's now much faster as it no longer converts to Spatial classes first. It still supports holes for PolySets.
  - 'importShapefileDBF()': Updated/simplified since DBF files contain one record per PID/EID.
	No longer reads in the shapefile to create the indices.
  - RS_Docs/calcConvexHull.Rd: Updated description of "xydata" to improve clarity.
  - RS_Docs/calcVoronoi.Rd: Created.
2.06f  2006-07-06  Nick
  - RS_Source/PBSmapping 'calcVoronoi()': Updated to create a consistent interface with other PBS Mapping functions.
  - 'calcVoronoi()': Resolved issue re: ordering of points.
2.06e  2006-07-05  Nick
  - RS_Source/PBSmapping 'calcVoronoi()': Added preliminary version of new "calcVoronoi" function.
  - RS_Docs/addPolys.Rd: Added "colHoles" argument.
  - RS_Docs/plotPolys.Rd: Added "colHoles" argument.
  - RS_Docs/plotMap.Rd: Added "colHoles" argument.
  - RS_Source/PBSmapping (addPolys): Finished adding a first version of the "colHoles" argument.
  - 'locatePolys()': If a variable named "SID" existed before the call, it would break the function. Fixed.
2.06d  2006-07-04  Nick
  - RS_Source/PBSmapping 'findCells()': Removed final call to 'as.LocationSet()' to 
	improve performance and added code to manually set the class.
  - 'plotMap()': Added "colHoles" argument for hole colours and included it in the call to '.plotMaps()'.
  - 'plotPolys()': Added "colHoles" argument and added it in the call to '.plotMaps()'.
  - '.plotMaps()': Added "colHoles" argument and included it in the call to 'addPolys()'.
  - 'addPolys()': Added "colHoles" argument.
  - '.preparePolyProps()': Simplified the code.
2.06c  2006-06-21  Nick
  - R_Other/DESCRIPTION (Suggests): Added suggests for "foreign",
	"sp", and "maptools" to use the new import functionality.
2.06b  2006-06-19  Nick
  - RS_Source/PBSmapping '.pbsproj()': Created function.
  - 'importShapefile()': Created function.
  - 'SpatialPolygons2PolySet()': Created function.
  - 'SpatialLines2PolySet()': Created function.
  - 'SpatialPoints2PolySet()': Created function.
  - 'importShapefileDBF()': Created function.
  - '.getBasename()': Created function.
2.06a  2006-05-24  Nick
  - C/Makefile: Added code that attempts to detect R < 2.3.0  to account for 
	the new DLL build procedure. No longer defines the CYG_DIR and R_DIR variables;
	instead, it expects them to be set in an environment variable.
  - Added new targets (depR and depCygwin) to check whether the appropriate environment variables are defined.
2.06  2006-05-17  Nick
  - SPLUS6.sh: Added the path to the S-PLUS 6.2 CHAPTER command.
  - RS_Source/PBSmapping '.getGridPars()': Replaced the call to 'identical()' with
	'!is.character(all.equal())' because S-PLUS 2000 lacks an 'identical' function.
  - POSTED ON CRAN.
2.05  2006-05-10  Nick
  - RS_Docs/makeGrid.Rd: Clarified the meaning of 'i' and 'j' in the details section.
	Corrected an off-by-one error with 'm' and 'n' in the details section.
  - RS_Docs/findPolys.Rd: Updated to reflect renaming the 'avg' argument to 'maxRows'.
  - RS_Source/PBSmapping 'findPolys()': Renamed the argument 'avg' to 'maxRows' so that 
	the user can now enter the estimated number of  rows in the output. 
	Behavior is consistent with 'joinPolys()', which has a 'maxVerts' argument.
  - 'findPolys()': Updated the error messages to match the 'maxRows' argument.
  - 'joinPolys()': Updated the error messages to match the 'maxVerts' argument.
  - 'joinPolys()': Removed dead code where it formerly calculated 'outCapacity'.
  - POSTED ON CRAN.
2.04  2004-11-14  Nick
  - Replaced all instances of long with PBSINT to quickly support R's use of 'int' rather than 'long'.
	Will make similar replacements in the dependent files.
  - Checked GPC functions to ensure appropriate types were being passed into the GPC,
	because I won't make similar replacements within that module
  - POSTED ON CRAN.
2.03  2005-06-01  Nick
  - POSTED ON CRAN.
2.02  2004-11-18  Nick
  - POSTED ON CRAN.
2.01  2004-09-22  Nick
  - POSTED ON CRAN.
2.00  2004-08-23  Nick
1.99b  2004-08-16  Nick
  - Moved 'isPolyConvex()' to polygons.c
  - Moved 'nPolyIntersects()' to polygons.c
  - Moved 'isRetrace()' to polygons.c
  - Moved 'linesIntersect()' to polygons.c
1.99a  2004-08-03  Nick
  - Added note to 'isPolyConvex()'
  - POSTED ON CRAN.
1.99  2004-07-29  Nick
  - Updated 'joinPolys()' to use existing PIDs when either 'polysA' or 'polysB' contains only one "generic" polygon
1.98  2004-07-28  Nick
  - Rewrote 'joinPolys()' and added several functions ('gpcOutputPoly()', 'gpcCreatePoly()')
	to support it; the code is much cleaner (and more powerful now).
1.93  2004-07-21  Nick
1.92  2004-07-18  Nick
1.91  2004-07-12  Nick
1.90d  2004-07-05  Nick
  - Renamed 'convexHull()' to 'calcConvexHull()';
	it called 'calcConvexHull()', and renamed this call to 'convexHull()'.
1.90c  2004-06-30  Nick
  - Added 'isConvex()'
  - Added 'nPolyIntersects()'
1.90b  2004-06-29  Nick
  - Added 'isRetrace()' to support 'isIntersecting()'.
  - Added 'lineIntersect()' to support 'isIntersecting()'.
1.90a  2004-06-28  Nick
  - Added 'isIntersecting()' to determine if a polygon is self-intersecting.
1.90  2004-06-22  Nick
1.80  2004-06-21  Nick
  - Changed 'calcArea()' to match new interface for 'calcPolyArea()'; 
	can now return negative areas for holes; substantially simplified function.
1.70  2004-06-18  Nick
  - Removed 'fixPOS()' and 'integrateHoles()'.
1.60  2004-06-17  Nick
  - Cleaning
  - Added 'rollupPolys()' to replace 'fixPOS()' and 'integrateHoles()' - but it does much more than those two.
1.50  2004-06-16  Nick
  - Adjusted paths to #include's
1.40  2004-06-15  Nick
  - Renamed 'integrateHoles()' to 'mergePolys()';
	now merges in all SIDs when specified as well as those representing holes.
  - Fixed huge memory leak and bug in 'joinPolys()' -- the clip polygon wasn't handled correctly.
1.30  2004-06-14  Nick
1.20d  2004-06-10  Nick
  - Gave 'fixPOS()' the ability to update X/Y values so that it can make polygons that follow
	the GIS standards for clockwise/counter-clockwise.
  - Renamed 'calcPolygonArea()' to 'calcPolyArea()'
1.20c  2004-06-09  Nick
  - Performed preliminary memory tests on all functions, and none appeared to have memory leaks.
  - Added 'calcOrientation()' to determine whether vertices are clockwise or counter-clockwise.
1.20b  2004-06-08  Nick
  - Added 'thickenPolys()' (only supports UTM).
1.20a  2004-06-02  Nick
  - Updated 'thinPolys()' to support UTM.
1.20  2004-05-30  Nick
1.10c  2004-05-26  Nick
  - Fixed huge memory leaks in 'joinPolys()'.
  - Added support for all R-accessible functions to interface with MemCheckDeluxe.
1.10b  2004-05-24  Nick
  - Fixed huge bug in 'joinPolys()', where an error would be signalled where one didn't really exist
	(check if all holes were processed was placed in the wrong spot...).
1.10a  2004-05-20  Nick
  - Added 'convexHull()'
1.10  2004-05-16  Nick
1.00e  2004-05-12  Nick
  - Renamed 'clipToPoly()' to 'joinPolys()'.
  - Extensively cleaned up 'joinPolys()' code.
  - Added 'extern gpc_success' to catch errors that occur within GPC.
  - Discovered setjmp.h (setjmp() and longjmp())!!!
	Now I can reliably detect memory allocation errors that occur in GPC!!!
1.00d  2004-05-11  Nick
  - Renamed 'clipPoly()' to 'clipToPoly()'.
1.00c  2004-05-10  Nick
  - Continued use of the Greiner/Hormann polygon clip routine would require accounting for numerous special cases;
	switching to the gpc (General Polygon Clipper) library.
  - Fully implemented an interface to the gpc library (holes and all).
  - We will need to rename the R function from 'clipPoly' to something more intuitive.
1.00b  2004-05-08  Nick
  - Added 'clipPoly()' function to clip a polygon against another polygon.
1.00a  2004-05-04  Nick
  - Added 'thinPolys()' function.
1.00  2004-01-04  Nick
  - Cosmetic changes to the code.
0.99  2003-12-22  Nick
  - Bug fix: previously, 'clip()' assumed that if the first vertex in a polygon was not equal to 1, then the 
	polygon must be a hole; now, it looks at the first two vertices to determine increasing or decreasing order.
0.98  2003-08-15  Nick
  - Renamed functions:
	'ulConv()' --> 'convUL()'
	'locateEvents()' --> 'findPolys()'
	'clipPolys()' --> 'clip()'
0.97  2003-08-14  Nick
  - Fixed bug in 'calcArea()' where polygons with multiple components were not being summed.
0.96  2003-08-05  Nick
  - Fixed epsilon.
0.95  2003-07-27  Nick
  - Rewrote 'closePolys()'
0.94  2003-07-23  Nick
  - Moved 'pointInPolygon' to polygons.c/.h
  - Renamed ulconv.c/.h to conversions.c/.h (in case we add more conversions).
  - Creating a "floating.h" for floating point equality test, etc.
  - Moved 'clipPolygon' to polygons.c/.h
0.93  2003-07-21  Nick
  - Removed 'lines_intersect()' from the file (not used).
  - Moved 'calcPolygonArea' to its own files, polygons.c/.h
  - In time, polygon clipping should be moved to the polygons.c/.h files.
0.92  2003-07-16  Nick
  - Changed the interface to 'fixPOS()' so that it will take floating-point POSs as input.
  - Moved 'fixBound()' to R.
0.91  2003-07-14  Nick
  - Started the change log