StatSVN - Directory src/dr/geo/

[root]/src/dr/geo

cartogram (1 files, 23 lines)

contouring (8 files, 1612 lines)

distributions (4 files, 92 lines)

math (3 files, 467 lines)

operators (2 files, 219 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	179 (100.0%)	11688 (100.0%)	65.2
alexei.drummond	100 (55.9%)	9239 (79.0%)	92.3
msuchard	43 (24.0%)	1886 (16.1%)	43.8
philippe.lemey@gmail.com	18 (10.1%)	336 (2.9%)	18.6
rambaut	14 (7.8%)	214 (1.8%)	15.2
jheled	1 (0.6%)	8 (0.1%)	8.0
dong.w.xie	3 (1.7%)	5 (0.0%)	1.6

Most Recent Commits

msuchard 2012-12-05 12:41 Rev.: 5275

Added transition kernel for disjoint geographic regions

30 lines of code changed in 4 files:

src/dr/geo: GeoSpatialDistribution.java (new), MultiRegionGeoSpatialDistribution.java (+29 -1)

msuchard 2012-09-27 21:22 Rev.: 5177

Extract leaf traits from the compound parameter constructed in an integrated continuous trait likelihood

14 lines of code changed in 1 file:

src/dr/geo: GeoSpatialDistribution.java (+14 -10)

msuchard 2011-03-17 10:51 Rev.: 3878

Tweaks to 2D KDEs.

20 lines of code changed in 2 files:

src/dr/geo: KernelDensityEstimator2D.java (new)

philippe.lemey@gmail.com 2010-12-21 09:34 Rev.: 3761

modifying KernelDensityEstimator2D constructor (that takes a gridsize argument) to set up bandwiths

1 lines of code changed in 1 file:

src/dr/geo: KernelDensityEstimator2D.java (+1 -1)

rambaut 2010-12-08 01:04 Rev.: 3744

Made some arrays final to ensure things weren't being changed

6 lines of code changed in 1 file:

src/dr/geo: KernelDensityEstimator2D.java (+6 -6)

philippe.lemey@gmail.com 2010-10-23 23:35 Rev.: 3667

TimeSlicer update for compatibility with Google Earth 5.2

43 lines of code changed in 2 files:

src/dr/geo: Polygon2D.java (new)

philippe.lemey@gmail.com 2010-10-09 17:20 Rev.: 3622

added a getCentroid method in Polygon2D

21 lines of code changed in 1 file:

src/dr/geo: Polygon2D.java (+21)

rambaut 2010-09-07 10:37 Rev.: 3497

Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.

6 lines of code changed in 12 files:

src/dr/geo: GTOPO30Browser.java (+1 -1), GTOPO30Panel.java (new), GTOPO30RandomWalk.java (new), GTOPO30Tile.java (+1 -1), InhomogeneousRandomWalk.java (+1 -1), VisualizeKMLNumericalProbs.java (new)

msuchard 2010-07-30 06:25 Rev.: 3346

Updating geo-spatial regions for Gibbs sampling

92 lines of code changed in 3 files:

src/dr/geo: GeoSpatialDistribution.java (+24 -18), MultiRegionGeoSpatialDistribution.java (+66), Polygon2D.java (+2 -2)

philippe.lemey@gmail.com 2010-07-19 17:50 Rev.: 3320

adding the ability to consider unions of polygons in GeoSpatialCollection

23 lines of code changed in 2 files:

src/dr/geo: GeoSpatialCollectionModel.java (new)

philippe.lemey@gmail.com 2010-07-19 17:50 Rev.: 3319

adding the ability to consider unions of polygons in GeoSpatialDistribution

17 lines of code changed in 1 file:

src/dr/geo: GeoSpatialDistribution.java (+17 -4)

msuchard 2010-06-30 00:27 Rev.: 3296

Tool for performing KDE using a Gaussian kernel (most standard approach)

1 lines of code changed in 1 file:

src/dr/geo: KernelDensityEstimator2D.java (+1 -1)

philippe.lemey@gmail.com 2010-06-29 11:28 Rev.: 3295

deleting MultiSpatial stuff

136 lines of code changed in 5 files:

src/dr/geo: GeoMultiSpatialCollectionModel.java (del), GeoMultiSpatialDistribution.java (del), GeoSpatialDistribution.java (+1), Polygon.java (new 110), Polygon2D.java (+25)

philippe.lemey@gmail.com 2010-06-29 10:31 Rev.: 3294

extending GeoMultiSpatialDistribution to accomodate arrays of polygons defining a region

0 lines of code changed in 1 file:

src/dr/geo: GeoMultiSpatialDistribution.java (new)

philippe.lemey@gmail.com 2010-06-29 10:29 Rev.: 3293

extending GeoSpatialCollectionModel to accomodate arrays of polygons in a GeoMultiSpatialDistribution defining a region

0 lines of code changed in 1 file:

src/dr/geo: GeoMultiSpatialCollectionModel.java (new)

alexei.drummond 2010-03-08 16:50 Rev.: 3033

Added elevation-based random walks on GTOPO30 maps

171 lines of code changed in 11 files:

src/dr/geo: GTOPO30Browser.java (+1), GTOPO30Panel.java (+67 -6), GTOPO30RandomWalk.java (+48), InhomogeneousRandomWalk.java (+38 -34), KMLRenderer.java (new), Lattice.java (new), Location.java (+4), RateMatrix.java (new 9)

alexei.drummond 2010-03-05 19:45 Rev.: 3024

Further tweaks on GTOPO30 support

118 lines of code changed in 2 files:

src/dr/geo: GTOPO30Browser.java (+79), GTOPO30Panel.java (+39 -12)

alexei.drummond 2010-03-05 15:40 Rev.: 3022

Added initial support for reading, tiling and coloring GTOPO30 digital elevation data

235 lines of code changed in 2 files:

src/dr/geo: GTOPO30Panel.java (+83), GTOPO30Tile.java (+152)

alexei.drummond 2010-02-15 16:25 Rev.: 2917

random walks improvement

9 lines of code changed in 1 file:

src/dr/geo: InhomogeneousRandomWalk.java (+9 -5)

alexei.drummond 2010-02-15 16:12 Rev.: 2916

implemented inhomogeneous random walk from KML-based lattice

355 lines of code changed in 4 files:

src/dr/geo: InhomogeneousRandomWalk.java (+34 -54), IslandLattice.java (new 232), KMLRenderer.java (+74 -1), Lattice.java (+15 -208)

alexei.drummond 2010-02-15 14:56 Rev.: 2914

Use image for rendering, started consolidating viewtransform code in single class

191 lines of code changed in 5 files:

src/dr/geo: KMLRenderer.java (+85), KMLViewer.java (new), Polygon2D.java (+15), ViewTransform.java (new 78)

alexei.drummond 2010-02-15 14:15 Rev.: 2912

LinkedList was horrifically slow in Polygon2D for polygons of >100000 vertices. Added a general KMLViewer...

267 lines of code changed in 7 files:

src/dr/geo: KMLCoordinates.java (+15 -16), KMLViewer.java (+194), Polygon2D.java (+56 -35), VisualizeKMLBrownianBridge.java (+1 -2), VisualizeKMLNumericalProbs.java (+1 -2)

alexei.drummond 2010-02-09 07:02 Rev.: 2898

Further work on geographic diffusion with boundaries

149 lines of code changed in 12 files:

src/dr/geo: NumericalSpaceTimeProbs2D.java (new), SpaceTimeSimulator.java (new), VisualizeBrownianBridge2D.java (-22), VisualizeKMLBrownianBridge.java (+5 -4), VisualizeKMLJointProb.java (+1 -1), VisualizeKMLNumericalProbs.java (+24 -5), VisualizeSpaceTimeSim2D.java (new)

alexei.drummond 2010-02-05 17:47 Rev.: 2895

Class to look at joint geographical diffusion probs

126 lines of code changed in 2 files:

src/dr/geo: VisualizeKMLJointProb.java (+126), VisualizeKMLNumericalProbs.java (-2)

alexei.drummond 2010-02-05 16:59 Rev.: 2894

Better color function for visualizing geographical transition probabilities

12 lines of code changed in 1 file:

src/dr/geo: VisualizeKMLNumericalProbs.java (+12 -4)

alexei.drummond 2010-02-05 15:42 Rev.: 2889

Computing numerical transition probabilities for 2D diffusion with arbitrary well boundaries

555 lines of code changed in 12 files:

src/dr/geo: MultivariateBrownianBridge.java (+1 -1), NumericalSpaceTimeProbs2D.java (+265), Reject.java (new), SpaceTimeRejector.java (+21 -4), SpaceTimeSimulator.java (+5 -5), VisualizeBrownianBridge2D.java (+5 -4), VisualizeKMLBrownianBridge.java (+7 -6), VisualizeKMLNumericalProbs.java (+234), VisualizeSpaceTimeSim2D.java (+4 -3)

alexei.drummond 2010-02-05 09:06 Rev.: 2884

Further work on SpaceTime simulation

474 lines of code changed in 8 files:

src/dr/geo: MultivariateBrownianBridge.java (+25), SpaceTime.java (+48), SpaceTimeRejector.java (+25), SpaceTimeSimulator.java (+92), VisualizeBrownianBridge2D.java (+27 -15), VisualizeKMLBrownianBridge.java (+26 -1), VisualizeSpaceTimeSim2D.java (+231)

alexei.drummond 2010-02-04 13:45 Rev.: 2881

Example reconstructs a phylogeographic path given a three taxa tree with specied end-point locations

58 lines of code changed in 2 files:

src/dr/geo: VisualizeBrownianBridge2D.java (+37 -41), VisualizeKMLBrownianBridge.java (+21 -5)

alexei.drummond 2010-02-04 11:24 Rev.: 2880

Added some cities and fixed the superclass

30 lines of code changed in 3 files:

src/dr/geo: SpaceTime.java (+9 -1), VisualizeBrownianBridge2D.java (+10 -5), VisualizeKMLBrownianBridge.java (+11 -4)

alexei.drummond 2010-02-02 14:57 Rev.: 2870

Alexei and Marc realizing that rejection sampling in 2D map of Europe is difficult: absorptive versus reflective coastlines should give different answers.

187 lines of code changed in 5 files:

src/dr/geo: MultivariateBrownianBridge.java (+11 -6), Reject.java (+27), SpaceTimeRejector.java (+12 -1), VisualizeBrownianBridge2D.java (+73 -15), VisualizeKMLBrownianBridge.java (+64 -8)

msuchard 2010-01-29 16:26 Rev.: 2861

Simple stupid solution to the Italian problem.

25 lines of code changed in 2 files:

src/dr/geo: MultivariateBrownianBridge.java (+20 -7), VisualizeBrownianBridge2D.java (+5 -1)

dong.w.xie 2010-01-29 16:09 Rev.: 2860

Trunk: Maintaining JDK 1.5 compatibility.

4 lines of code changed in 2 files:

src/dr/geo: VisualizeBrownianBridge2D.java (+2 -2), VisualizeKMLBrownianBridge.java (+2 -2)

alexei.drummond 2010-01-29 15:41 Rev.: 2859

Alexei and Marc adding 2-dimensional brownian bridge with rejection-sampling on map of Europe :-)

278 lines of code changed in 4 files:

src/dr/geo: MultivariateBrownianBridge.java (+14 -13), SpaceTime.java (+13), VisualizeBrownianBridge2D.java (+156), VisualizeKMLBrownianBridge.java (+95)

msuchard 2010-01-29 11:08 Rev.: 2856

Refactoring multivariate normal distribution to support nice Brownian bridge features

36 lines of code changed in 1 file:

src/dr/geo: MultivariateBrownianBridge.java (+36 -18)

alexei.drummond 2010-01-29 09:53 Rev.: 2855

Alexei and Marc adding N-dimensional brownian bridge with rejection-sampling!

197 lines of code changed in 5 files:

src/dr/geo: BrownianBridge1D.java (new 91), MultivariateBrownianBridge.java (+65), SpaceTime.java (+23), SpaceTimeRejector.java (+9), SpaceTimeRejector1D.java (new 9)

msuchard 2009-12-24 06:17 Rev.: 2721

Fixed regular polygon parser

112 lines of code changed in 1 file:

src/dr/geo: Polygon2D.java (+112 -70)

philippe.lemey@gmail.com 2009-12-24 04:15 Rev.: 2719

DiscreteRatePriorGenerator tweaks

68 lines of code changed in 1 file:

src/dr/geo: Polygon2D.java (+68 -9)

msuchard 2009-12-15 06:40 Rev.: 2697

Refactoring geo-specific functionality into dr.geo (step 1). Also, adding in shell classes for many different spatial distributions

1 lines of code changed in 2 files:

src/dr/geo: GreatCircleDistances.java (+1 -1)

dong.w.xie 2009-12-10 16:15 Rev.: 2688

Trunk: merge from branch 1.5 in

1 lines of code changed in 1 file:

src/dr/geo: GreatCircleDistances.java (+1 -1)

philippe.lemey@gmail.com 2009-07-31 00:05 Rev.: 1954

Tracer tweaks

2 lines of code changed in 1 file:

src/dr/geo: Polygon2D.java (+2 -2)

(27 more)

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