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PoonLab
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Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Make ECctmc package optional
#47
MathiasRenaud
closed
7 years ago
3
Problems running Kaphi tests
#46
0ldM4j0r
closed
7 years ago
14
problem cloning igraph with fresh clone of repo
#45
ArtPoon
closed
7 years ago
1
allow Kaphi to fit model to more than one tree
#44
ArtPoon
opened
7 years ago
0
Implement skyline coalescent simulator
#43
ArtPoon
opened
7 years ago
2
Validate ABC-SMC estimation for compartmental (SIR) models
#42
ArtPoon
closed
6 years ago
35
Incorporate tree shape statistics into SMC-ABC
#41
ArtPoon
closed
7 years ago
12
Possible for cherries to have label mismatch
#40
ArtPoon
closed
7 years ago
2
Tree kernel requires exact label matches
#39
ArtPoon
opened
7 years ago
1
Write manual .Rd pages
#38
ArtPoon
closed
7 years ago
16
tree simulation code is locking up
#37
ArtPoon
closed
7 years ago
1
.simulate.tree loop terminates early
#36
ArtPoon
closed
7 years ago
8
Mapping `phylo` to `z` is failing
#35
ArtPoon
closed
7 years ago
1
Coalescent events are lower in tree than sample times
#34
ArtPoon
closed
7 years ago
2
Problem simulating tree from RP model
#33
ArtPoon
closed
7 years ago
10
Map edges to ape:phylo edges
#32
ArtPoon
closed
7 years ago
0
Problem with coalescent tree simulation for multiple demes
#31
ArtPoon
closed
7 years ago
0
Store deme migration events in coalescent tree as internal nodes
#30
ArtPoon
closed
7 years ago
1
Unit testing coalescent simulation
#29
ArtPoon
closed
7 years ago
2
Linear interpolation for not-yet-sampled lineages
#28
ArtPoon
closed
7 years ago
0
Port/refactor wrapper function for deSolve
#27
ArtPoon
closed
7 years ago
0
Parallelize SMC routines
#26
ArtPoon
closed
7 years ago
5
In coalescent example, particles are not being resampled
#25
ArtPoon
closed
7 years ago
1
uniroot fails in run.smc
#24
ArtPoon
closed
7 years ago
2
const.coalescent is producing trees with nonsense tip labels
#23
ArtPoon
closed
7 years ago
1
Kernel normalization problem
#22
ArtPoon
closed
7 years ago
10
Unit test failure
#21
ArtPoon
closed
7 years ago
1
Write unit tests for main SMC loop
#20
ArtPoon
closed
7 years ago
4
plot.smc.config should show multiple prior distributions
#19
ArtPoon
closed
7 years ago
3
Merge labeled kernel
#18
brj1
closed
7 years ago
3
R crashes when I run tests/test_kernel.R
#17
brj1
closed
7 years ago
2
R yaml.load_file fails to parse 1e-5 as float in scientific notation
#16
ArtPoon
closed
7 years ago
2
Port bisection solver for updating epsilon from C to R
#15
ArtPoon
closed
7 years ago
2
How are we going to implement prior distributions?
#14
ArtPoon
closed
7 years ago
1
Write unit tests for R_Kaphi_parse_newick
#13
ArtPoon
closed
5 years ago
8
Write Makefile to build newick_parser.h from .l and .y sources
#12
ArtPoon
closed
5 years ago
1
Judy problem
#11
ArtPoon
closed
7 years ago
1
Can't compile igraph
#10
ArtPoon
closed
7 years ago
3
Generate newick_parser.h from .y and .l files
#9
ArtPoon
closed
7 years ago
7
Failing to set C igraph attributes
#8
ArtPoon
closed
7 years ago
0
confirm that branch lengths and topology in igraph object is correctly passed from R to C
#7
ArtPoon
closed
7 years ago
2
Minimize rinterface code but keep acknowledgement and license
#6
ArtPoon
closed
7 years ago
1
Pass an igraph object from R to C
#5
ArtPoon
closed
7 years ago
8
Need R header files (R.h) to compile C extensions for R
#4
ArtPoon
closed
7 years ago
1
compiling igraph from source
#3
ArtPoon
closed
7 years ago
4
Refactor deSolve:ode(method="rk4")
#2
ArtPoon
closed
7 years ago
1
Pass tree as igraph object from R to tree.c:height()
#1
ArtPoon
closed
7 years ago
0
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