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ArtPoon
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kamphir
Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework
BSD 3-Clause "New" or "Revised" License
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Use sequential Monte Carlo instead of MCMC
#52
ArtPoon
opened
8 years ago
0
Reimplement tree shape kernel as C shared library
#51
ArtPoon
opened
8 years ago
3
Subtree kernel may not be positive definite
#50
rmcclosk
opened
9 years ago
0
delimiter + tipdate doesn't work as expected
#49
rmcclosk
opened
9 years ago
0
Rcolgem non-fatal error
#48
rmcclosk
opened
9 years ago
0
Priors don't work
#47
rmcclosk
closed
9 years ago
0
Error in approx()
#46
ArtPoon
closed
9 years ago
5
Maximum recursion depth crash
#45
ArtPoon
closed
9 years ago
4
Getting negative values for coalescent dot-product kernel
#44
ArtPoon
closed
9 years ago
3
Run hangs on OS-X
#43
ArtPoon
opened
9 years ago
0
Bugfix
#42
rmcclosk
closed
9 years ago
1
Stop if a non-ultrametric tree is passed without delimiter+position
#41
rmcclosk
opened
9 years ago
0
Zero division error
#40
rmcclosk
closed
9 years ago
4
Kamphir won't run on cluster
#39
rmcclosk
opened
9 years ago
0
Unit tests and one-deme sims
#38
rmcclosk
closed
9 years ago
0
Implement adaptive MCMC for automatically tuning proposal variances
#37
ArtPoon
opened
9 years ago
0
Implement coalescent times kernel
#36
ArtPoon
closed
9 years ago
0
Possible rcolgem off-by-one error
#35
rmcclosk
opened
9 years ago
0
Don't create an R cluster when ncores = 1
#34
rmcclosk
opened
9 years ago
0
Repeating serialization error
#33
rmcclosk
closed
9 years ago
7
Unit tests and install instructions
#32
rmcclosk
closed
9 years ago
0
New options, logging, install instructions
#31
rmcclosk
closed
9 years ago
1
Missing factor of 2 in kernal computation
#30
rmcclosk
closed
9 years ago
1
using mclapply within rcolgem locking up Kamphir
#29
ArtPoon
opened
9 years ago
11
dill crash on cluster
#28
ArtPoon
opened
9 years ago
2
rcolgem crash
#27
ArtPoon
opened
9 years ago
0
crash in Rcolgem, no trees
#26
ArtPoon
closed
9 years ago
1
rcolgem: Generate sampleStates at respective tip heights
#25
ArtPoon
opened
9 years ago
0
Control-C does not exit kamphir because of multithreading
#24
ArtPoon
opened
9 years ago
0
Implement change point in ODE for rcolgem
#23
ArtPoon
closed
9 years ago
1
Processing large trees is unusually slow
#22
ArtPoon
closed
9 years ago
0
rcolgem: ODE error
#21
ArtPoon
closed
9 years ago
2
rcolgem: Object 'v' not found
#20
ArtPoon
opened
9 years ago
0
Seg fault in rcolgem, memory not mapped
#19
ArtPoon
opened
9 years ago
1
Pickle crash
#18
ArtPoon
closed
9 years ago
2
Time-out tree simulation if MASTER takes too long to simulate trees.
#17
ArtPoon
closed
9 years ago
2
MASTER is extremely slow if requesting exact number of tips
#16
ArtPoon
closed
9 years ago
1
Python not waiting for MASTER to complete
#15
ArtPoon
closed
9 years ago
0
Method validation
#14
ArtPoon
closed
9 years ago
7
Auto-optimization of proposal distribution
#13
ArtPoon
opened
9 years ago
0
IndexError in multiprocessing async_results
#12
ArtPoon
closed
9 years ago
1
pthread_cond_wait: Resource busy
#11
ArtPoon
closed
9 years ago
1
R parallel appears to be only spawning 2 processes in mclapply()
#10
ArtPoon
closed
9 years ago
1
Restore chain from logfile
#9
ArtPoon
opened
9 years ago
0
NewickIO bug
#8
ArtPoon
opened
9 years ago
3
Parallelize kernel computation
#7
ArtPoon
closed
9 years ago
1
Bug in simulate.binary.dated.tree.0 [known issue for rcolgem]
#6
ArtPoon
closed
9 years ago
1
Error in computing make.fgy() in rcolgem
#5
ArtPoon
closed
9 years ago
5
Use prior distributions in calculating kernel score
#4
ArtPoon
closed
9 years ago
2
Allow user to set arbitrary Rscript driver
#3
ArtPoon
closed
9 years ago
1
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