PoonLab Kaphi issues - Githubissues

PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference

GNU Affero General Public License v3.0

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TripL distance calculation with n random trees

#147 Jigyasa3 opened 3 years ago
0
Reproducing Figure7 from Avino et al paper + grouping the cophylogeny analysis as high or low

#146 Jigyasa3 opened 3 years ago
10
Native R kernel computation is slow

#145 ArtPoon opened 5 years ago
2
test.speciation.model not passing

#144 ArtPoon closed 5 years ago
1
Re-implementation of kernel in native R failing unit tests

#143 ArtPoon closed 5 years ago
1
Broken unit test using R-native tree.kernel()

#142 ArtPoon closed 5 years ago
0
Cannot install Kaphi on cluster (CentOS)

#141 mavino closed 5 years ago
2
Cannot install Kaphi on cluster (CentOS)

#140 mavino closed 5 years ago
1
Clean up branches

#139 ArtPoon closed 4 years ago
1
Problem compiling igraph on Ubuntu 16.04

#138 ArtPoon closed 5 years ago
3
Trip is not working with the BiSSE model

#137 helenhe96 closed 6 years ago
1
Setting \rho without tip labels in tree.kernel() generates strange outputs

#136 ArtPoon opened 6 years ago
1
make configure.ac script

#135 ArtPoon opened 6 years ago
2
normalizing kernels and branch lengths

#134 ArtPoon closed 6 years ago
0
Incorporating binary labels into kernel distance

#133 helenhe96 opened 6 years ago
9
System freezes on running mclapply

#132 ArtPoon opened 6 years ago
1
Computer crashes when using multi-threads on BiSSE model

#131 helenhe96 closed 6 years ago
1
Compiling requires non-CRAN package dependencies

#130 ArtPoon closed 6 years ago
1
Align is not working

#129 mavino closed 6 years ago
2
MAST is slow

#128 ArtPoon closed 6 years ago
12
Incorporating 'k' into TripL implementation and bug in Node.dist implementation

#127 gtng92 closed 6 years ago
0
Look into dropping igraph submodule

#126 ArtPoon closed 5 years ago
34
Note that some distances cannot be used with forward-time simulation

#125 ArtPoon closed 6 years ago
2
Hard code in max number of iterations for SMC run?

#124 gtng92 closed 6 years ago
5
Comprehensive overview of past runs of SIR models using rcolgem vs MASTER frameworks

#123 gtng92 closed 6 years ago
5
Alternative distance metrics back-end formula

#122 gtng92 closed 6 years ago
0
MASTER: regularizing the size of the tree

#121 ArtPoon closed 6 years ago
1
MASTER Newick output tree errors

#120 gtng92 closed 6 years ago
12
MASTER: R abort session from infinite Rejections of end conditions

#119 gtng92 closed 6 years ago
5
'undefined symbol: __gmpz_set_si' when installing Kaphi

#118 kstanski closed 6 years ago
7
Robinson-Foulds distance calculations not consistent with Kuhner-Yamato

#117 ArtPoon closed 6 years ago
4
Need to be running test suite

#116 ArtPoon closed 6 years ago
2
Where is `timefromtips` defined in Kuhner program?

#115 ArtPoon closed 6 years ago
3
Munkres algorithm for Align distance metric

#114 gtng92 closed 6 years ago
3
Generating MASTER replicates

#113 gtng92 closed 6 years ago
2
MASTER simulation distances in .tsv are not being populated

#112 gtng92 closed 6 years ago
4
Align distance metric cannot be zero for both subsets

#111 gtng92 closed 6 years ago
1
Incorporate helpful error messages when MASTER is unable to generate newick/nexus trees

#110 gtng92 closed 6 years ago
2
R cannot read Newick tree file returned from MASTER

#109 gtng92 closed 6 years ago
2
Implement wrapper for MASTER simulations of SI models

#108 ArtPoon closed 6 years ago
2
MASTER simulations producing trees with too many tips

#107 ArtPoon closed 6 years ago
0
Cannot find test.json when compiling Kaphi

#106 0ldM4j0r closed 6 years ago
3
Meaning of attribute 'simulationTime' in XML template for MASTER

#105 gtng92 closed 6 years ago
0
Kernel may not be positive semi-definite for labelled subtrees

#104 ArtPoon opened 6 years ago
4
Stochastic subscript out of bounds error (parallelized run.smc)

#103 gtng92 closed 6 years ago
1
ws$accept hits 0 after first iteration again (for parallelization)

#102 gtng92 closed 6 years ago
7
Validate ABC-SMC parameter estimation on BiSSE model

#101 MathiasRenaud opened 6 years ago
12
Use additional or different tree statistics to fit speciation models (yule, bd)

#100 MathiasRenaud closed 6 years ago
2
Make phyloTop and phangorn optional packages

#99 MathiasRenaud closed 6 years ago
1
Extend speciation model simulation with "relaxed clock"

#98 ArtPoon opened 6 years ago
2