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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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Question about updating mh.ratio
#97
gtng92
closed
7 years ago
1
Decide on specification scheme for distance functions
#96
ArtPoon
closed
7 years ago
1
Direct-descendant particles are not perturbed to new values
#95
ArtPoon
closed
7 years ago
4
Kaphi implementation of cophenetic causes error
#94
MathiasRenaud
closed
7 years ago
3
Overestimating beta parameter value for compartmental (SIR) models
#93
gtng92
closed
7 years ago
5
run.smc breaks when ws$weights are assigned to NaN value
#92
gtng92
closed
7 years ago
8
Write YAML specification documentation
#91
ArtPoon
closed
7 years ago
1
Drop particles where mu is greater than lambda (speciation models)
#90
MathiasRenaud
closed
7 years ago
3
Extra attributes in simulate.binary.dated.tree.fgy output uses a lot of space
#89
gtng92
closed
7 years ago
1
If NA is returned by one of the measures used, the final value is coerced to NA
#88
MathiasRenaud
closed
7 years ago
1
Some tree statisitic functions have incompatible outputs
#87
MathiasRenaud
closed
7 years ago
22
Quantile is not allowing the plotting of Ne.tau
#86
0ldM4j0r
closed
7 years ago
2
Implement Tree Comparison Metrics from Kuhner & Yamato paper
#85
MathiasRenaud
closed
6 years ago
18
.preprocess.tree crashes when the tree is labelled
#84
0ldM4j0r
closed
7 years ago
6
Attempting fresh install throws igraph exception
#83
gtng92
closed
7 years ago
2
Malformed newick error when running `run.smc` with >100 particles
#82
MathiasRenaud
closed
7 years ago
16
Confirm that if we rescale trees, it is not possible to estimate Yule model lambda
#81
ArtPoon
closed
7 years ago
2
Validate parameter identifiabiltiy by speciation models
#80
MathiasRenaud
closed
7 years ago
8
Retesting cast of simulate.binary.dated.tree.fgy output to phylo object
#79
gtng92
closed
7 years ago
9
Consistent style
#78
ArtPoon
closed
7 years ago
0
Shiny: Generating a selectInput from a list of lists goes directly to the deepest layer
#77
0ldM4j0r
closed
7 years ago
2
ws$sim.trees contains integers, not tree objects after run.smc is finished
#76
MathiasRenaud
closed
7 years ago
7
Acceptance rate becomes zero after one iteration with Yule model.
#75
MathiasRenaud
closed
7 years ago
2
Populate Shiny config menu from R list objects
#74
ArtPoon
closed
7 years ago
2
Are the config files to be created on the server or downloaded to the user computer
#73
0ldM4j0r
closed
7 years ago
1
User can't download tree plot with updated dimensions
#72
0ldM4j0r
closed
7 years ago
3
simulate.trees should provide different arguments to config$model
#71
MathiasRenaud
closed
7 years ago
1
Implement a check for malformed Newick tree strings
#70
gtng92
closed
7 years ago
6
Create INSTALL.md documentation for Mac
#69
ArtPoon
closed
7 years ago
2
Plan interface for Shiny app
#68
ArtPoon
closed
7 years ago
1
Install Shiny on development server
#67
ArtPoon
closed
7 years ago
1
Create Kaphi.github.io page
#66
ArtPoon
opened
7 years ago
2
Install Discourse
#65
ArtPoon
closed
7 years ago
0
Make Django app
#64
ArtPoon
closed
7 years ago
0
Select paper for JC that is relevant to using Kaphi speciation/compartmental models
#63
ArtPoon
closed
7 years ago
0
Validate ABC-SMC parameter estimation on speciation models
#62
ArtPoon
closed
7 years ago
15
Unit testing speciation model simulation wrappers
#61
ArtPoon
closed
7 years ago
10
Unit test compartmental model simulations
#60
ArtPoon
closed
7 years ago
3
Add refactored rcolgem code to our organization fork of Erik's code
#59
ArtPoon
closed
6 years ago
3
Require installing additional dependency "inline" for "rcolgem"
#58
gtng92
closed
7 years ago
1
Refactor tree vector parsing to its own generic function in smcConfig.R
#57
ArtPoon
closed
7 years ago
2
Allow user to set model parameters for simulating trees
#56
ArtPoon
closed
7 years ago
1
Configuration settings required to call tree statistics functions
#55
gtng92
closed
7 years ago
12
Correct markdown formatting used in INSTALL.md
#54
0ldM4j0r
closed
7 years ago
1
Unit test for .get.node.heights function in smcWorkspace.R
#53
MathiasRenaud
closed
7 years ago
2
Implement simple compartmental models
#52
ArtPoon
closed
7 years ago
5
Change tips argument for template for simulation function
#51
ArtPoon
closed
7 years ago
1
Implement standard speciation models
#50
ArtPoon
closed
7 years ago
5
Check if nLTT statistic actually works
#49
ArtPoon
closed
6 years ago
1
Refactor R code so that non-user functions have dot prefix
#48
ArtPoon
closed
7 years ago
7
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