e3bo 2015phylo issues - Githubissues

e3bo / 2015phylo

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refactor mle.r to support mansuscript outline

#44 e3bo opened 9 years ago
0
Calculate updated flow matrix based on norm between 2001 matrix and estimated outshipments

#43 e3bo closed 9 years ago
1
Add function to calculate likelihood of saturated model

#42 e3bo opened 9 years ago
1
Discuss how structured coalescent with estimated migration rates could explain observed deviations from exponentiality, and may mask signal of population growth

#41 e3bo opened 9 years ago
0
Study power to reject exponentiality

#40 e3bo closed 9 years ago
0
Determine why branching.times() gives some negatives

#39 e3bo closed 9 years ago
1
Determine if separation of migration and coalescent time scales is consistent with estimates

#38 e3bo closed 9 years ago
1
simulation test of variable selection via cross validation

#37 e3bo opened 9 years ago
0
cross validation to regularization paths on larger set of PEDV predictors

#36 e3bo opened 9 years ago
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create plotting function for cross validation results

#35 e3bo opened 9 years ago
0
Develop additional predictors for pedv data

#34 e3bo opened 9 years ago
0
Try elastic net penalty in optimization

#33 e3bo closed 9 years ago
0
Increase speed of optimization for penalized models

#32 e3bo opened 9 years ago
0
Figure out why multiple cycles of coordinate descent seems not to work very well

#31 e3bo closed 9 years ago
0
Add code to do cross validation

#30 e3bo closed 9 years ago
0
Check that p-values for chi square test are correct

#29 e3bo opened 9 years ago
0
Add code to fit model where coefficients have L1 penalty

#28 e3bo closed 9 years ago
0
Increase simulation R for likelihood ratio tests

#27 e3bo opened 9 years ago
0
Update test of consistency

#26 e3bo opened 9 years ago
0
Calculate likelihood of ancestral states of root node

#25 e3bo opened 9 years ago
0
Try unlinking clocks between S INDEL and non-S INDEL strains

#24 e3bo closed 9 years ago
1
Determine if likelihood ratio test valid when using expected log likelihood over random trees

#23 e3bo closed 9 years ago
1
Get Makefile recipes to kill beast after run is completed

#22 e3bo opened 9 years ago
0
Make publication-quality plot of posterior trees

#21 e3bo closed 9 years ago
0
Sample from priors and compare posterior and prior densities for node heights of INDEL and nonINDEL clades

#20 e3bo closed 9 years ago
2
Try unlinking trees for INDEL and nonINDEL strains

#19 e3bo closed 9 years ago
0
Get XML generation script to update sampling frequency of trees correctly

#18 e3bo closed 9 years ago
1
read and probably cite POTN paper

#17 e3bo opened 9 years ago
0
Create figure of mcc tree

#16 e3bo closed 9 years ago
2
Write down rationale for all choices of priors for BEAST analysis

#15 e3bo closed 9 years ago
4
Check for convergence of BEAST MCMC chains from multiple starting points

#14 e3bo closed 9 years ago
5
Create figure illustrating statistical power vs sample size

#13 e3bo opened 9 years ago
0
Create figure illustrating consistency

#12 e3bo closed 9 years ago
0
Change parameterization so that intercept estimates scaling for branch lengths

#11 e3bo closed 9 years ago
0
Determine if passaged sequences have shared traits that are affecting trees

#10 e3bo closed 9 years ago
2
Compute likelihood over sample of trees from posterior

#9 e3bo closed 9 years ago
0
Determine how errors in numerical derivatives may be causing problems in optimization

#8 e3bo opened 9 years ago
0
Allow variable alphabet length for substitution model, make sure mapping is correct

#7 e3bo closed 9 years ago
0
Check genbank records to see which sequences are from field samples versus experiments

#6 e3bo closed 9 years ago
0
Enforce monophyly of strains with S-INDEL

#5 e3bo closed 9 years ago
0
try fitting tree with relaxed clock

#4 e3bo closed 9 years ago
0
incorporate variable precision of tip dates into beast analysis

#3 e3bo closed 9 years ago
2
Create decent multiple sequence alignment

#2 e3bo closed 9 years ago
1
Decide workflow for drafting writing

#1 e3bo closed 9 years ago
0