xavierdidelot BactDating issues

xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees

https://xavierdidelot.github.io/BactDating

MIT License

79 stars 14 forks source link

issues

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Question–– model selection with pstrict vs. other criteria?

#69 amyecampbell closed 1 month ago
2
Export BactDating object to SPREAD

#68 Leytoncito opened 5 months ago
0
Error in if (log(runif(1)) < l2 - l + dgamma(mu2, shape = 0.001, scale = 1000, : missing value where TRUE/FALSE needed

#67 varunshamanna closed 6 months ago
1
Uncertain error message

#66 MaitiuMarm closed 8 months ago
2
Error to BactDating

#65 STChoudhury closed 9 months ago
3
Question: BactDating usage (one gene)!

#64 maesaar closed 10 months ago
1
the node data on exported plot

#63 chaolv123 closed 1 year ago
1
Error in if (log(runif(1)) < l2 - l + dgamma(mu2, shape = 0.001, scale = 1000, : missing value where TRUE/FALSE needed

#62 appliedmicrobiologyresearch closed 1 year ago
8
Possible for parallel running?

#61 Tonny-zhou closed 1 year ago
1
Error when specifying isolation date intervals

#60 acrespo-virevol closed 1 year ago
1
plotting 95CI for MCMC analysis

#59 drxilu closed 1 year ago
1
t$unrec values are negative or larger than 1

#58 drxilu closed 2 years ago
2
Bacdating not installed on R

#57 krishna1925 closed 2 years ago
1
Is it possibile for providing the outgroup taxa to root the tree?

#56 Tonny-zhou closed 2 years ago
3
#Acquire the estimated time for each node and add time axis when plotting the result tree

#55 QianGuoPKU closed 2 years ago
1
Extract isolation dates from tip labels

#54 amymariecampbell closed 2 years ago
1
ESS values when nbIts increase

#53 snakano0527 closed 2 years ago
4
Title : Error with bactdate : Error in if [...] missing value where TRUE/FALSE needed

#52 fredericQC closed 2 years ago
2
effectiveSize function from coda package cannot read object from

#51 hcc14 closed 2 years ago
1
Help on interpreting results - strenght of temporal signal

#50 andreaniml closed 2 years ago
5
calculation of mutation rate and DIC value

#49 LeonardosMageiros closed 2 years ago
3
Bactdating convergence and root to tip plot

#48 LeonardosMageiros closed 2 years ago
2
Missing dates

#47 LeonardosMageiros closed 2 years ago
2
Question about the strength of signal requirements.

#46 martinastoycheva closed 3 years ago
1
incompatible dimensions

#45 jts1044 closed 3 years ago
1
questions on interpreting results

#44 fengyuchengdu closed 3 years ago
1
Invariant sites for snp tree?

#43 Tonny-zhou closed 3 years ago
3
Incorrect dimensions

#42 furqan915 closed 3 years ago
1
Sigma value 501.000 on multiple runs on same dataset!

#41 maesaar closed 3 years ago
12
Model Comparison

#40 dnanto closed 3 years ago
3
mixedgamma vs mixedcarc model

#39 maesaar closed 3 years ago
12
branch/subtree statistics

#38 fengyuchengdu closed 3 years ago
1
Please Host BactDating on the Anaconda R Channel

#37 dnanto closed 3 years ago
3
seems like the as.mcmc function behaves differently between R versions

#36 fengyuchengdu closed 3 years ago
3
Extracting node height and CI

#35 GonzaloYebra closed 3 years ago
4
Can BactDating run on R3.6.1?

#34 StephanieWLo closed 3 years ago
3
Help wanted: how to inerpret mu?

#33 nbawe closed 4 years ago
4
Root-to-tip R2 value?

#32 nbawe closed 4 years ago
4
How to export BactDating tree to newick?

#31 maesaar closed 4 years ago
2
export to figtree

#30 fengyuchengdu closed 4 years ago
7
95%CI association with tip and node labels?

#29 maesaar closed 4 years ago
2
error after updating to 1.0.9

#28 fengyuchengdu closed 4 years ago
5
Error in if (log(runif(1)) < l2 - l + pratio + qratio) { : missing value where TRUE/FALSE needed

#27 nbawe closed 4 years ago
7
Posterior support values of the result tree?

#26 Tonny-zhou closed 4 years ago
2
pstrict value explanation!

#25 nbawe closed 4 years ago
4
Is it possible to combine different date formats?

#24 maesaar closed 4 years ago
7
Rooted and unrooted trees in BactDating analysis!

#23 nbawe closed 4 years ago
11
Write result tree to nexus

#22 ConstantinV closed 4 years ago
2
export bactdating object to tree

#21 clydeandforth closed 4 years ago
2
estimated substitution rate - no temporal data

#20 clydeandforth closed 4 years ago
3