acope3 RibModelFramework issues

acope3 / RibModelFramework

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Panse ignore positions

#401 acope3 closed 1 month ago
0
Allow independent fitting of mu_phi and s_phi parameters

#400 mikegilchrist opened 5 months ago
0
CHange plotting behavior of LLik and Log PPr to avoid zoom window

#399 mikegilchrist opened 5 months ago
0
Add Selection prior function

#398 mikegilchrist closed 7 months ago
1
With phi segfault 395

#397 acope3 closed 10 months ago
0
Remove code Alex commented out, fix minor bugs related to aa.names an…

#396 mikegilchrist closed 10 months ago
0
Can't run code with obs phi values

#395 mikegilchrist closed 10 months ago
5
Add priors for all parameters and make defining these priors more flexible

#394 acope3 opened 1 year ago
2
Testing Failure when Running ROC's MCMC Object

#393 mikegilchrist opened 1 year ago
0
Minor edits to documentation and gitignore, but ...

#392 mikegilchrist closed 1 year ago
1
tests for writing and loading MCMC objects

#391 ebarne24 closed 1 year ago
0
Additional tweaks to test code

#390 mikegilchrist closed 2 years ago
1
tests for writing and loading MCMC objects

#389 ebarne24 closed 2 years ago
1
saving and loading MCMC object results in loss of first element

#388 mikegilchrist opened 2 years ago
1
Create tests for saving and loading model and parameter objects

#387 mikegilchrist opened 2 years ago
0
Improved vignette

#386 acope3 opened 2 years ago
0
Error in `loadParameterObject` for CRAN version

#385 acope3 opened 2 years ago
1
Add stop codons to analysis

#384 mikegilchrist opened 2 years ago
0
Catching develop up with master

#383 acope3 closed 2 years ago
0
Output sigma 379

#382 acope3 closed 2 years ago
0
Output expected waiting times for PA and PANSE

#381 acope3 opened 2 years ago
0
Add functions for calculating DIC for ROC

#380 acope3 opened 2 years ago
0
Add function to output sigma values from PANSE

#379 acope3 closed 2 years ago
1
Move with.phi functions to parent class Model.cpp

#378 acope3 closed 2 years ago
1
Error when loading first parameter object in a session

#377 mikegilchrist opened 2 years ago
1
Added hook to update DESCRIPTION file after every commit.

#376 mikegilchrist closed 2 years ago
2
updating getExpressionEstimate to resolve issue with numerics being c…

#375 acope3 closed 2 years ago
0
Get expression estimate 370

#374 acope3 closed 2 years ago
0
Diverging from initial conditions with PA/PANSE causes values to start at NA

#373 acope3 opened 2 years ago
0
Deprecate split.serine for initializeParameterObject

#372 acope3 opened 2 years ago
0
fixed gene.assignment typo

#371 mikegilchrist closed 2 years ago
0
Using genome argument in getExpressionEstimates converts numeric to char

#370 mikegilchrist closed 2 years ago
2
Fix set samples

#369 mikegilchrist closed 2 years ago
0
fixed 'end <- trace2' with 'end <- length(trace2)'.

#368 mikegilchrist closed 3 years ago
0
Yet another attempt to fix bug in combineTwoDimensionalTrace

#367 mikegilchrist closed 3 years ago
0
Fix issue with combineTwoDimensionalTrace

#366 mikegilchrist closed 3 years ago
0
Move diag calculations within convergence test

#365 mikegilchrist opened 3 years ago
1
Proposed Change: Adopt Better Adaptive Beahvior for MCMC

#364 mikegilchrist opened 3 years ago
0
std_csp still needed for ROC/FONSE

#363 acope3 opened 3 years ago
0
Bug in AAToCodon?

#362 mikegilchrist opened 3 years ago
2
Update documentation to reflect that CodonTable.cpp is not currently used in production code

#361 acope3 opened 3 years ago
0
Update autocorrelation plots

#360 acope3 opened 3 years ago
0
Don't update std_csp when elongation parameters are fixed

#359 acope3 opened 3 years ago
0
Acceptance Rates of 1 when parameters fixed

#358 acope3 opened 3 years ago
0
fixed a typo in variable name

#357 clandere closed 4 years ago
0
fixed weird mismatch in PA proposal function

#356 clandere closed 4 years ago
0
This is the current version submitted to CRAN

#355 clandere closed 4 years ago
0
Minor edits to labeling of output (as I was trying to ensure Std.Dev is not being divided by anything)

#354 mikegilchrist closed 4 years ago
0
Improve terminology in code and output related to 'step', 'sample' and 'iteration'

#353 mikegilchrist opened 4 years ago
0
Change Behavior: Should return NA when length not a multiple of 3

#352 mikegilchrist opened 4 years ago
1