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ScottClaessens
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coevolve
coevolve R package for Bayesian dynamic coevolutionary models using Stan
GNU General Public License v2.0
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`coev_plot_flowfield()` for more than 2 traits
#82
ErikRingen
opened
2 days ago
3
Add `complete_cases` argument
#81
ScottClaessens
closed
4 days ago
1
Build package website using `pkgdown`
#80
ScottClaessens
opened
1 week ago
0
Inform users about missing data imputation and provide option for complete case analysis
#79
ErikRingen
closed
4 days ago
9
adapt_delta = 0.95 by default
#78
ErikRingen
closed
2 weeks ago
0
Increase default adapt_delta
#77
ErikRingen
closed
2 weeks ago
1
Function to save coevolve fits as rds
#76
ErikRingen
opened
2 weeks ago
1
Positive definite warnings
#75
ScottClaessens
opened
2 weeks ago
2
multiPhylo trees with different numbers of internal nodes
#74
ScottClaessens
opened
2 weeks ago
3
Prior specification throws error when trying to set Q_sigma
#73
ErikRingen
closed
2 weeks ago
2
Generation of yrep for predictive checks leaks information
#72
ErikRingen
opened
3 weeks ago
21
Gaussian measurement error
#71
ErikRingen
opened
4 weeks ago
17
Implement log_lik argument
#70
ScottClaessens
closed
1 month ago
0
Implementing the gamma distribution
#69
ScottClaessens
closed
1 month ago
0
Why are autoregressive effects constrained to be negative?
#68
ScottClaessens
closed
1 month ago
2
66 allow coev pred series to accept intervention values
#67
ErikRingen
closed
1 month ago
0
Allow `coev_pred_series()` to accept intervention values
#66
ErikRingen
closed
1 month ago
2
55 fixing drift
#65
ErikRingen
closed
1 month ago
1
55 fixing drift
#64
ErikRingen
closed
1 month ago
0
allow non-intervention values in calculate_theta()
#63
ErikRingen
closed
1 month ago
0
coev_calculate_theta() for non-interventions
#62
ErikRingen
closed
1 month ago
0
Only calculate pointwise log likelihood when `log_lik = TRUE`
#61
ScottClaessens
closed
1 month ago
0
48 function to predict an evolutionary time series given some initial values
#60
ErikRingen
closed
1 month ago
1
`coev_plot_predictive_check()` requires ndraws and tree_id to be declared as integers
#59
ErikRingen
closed
1 month ago
2
Integrate phylo uncertainty by default in coev_plot_predictive_check()
#58
ErikRingen
closed
1 month ago
0
Integration of tree uncertainty into coev_plot_predictive_check()
#57
ErikRingen
closed
1 month ago
4
replace log normal with gamma
#56
ErikRingen
closed
1 month ago
14
Gaussian/student-t responses handle drift incorrectly
#55
ErikRingen
closed
1 month ago
25
Pairs plot of model-implied trait values
#54
ScottClaessens
closed
4 weeks ago
9
Update vignette with multiPhylo and other features
#53
ScottClaessens
opened
1 month ago
2
Require multiPhylo objects to have same number of branches
#52
ScottClaessens
closed
1 month ago
1
Set limits automatically for `coev_plot_delta_theta()`
#51
ScottClaessens
closed
1 month ago
1
#47 Estimated correlated drift by default
#50
ScottClaessens
closed
1 month ago
0
`coev_simulate_coevolution()` with non-zero means and ancestral states
#49
ErikRingen
closed
1 month ago
1
Function to predict an evolutionary time series given some initial values
#48
ScottClaessens
closed
1 month ago
4
Full Q matrices by default
#47
ScottClaessens
closed
1 month ago
4
`coev_plot_predictive_check()` includes NA values represented as -9999
#46
ScottClaessens
closed
1 month ago
1
Full Q matrices by default
#45
erik-ringen
closed
2 weeks ago
1
Including multiPhylo objects
#44
ScottClaessens
closed
1 month ago
0
Choice of covariance kernels for distance GPs
#43
ScottClaessens
closed
1 month ago
4
`coev_plot_delta_theta()` should produce smoother posterior distributions
#42
ScottClaessens
closed
1 month ago
1
`coev_fit()` accepts trees when some edge lengths = 0 then fails to converge
#41
ScottClaessens
closed
1 month ago
1
Axis limits and fill colour for `coev_plot_selection_gradient()` and `coev_plot_flowfield()`
#40
ScottClaessens
closed
1 month ago
1
Restrict to rooted trees
#39
ScottClaessens
closed
2 months ago
1
What are the default priors?
#38
adrianjaeggi
closed
2 months ago
2
Produce warning when random effects / Gaussian processes are added to the model
#37
ScottClaessens
closed
2 months ago
1
Additional information in documentation
#36
ScottClaessens
closed
2 months ago
2
Further help for users about integer and ordered factors
#35
ScottClaessens
closed
2 months ago
1
Tibbles not accepted
#34
ScottClaessens
closed
2 months ago
1
Print error message if tree has no branch lengths
#33
ScottClaessens
closed
2 months ago
1
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