Ecosyste.ms: Issues

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GitHub / lamho86/phylolm issues and pull requests

#76 - Update phylolm-methods.Rd

Pull Request - State: closed - Opened by AMBarbosa about 1 month ago

#75 - Update predict.phylolm() to allow na.action argument

Pull Request - State: closed - Opened by AMBarbosa about 1 month ago

#74 - predict.phylolm() returns fewer values when newdata has NAs

Issue - State: closed - Opened by AMBarbosa about 1 month ago - 2 comments

#73 - `predict.phylolm` fails for `phylostep` models

Issue - State: closed - Opened by AMBarbosa about 2 months ago - 1 comment

#72 - phylolm() obscure errors when a predictor has unused levels

Issue - State: open - Opened by AMBarbosa 5 months ago - 2 comments

#71 - phyloglm coefficient=0 P value=1

Issue - State: open - Opened by lfdelzam 6 months ago - 2 comments

#70 - Prediction accounting for phylogenetic

Issue - State: closed - Opened by MorceletL 7 months ago - 1 comment

#69 - trouble interpreting alpha

Issue - State: closed - Opened by reillybren 8 months ago - 1 comment

#67 - Guidance on the visualization of phylolm models

Issue - State: closed - Opened by MarcRieraDominguez about 1 year ago

#66 - Make logLik functions more compatible.

Pull Request - State: closed - Opened by Ax3man about 1 year ago - 1 comment

#65 - logLik method and compatibility with MuMIn functions

Issue - State: closed - Opened by MarcRieraDominguez about 1 year ago - 2 comments

#64 - Compatibility between phylolm and visreg

Issue - State: closed - Opened by MarcRieraDominguez about 1 year ago - 2 comments

#62 - null p-values for logistic phyloglm seem biased?

Issue - State: open - Opened by pbradz over 1 year ago - 1 comment

#61 - Fitting models with REML.

Pull Request - State: closed - Opened by pbastide over 1 year ago - 2 comments

#60 - One-way ANOVA with phylolm

Issue - State: closed - Opened by matthieu-haudiquet almost 2 years ago - 3 comments

#59 - Interpret scale parameter when estimating dispersion in Poisson model

Issue - State: closed - Opened by ashdederich about 2 years ago - 1 comment

#58 - Interpreting alpha in phyloglm

Issue - State: closed - Opened by Madeleinecg about 2 years ago - 1 comment

#57 - Different p-value for same tree with different species sort

Issue - State: closed - Opened by GrRomas over 2 years ago - 3 comments

#56 - nobs and logLik for phyloglm

Issue - State: closed - Opened by dramanica over 2 years ago

#55 - nobs and loglik fixes

Pull Request - State: closed - Opened by dramanica over 2 years ago - 1 comment

#53 - Best practices for phyloglm input phylogeny - ultrametric or not?

Issue - State: open - Opened by marybelsoto over 2 years ago - 2 comments

#52 - 'Both' model selection gives worse results than 'forward'?

Issue - State: closed - Opened by rvosa over 2 years ago - 2 comments

#50 - Phyloglm univariate case: testing for phylogenetic signal

Issue - State: closed - Opened by gcjarvis over 2 years ago - 4 comments

#49 - R-squared and Adjusted R-squared

Issue - State: closed - Opened by paternogbc almost 3 years ago - 3 comments

#48 - Error: two or more sister external edges have length 0, V is singular

Issue - State: closed - Opened by jasminelmah almost 3 years ago - 6 comments

#47 - Sign problem in phyloglmstep and phyloglm results

Issue - State: closed - Opened by yuxin0406 about 3 years ago - 5 comments

#46 - phyloglm troubleshooting

Issue - State: closed - Opened by jakeberv about 3 years ago - 11 comments

#45 - What's the order of residuals in the result of phyloglm?

Issue - State: closed - Opened by yuxin0406 over 3 years ago - 1 comment

#44 - Using models with lambda input.

Issue - State: closed - Opened by Syrph over 3 years ago - 3 comments

#43 - added arguement check.precision in three.point.compute

Pull Request - State: closed - Opened by jboyko over 3 years ago

#42 - sigma2_error bound warning

Pull Request - State: closed - Opened by pbastide over 3 years ago

#41 - Add a `confint` method for `phylolm` objects

Pull Request - State: closed - Opened by pbastide over 3 years ago

#40 - Check that the response is univariate (vector or only one column).

Pull Request - State: closed - Opened by pbastide over 3 years ago

#39 - Handling bounds and starting values for sigma2_error (with tests).

Pull Request - State: closed - Opened by lamho86 over 3 years ago

#38 - Starting values and bounds for `sigma2_error`

Issue - State: closed - Opened by pbastide almost 4 years ago - 3 comments

#37 - predict () does not work with 'phyloglm' object

Issue - State: closed - Opened by rosbakh almost 4 years ago - 1 comment

#36 - Relax dependency on R >= 3.0

Pull Request - State: closed - Opened by jmaspons about 4 years ago - 1 comment

#35 - Minor issue when using my own transformed tree.

Pull Request - State: closed - Opened by jboyko about 4 years ago - 4 comments

#34 - Phylolm functionality with emmeans/emtrends

Issue - State: open - Opened by iausprey over 4 years ago - 1 comment

#33 - Alpha warning when performing phylostep/phyloglmstep

Issue - State: closed - Opened by estherdr over 4 years ago - 1 comment

#32 - phyloglmstep

Pull Request - State: closed - Opened by rvosa over 4 years ago - 2 comments

#31 - phyloglmstep

Issue - State: closed - Opened by rvosa over 4 years ago - 2 comments

#30 - LRT using parametric bootstrap?

Issue - State: closed - Opened by courtiol over 4 years ago - 1 comment

#29 - Back-transformation of phylogenetic logistic regression

Issue - State: closed - Opened by rosbakh almost 5 years ago - 3 comments

#28 - Alpha parameter >50

Issue - State: closed - Opened by matthieu-haudiquet almost 5 years ago - 17 comments

#27 - Residuals check for phyloglm ()

Issue - State: closed - Opened by rosbakh almost 5 years ago - 26 comments

#26 - phylolm results do not match binary.PGLMM results. How to explain that?

Issue - State: closed - Opened by Jigyasa3 about 5 years ago - 3 comments

#25 - fix #24

Pull Request - State: closed - Opened by cecileane over 5 years ago

#24 - How to solve "Error in lenth(taxa_without_data) : could not find function "lenth""

Issue - State: closed - Opened by jeagull over 5 years ago - 2 comments

#23 - match taxa between data and tree

Pull Request - State: closed - Opened by cecileane over 5 years ago

#22 - Post hoc test in phyloglm?

Issue - State: closed - Opened by rosbakh over 5 years ago - 2 comments

#21 - Error when using continuous predictor

Issue - State: closed - Opened by minicola2 over 5 years ago - 9 comments

#20 - Taxon-specific measurement error

Issue - State: open - Opened by wrshoemaker over 5 years ago - 4 comments

#19 - How to explain the phylolm results

Issue - State: closed - Opened by lychen83 over 5 years ago - 1 comment

#18 - Error running phyloglm, number of species

Issue - State: closed - Opened by diogoprov over 5 years ago - 8 comments

#17 - Implement phylogenetic PCA

Issue - State: closed - Opened by jmaspons about 6 years ago - 1 comment

#16 - Add 'BugReports' and update 'URL'

Pull Request - State: closed - Opened by HenrikBengtsson about 6 years ago

#15 - Add r.squared and adj.r.squared to the phylolm result

Pull Request - State: closed - Opened by jmaspons over 6 years ago - 9 comments

#14 - Change bootstrap implementation to future.

Pull Request - State: closed - Opened by Ax3man over 6 years ago - 2 comments

#13 - boot parameter is silently ignored for Poisson glm, and summary yields an error

Issue - State: open - Opened by Ax3man over 6 years ago - 5 comments

#12 - Implement parallel bootstrap to glm (#10)

Pull Request - State: closed - Opened by Ax3man over 6 years ago - 1 comment

#11 - Implement parallel bootstrap to lm (#10).

Pull Request - State: closed - Opened by Ax3man over 6 years ago - 4 comments

#10 - Parallel support for bootstrapping

Issue - State: closed - Opened by Ax3man about 7 years ago - 2 comments

#9 - p-values in exp format for phyloglm

Pull Request - State: closed - Opened by cecileane over 8 years ago

#8 - Added parametric bootstrap for phylolm

Pull Request - State: closed - Opened by yuqing19118 over 8 years ago - 2 comments

#7 - small bug fixes for test of the coalescent on a tree

Pull Request - State: closed - Opened by cecileane over 8 years ago

#6 - examples >5sec not tested for CRAN submission

Pull Request - State: closed - Opened by cecileane almost 9 years ago - 1 comment

#5 - added functions & data examples for TICR test

Pull Request - State: closed - Opened by cecileane almost 9 years ago

#4 - significance in phylolm analysis

Issue - State: closed - Opened by paternogbc almost 9 years ago - 8 comments

#3 - Warning using phyloglm

Issue - State: closed - Opened by paternogbc about 9 years ago - 11 comments

#2 - fixed AIC bug and summary output, phyloglm

Pull Request - State: closed - Opened by cecileane about 9 years ago

#1 - phylostep: added k option and other changes

Pull Request - State: closed - Opened by cecileane about 9 years ago