Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bryandmartin/corncob issues and pull requests

#148 - Model failing to converge -- small sample size

Issue - State: open - Opened by cbahern57 over 1 year ago

#147 - plot options- dotplot

Issue - State: open - Opened by AnnaAntonatouPap over 1 year ago - 2 comments

#146 - corncob does not work for continuous covariates, vignette has no examples

Issue - State: open - Opened by AustinLG over 1 year ago - 4 comments

#145 - Output models despite unable to converge

Issue - State: open - Opened by jorondo1 almost 2 years ago

#144 - plot options

Issue - State: open - Opened by jorondo1 about 2 years ago - 1 comment

#143 - differentialTest Error (All models failed to converge)

Issue - State: closed - Opened by SevanEsaian about 2 years ago - 4 comments

#142 - CRAN problem fixes

Pull Request - State: closed - Opened by david-barnett about 2 years ago - 2 comments

#141 - All models failed to converge! with vignette data

Issue - State: closed - Opened by xec-cm about 2 years ago - 6 comments
Labels: urgent

#140 - Update plot_differentialTest.R

Pull Request - State: closed - Opened by gcuster1991 over 2 years ago

#139 - Model not converging

Issue - State: closed - Opened by Auerilas over 2 years ago - 1 comment

#138 - N/A P-Values

Issue - State: closed - Opened by Desorcy91 over 2 years ago - 1 comment

#137 - Dispersion

Issue - State: open - Opened by kmdesorcy over 2 years ago

#136 - Apply Corncob into multi-datasets

Issue - State: open - Opened by Zhujun-zhujun over 2 years ago

#135 - Model does not converge

Issue - State: open - Opened by kmdesorcy over 2 years ago - 1 comment

#134 - `differentialTest` is way to verbose by default now

Issue - State: open - Opened by cdiener over 2 years ago

#132 - multithread computation

Issue - State: closed - Opened by g-antonello over 2 years ago

#130 - contrastsTest issue

Issue - State: closed - Opened by msmcfarlin almost 3 years ago - 1 comment

#129 - differentialTest failing on relatively simple model

Issue - State: open - Opened by mirpie almost 3 years ago - 3 comments

#128 - `differentialTest` fails with `boot = TRUE`

Issue - State: open - Opened by amorris28 almost 3 years ago - 7 comments

#127 - Appropriate use of corncob?

Issue - State: closed - Opened by msmcfarlin about 3 years ago - 2 comments

#126 - Pairwise contrasts

Issue - State: open - Opened by gcuster1991 about 3 years ago - 1 comment

#125 - Add verbosity for differentialTest and suggest `slam`

Pull Request - State: closed - Opened by nickp60 about 3 years ago - 4 comments

#124 - error in demo data

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

#123 - Runs fine w/ Boot = FALSE, error when BOOT = TRUE

Issue - State: open - Opened by eveistswp over 3 years ago - 3 comments

#122 - Change the baseline

Issue - State: closed - Opened by eveistswp over 3 years ago - 6 comments

#121 - model optimization error bbdml and differentialTest

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

#120 - Interpreting beta coefficients for binary co-variates

Issue - State: closed - Opened by mnadim01 over 3 years ago - 1 comment

#119 - Different results under different OS

Issue - State: closed - Opened by ashishdamania over 3 years ago - 4 comments

#118 - Don't have a problem, just a comment

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

#117 - editing bbdml plots

Issue - State: closed - Opened by mtswanson2017 over 3 years ago - 1 comment

#116 - Cannot install the package

Issue - State: closed - Opened by NicolasLouw over 3 years ago - 5 comments

#115 - biased estimation of model parameters?

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

#114 - parallel processing

Issue - State: open - Opened by Midnighter over 3 years ago - 5 comments

#113 - extract model data

Issue - State: open - Opened by Midnighter over 3 years ago - 5 comments

#112 - Error with nesting of abundance models

Issue - State: closed - Opened by mirpie over 3 years ago - 5 comments

#111 - Random effects for individuals ?

Issue - State: closed - Opened by Harithaa-Anandakumar over 3 years ago - 4 comments

#110 - Update install instructions and badges to include CRAN

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

#109 - Ubuntu release can't load phyloseq

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

#108 - Migrate from travis to GitHub Actions, speed up examples

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

#107 - Many ASVs with a high absolute mu but insignificant

Issue - State: closed - Opened by roey-angel over 3 years ago - 9 comments

#106 - edit/fix examples for CRAN

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

#105 - Capitalize DOI and add pipe for CRAN

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

#104 - Documentation revisions for CRAN

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

#103 - Minor tweaks for CRAN compatability

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

#102 - Fix try_only bug

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

#101 - Pull in various minor changes

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

#100 - Differential tests do not recognise groups with zero reads

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

#99 - corncob in CRAN or bioconductor

Issue - State: closed - Opened by Russel88 almost 4 years ago - 3 comments

#98 - waldchisq_test - silently fails when limma is missing

Issue - State: closed - Opened by AdrianS85 about 4 years ago - 2 comments

#97 - continuous covariate

Issue - State: closed - Opened by Ivy-ops about 4 years ago - 1 comment

#95 - Outliers & best practices

Issue - State: closed - Opened by ianartmor about 4 years ago - 1 comment

#94 - Feature request sent via email: prediction intervals

Issue - State: open - Opened by bryandmartin about 4 years ago - 1 comment

#93 - Feature request sent via email: extracting estimates

Issue - State: open - Opened by bryandmartin about 4 years ago - 2 comments

#92 - Error in `differentialTest` when phyloseq is not imported

Issue - State: closed - Opened by mikemc about 4 years ago - 1 comment

#91 - Consider updating package versions when changes are made

Issue - State: closed - Opened by mikemc about 4 years ago - 1 comment

#90 - Fix factor ordering for plots with numeric. Fixes #80

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

#89 - Fixing some old issues

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

#88 - Modify try_only and add full_output

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

#87 - differentialTest seems broken

Issue - State: closed - Opened by cdiener about 4 years ago - 7 comments

#86 - ERROR: compilation failed for package ‘lpSolveAPI’

Issue - State: closed - Opened by Ivy-ops over 4 years ago - 3 comments

#85 - Feature request: Allow `try_only` to define specific taxa to test in `differentialTest()`

Issue - State: closed - Opened by mikemc over 4 years ago - 8 comments
Labels: enhancement

#84 - easy way to get differentialTest() to return full bbdml objects for automatic plotting?

Issue - State: closed - Opened by gzahn over 4 years ago - 3 comments
Labels: enhancement

#83 - Use of `offset()` in formulas to specify fixed coefficients

Issue - State: open - Opened by mikemc over 4 years ago - 3 comments
Labels: enhancement

#81 - At long last, contrasts!

Pull Request - State: closed - Opened by bryandmartin over 4 years ago - 1 comment

#80 - plot.bbdml - reorder functionality can break if factor levels begin with numerals

Issue - State: closed - Opened by gzahn over 4 years ago - 5 comments
Labels: enhancement

#79 - [question] how to get the covariance matrix from a corncob fit

Issue - State: closed - Opened by cdiener almost 5 years ago - 2 comments

#78 - Filter for differential abundance

Issue - State: closed - Opened by kunstner almost 5 years ago - 1 comment

#77 - estimateRA

Pull Request - State: closed - Opened by JacobRPrice almost 5 years ago - 2 comments

#76 - Clear up paragraph in vignette

Pull Request - State: closed - Opened by bryandmartin almost 5 years ago

#75 - (Possible) Vignette correction?

Issue - State: closed - Opened by JacobRPrice almost 5 years ago - 1 comment

#74 - Visualizing corncob output

Issue - State: closed - Opened by kattihorng almost 5 years ago - 4 comments

#72 - Intuition adding covariates in formula

Issue - State: closed - Opened by adriaaula about 5 years ago - 6 comments

#71 - Updates to initializations, testing for proper optimization

Pull Request - State: closed - Opened by bryandmartin about 5 years ago - 1 comment

#70 - corncob and phyloseq objects: invalid class for otu_table

Issue - State: closed - Opened by emilyjunkins about 5 years ago - 10 comments

#69 - Handling taxa/OTUs which have singular Hessian matrices?

Issue - State: closed - Opened by JacobRPrice about 5 years ago - 4 comments

#68 - Adding a contrasts argument

Issue - State: closed - Opened by BrandonDKayser about 5 years ago - 14 comments

#67 - Add differentialTest warning for overspecified models.

Pull Request - State: closed - Opened by bryandmartin about 5 years ago - 1 comment

#66 - Add Dockerfile and reference to hosted Docker image

Pull Request - State: closed - Opened by sminot about 5 years ago - 3 comments

#65 - Issue including co-variate in phi formula but not formula

Issue - State: closed - Opened by nearinj over 5 years ago - 4 comments

#64 - Interpreting Effect Sizes

Issue - State: closed - Opened by nearinj over 5 years ago - 3 comments

#63 - application of corncob to longitudinal data

Issue - State: closed - Opened by slhogle over 5 years ago - 10 comments

#62 - Testing

Pull Request - State: closed - Opened by bryandmartin over 5 years ago - 1 comment

#61 - phyloseq as suggests not depends

Issue - State: closed - Opened by adw96 over 5 years ago - 1 comment
Labels: enhancement, urgent

#59 - Error in trust::trust -- parinit not feasible

Issue - State: closed - Opened by adw96 over 5 years ago - 2 comments

#58 - Testing

Pull Request - State: closed - Opened by bryandmartin over 5 years ago - 1 comment

#57 - Remove term absolute abundances from vignette

Issue - State: closed - Opened by adw96 over 5 years ago - 1 comment

#56 - Fix issue if first model is discriminant

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

#55 - genInits for bstar

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

#54 - Include option to remove sample names in plot

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

#53 - any(phi >= : missing value where TRUE/FALSE needed

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

#52 - Fixing citations for ibd data

Pull Request - State: closed - Opened by bryandmartin over 5 years ago - 2 comments

#51 - Save ibd_phylo using older version

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

#49 - New IBD data, other minor updates

Pull Request - State: closed - Opened by bryandmartin over 5 years ago - 1 comment