Ecosyste.ms: Issues

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GitHub / epiverse-trace/episoap issues and pull requests

#158 - Severity pipeline: linelist data

Pull Request - State: open - Opened by CarmenTamayo 4 months ago

#157 - Use incidence2 + MASS directly instead of i2extras

Pull Request - State: closed - Opened by Bisaloo 8 months ago

#156 - Remove i2extras usage

Issue - State: closed - Opened by TimTaylor 9 months ago

#155 - Name all code chunks

Pull Request - State: closed - Opened by Bisaloo 9 months ago

#153 - To include all rmd chunks in the reports or not?

Issue - State: open - Opened by CarmenTamayo 10 months ago
Labels: discussion

#152 - Bad visibility of plots in R0 chunk

Issue - State: closed - Opened by CarmenTamayo 10 months ago - 2 comments
Labels: bug

#151 - Template still says that {linelist} isn't used?

Issue - State: closed - Opened by CarmenTamayo 10 months ago - 2 comments

#149 - Add `run_pipeline()` first draft

Pull Request - State: open - Opened by Bisaloo 10 months ago - 4 comments

#148 - Add showtext+sysfonts and required Rmd options

Pull Request - State: closed - Opened by Bisaloo 10 months ago - 2 comments

#146 - Allowed input file types for {episoap}?

Issue - State: closed - Opened by CarmenTamayo 10 months ago - 2 comments
Labels: question

#145 - "i_recent" incidence object

Issue - State: closed - Opened by CarmenTamayo 10 months ago - 1 comment
Labels: question

#144 - Updating transmissibility template

Pull Request - State: closed - Opened by CarmenTamayo 10 months ago - 1 comment

#143 - Update gitignore

Pull Request - State: closed - Opened by CarmenTamayo 10 months ago

#142 - Use tracetheme R package and Epiverse-TRACE fonts

Pull Request - State: closed - Opened by Bisaloo 11 months ago

#141 - Missing info in EpiNow2 chunk

Issue - State: closed - Opened by CarmenTamayo 11 months ago - 4 comments

#139 - Epicurves description in transmissibility report

Issue - State: closed - Opened by CarmenTamayo 11 months ago - 4 comments

#137 - Use linelist data source in transmissibility report

Pull Request - State: closed - Opened by Bisaloo 11 months ago - 2 comments

#136 - Update renv lockfile and drop unused packages

Pull Request - State: closed - Opened by Bisaloo 11 months ago

#135 - Set up spellcheck

Pull Request - State: closed - Opened by Bisaloo 11 months ago

#134 - Address {incidence2} grouped data not working with `EpiNow2::regional_epinow()`

Pull Request - State: closed - Opened by jamesmbaazam 12 months ago - 4 comments

#133 - Install episoap itself in test-reports workflow

Pull Request - State: closed - Opened by Bisaloo 12 months ago - 1 comment

#132 - Get child chunks to work with SI passed as epidist objects

Pull Request - State: closed - Opened by Bisaloo 12 months ago

#131 - replace `EpiNow2::dist_spec()` with `EpiNow2::pmf()` when appropriate

Issue - State: closed - Opened by avallecam about 1 year ago - 1 comment

#130 - update how to plug in `<epidist>` object to `epinow2`

Issue - State: closed - Opened by avallecam about 1 year ago - 4 comments

#128 - `epitrix` dependency - possible to remove?

Issue - State: open - Opened by chartgerink about 1 year ago - 1 comment

#127 - EpiEstim rmd chunk- use of {distcrete}

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 6 comments
Labels: question

#126 - Update Markdown to recommended best practices

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

#125 - Missing reference `Wallinga2007-hw?` in `.bib`

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

#124 - Add system dependency instruction

Pull Request - State: closed - Opened by chartgerink about 1 year ago - 2 comments

#123 - Data preparation for episoap pipelines

Issue - State: open - Opened by CarmenTamayo about 1 year ago - 3 comments
Labels: discussion

#122 - what is the difference between `orderly2` and `episoap`?

Issue - State: closed - Opened by avallecam about 1 year ago - 1 comment

#121 - `git-lfs` dependency not documented

Issue - State: open - Opened by chartgerink about 1 year ago - 1 comment

#120 - Changing content of the output of `episoap` templates

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 12 comments

#119 - Add lint-changed-files GHA workflow

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

#118 - Errors with `regional_epinow`

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 5 comments
Labels: help wanted

#117 - Preparing data for {EpiNow2}

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

#116 - Do not trigger test report CI more than necessary

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

#115 - Extracting parameters on the transmissibility template

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 8 comments

#114 - What to do if parameterised distributions are not on {epiparameter}?

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 4 comments

#113 - Distributions in Rt estimation using {EpiNow2}

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 10 comments

#112 - Creating epidist objects allowing flexibility for distribution parameters

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 13 comments
Labels: help wanted

#111 - Try adding report testing to CI

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

#110 - Remove deprecated select_tags() function

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

#107 - Plotting SI with negative values in {episoap} templates

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 7 comments

#106 - What should the maximum number of parameters on {episoap} templates be?

Issue - State: open - Opened by CarmenTamayo about 1 year ago - 1 comment

#104 - Update .lintr

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

#103 - Update .lintr

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

#102 - Update lockfiles

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

#101 - Add short gifs or videos for the GUI interaction

Issue - State: open - Opened by Bisaloo about 1 year ago - 2 comments
Labels: good first issue, help wanted

#100 - Update {epiparameter} usage

Pull Request - State: closed - Opened by CarmenTamayo about 1 year ago - 11 comments

#99 - Error when knitting template- renv?

Issue - State: closed - Opened by CarmenTamayo about 1 year ago - 10 comments

#98 - Warn on partial matching in tests & run tests in parallel

Pull Request - State: closed - Opened by Bisaloo over 1 year ago - 1 comment

#97 - {renv} integration (user experience on system requiring source packages)

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

#96 - Provide mechanism to consolidate several pipelines into a single report

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

#95 - Split pipelines as smallest units for a given task

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

#94 - Investigate ggautomap for descriptive statistics pipeline

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

#93 - Add release item reminding to bump episoap versio number

Pull Request - State: closed - Opened by Bisaloo over 1 year ago

#92 - Add missing packages to renv

Pull Request - State: closed - Opened by joshwlambert over 1 year ago - 4 comments

#91 - Use explicit namespacing in reports

Issue - State: open - Opened by jamesmbaazam over 1 year ago - 3 comments
Labels: good first issue, help wanted

#90 - Report not rendering

Issue - State: closed - Opened by joshwlambert over 1 year ago - 2 comments
Labels: bug

#89 - Use a line list as default pipeline data

Issue - State: closed - Opened by joshwlambert over 1 year ago - 3 comments
Labels: good first issue, help wanted

#88 - Add documentation on saving and loading data

Issue - State: open - Opened by joshwlambert over 1 year ago
Labels: documentation

#87 - Download lfs files in pkgdown workflow on push

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#86 - Use Clash Display font for logo

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#85 - Add CFR pipeline

Issue - State: open - Opened by Bisaloo almost 2 years ago
Labels: blocked

#84 - Switch to CRAN version of epiparameter

Issue - State: open - Opened by Bisaloo almost 2 years ago
Labels: blocked

#83 - Broken image path?

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

#82 - Convert POSIXct columns to Date

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#81 - Switch to grateful CRAN version

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#80 - Add Sam in the acknowledgement section for #35

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#79 - Use incidence2 accessor functions or subset columns directly?

Issue - State: open - Opened by Bisaloo almost 2 years ago - 2 comments
Labels: discussion

#78 - Spring cleaning 2023

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#77 - Updates transmissibility report lockfiles and deal with incidence2 breaking changes

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

#76 - Add background to logo

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#75 - Resize logo

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#74 - Add logo file

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#73 - Polish README

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#72 - Add design vignette with section on version management

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#71 - Fix typo

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#70 - Rationalise use of `renv::use()`

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago - 1 comment

#69 - Handling dependencies of skeleton reports

Issue - State: closed - Opened by TimTaylor almost 2 years ago - 9 comments

#68 - Add release checklist bullets

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago - 1 comment

#67 - Add Thibaut as author

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#66 - Pin version of epiparameter

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago - 1 comment

#65 - Fix typo

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#64 - Use epiversetheme

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#63 - Fail on linux specifically

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#62 - Move pkgdown config file to pkgdown/ folder

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#61 - Add data.org as fnd

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago

#60 - Copy new "green" workflows

Pull Request - State: closed - Opened by Bisaloo almost 2 years ago - 1 comment

#59 - Restore workflows

Pull Request - State: closed - Opened by Bisaloo about 2 years ago - 1 comment