epiverse-trace episoap issues

epiverse-trace / episoap

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates

https://epiverse-trace.github.io/episoap/

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issues

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Use incidence2 + MASS directly instead of i2extras

#157 Bisaloo closed 1 week ago
0
Remove i2extras usage

#156 TimTaylor closed 1 week ago
0
Name all code chunks

#155 Bisaloo closed 2 weeks ago
0
Consider building templates for pipelines explicitly using pipeline software

#154 papsti opened 1 month ago
1
To include all rmd chunks in the reports or not?

#153 CarmenTamayo opened 2 months ago
0
Bad visibility of plots in R0 chunk

#152 CarmenTamayo closed 2 months ago
2
Template still says that {linelist} isn't used?

#151 CarmenTamayo closed 2 months ago
2
ggplot wrapper function that provide their own theme() instructions do not use our default theme

#150 Bisaloo opened 2 months ago
0
Add `run_pipeline()` first draft

#149 Bisaloo opened 2 months ago
4
Add showtext+sysfonts and required Rmd options

#148 Bisaloo closed 2 months ago
2
Plotting errors in transmissibility template due to font change

#147 CarmenTamayo closed 2 months ago
0
Allowed input file types for {episoap}?

#146 CarmenTamayo closed 2 months ago
2
"i_recent" incidence object

#145 CarmenTamayo closed 2 months ago
1
Updating transmissibility template

#144 CarmenTamayo closed 1 month ago
1
Update gitignore

#143 CarmenTamayo closed 2 months ago
0
Use tracetheme R package and Epiverse-TRACE fonts

#142 Bisaloo closed 2 months ago
0
Missing info in EpiNow2 chunk

#141 CarmenTamayo closed 2 months ago
4
Referring to template parameters in the text of the transmissibility report

#140 CarmenTamayo closed 2 months ago
1
Epicurves description in transmissibility report

#139 CarmenTamayo closed 2 months ago
4
Description of serial interval in transmissibility report

#138 CarmenTamayo closed 2 months ago
0
Use linelist data source in transmissibility report

#137 Bisaloo closed 2 months ago
2
Update renv lockfile and drop unused packages

#136 Bisaloo closed 3 months ago
0
Set up spellcheck

#135 Bisaloo closed 3 months ago
0
Address {incidence2} grouped data not working with `EpiNow2::regional_epinow()`

#134 jamesmbaazam closed 2 months ago
4
Install episoap itself in test-reports workflow

#133 Bisaloo closed 4 months ago
1
Get child chunks to work with SI passed as epidist objects

#132 Bisaloo closed 3 months ago
0
replace `EpiNow2::dist_spec()` with `EpiNow2::pmf()` when appropriate

#131 avallecam closed 1 month ago
1
update how to plug in `<epidist>` object to `epinow2`

#130 avallecam closed 4 months ago
4
evaluate to replace `$qf()` by `$q()` to use the output of a discretised function

#129 avallecam closed 3 months ago
1
`epitrix` dependency - possible to remove?

#128 chartgerink opened 4 months ago
1
EpiEstim rmd chunk- use of {distcrete}

#127 CarmenTamayo closed 3 months ago
6
Update Markdown to recommended best practices

#126 chartgerink closed 4 months ago
1
Missing reference `Wallinga2007-hw?` in `.bib`

#125 chartgerink closed 4 months ago
2
Add system dependency instruction

#124 chartgerink closed 4 months ago
2
Data preparation for episoap pipelines

#123 CarmenTamayo opened 5 months ago
3
what is the difference between `orderly2` and `episoap`?

#122 avallecam closed 5 months ago
1
`git-lfs` dependency not documented

#121 chartgerink opened 5 months ago
1
Changing content of the output of `episoap` templates

#120 CarmenTamayo closed 2 months ago
12
Add lint-changed-files GHA workflow

#119 Bisaloo closed 5 months ago
0
Errors with `regional_epinow`

#118 CarmenTamayo closed 2 months ago
5
Preparing data for {EpiNow2}

#117 CarmenTamayo closed 1 month ago
2
Do not trigger test report CI more than necessary

#116 Bisaloo closed 6 months ago
0
Extracting parameters on the transmissibility template

#115 CarmenTamayo closed 4 months ago
8
What to do if parameterised distributions are not on {epiparameter}?

#114 CarmenTamayo closed 5 months ago
4
Distributions in Rt estimation using {EpiNow2}

#113 CarmenTamayo closed 5 months ago
10
Creating epidist objects allowing flexibility for distribution parameters

#112 CarmenTamayo closed 4 months ago
13
Try adding report testing to CI

#111 Bisaloo closed 6 months ago
1
Remove deprecated select_tags() function

#110 Bisaloo closed 6 months ago
0
Distributions for parameters from {epiparameter} vs manual input in transmissibility report

#109 CarmenTamayo opened 6 months ago
10
Allowing flexibility for probability distributions in transmissibility template

#108 CarmenTamayo closed 6 months ago
2