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epiverse-trace
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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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Use incidence2 + MASS directly instead of i2extras
#157
Bisaloo
closed
3 months ago
0
Remove i2extras usage
#156
TimTaylor
closed
3 months ago
0
Name all code chunks
#155
Bisaloo
closed
3 months ago
0
Consider building templates for pipelines explicitly using pipeline software
#154
papsti
opened
4 months ago
1
To include all rmd chunks in the reports or not?
#153
CarmenTamayo
opened
5 months ago
0
Bad visibility of plots in R0 chunk
#152
CarmenTamayo
closed
5 months ago
2
Template still says that {linelist} isn't used?
#151
CarmenTamayo
closed
5 months ago
2
ggplot wrapper function that provide their own theme() instructions do not use our default theme
#150
Bisaloo
opened
5 months ago
0
Add `run_pipeline()` first draft
#149
Bisaloo
opened
5 months ago
4
Add showtext+sysfonts and required Rmd options
#148
Bisaloo
closed
5 months ago
2
Plotting errors in transmissibility template due to font change
#147
CarmenTamayo
closed
5 months ago
0
Allowed input file types for {episoap}?
#146
CarmenTamayo
closed
5 months ago
2
"i_recent" incidence object
#145
CarmenTamayo
closed
5 months ago
1
Updating transmissibility template
#144
CarmenTamayo
closed
4 months ago
1
Update gitignore
#143
CarmenTamayo
closed
5 months ago
0
Use tracetheme R package and Epiverse-TRACE fonts
#142
Bisaloo
closed
5 months ago
0
Missing info in EpiNow2 chunk
#141
CarmenTamayo
closed
5 months ago
4
Referring to template parameters in the text of the transmissibility report
#140
CarmenTamayo
closed
5 months ago
1
Epicurves description in transmissibility report
#139
CarmenTamayo
closed
5 months ago
4
Description of serial interval in transmissibility report
#138
CarmenTamayo
closed
5 months ago
0
Use linelist data source in transmissibility report
#137
Bisaloo
closed
5 months ago
2
Update renv lockfile and drop unused packages
#136
Bisaloo
closed
6 months ago
0
Set up spellcheck
#135
Bisaloo
closed
6 months ago
0
Address {incidence2} grouped data not working with `EpiNow2::regional_epinow()`
#134
jamesmbaazam
closed
5 months ago
4
Install episoap itself in test-reports workflow
#133
Bisaloo
closed
7 months ago
1
Get child chunks to work with SI passed as epidist objects
#132
Bisaloo
closed
7 months ago
0
replace `EpiNow2::dist_spec()` with `EpiNow2::pmf()` when appropriate
#131
avallecam
closed
4 months ago
1
update how to plug in `<epidist>` object to `epinow2`
#130
avallecam
closed
7 months ago
4
evaluate to replace `$qf()` by `$q()` to use the output of a discretised function
#129
avallecam
closed
7 months ago
1
`epitrix` dependency - possible to remove?
#128
chartgerink
opened
7 months ago
1
EpiEstim rmd chunk- use of {distcrete}
#127
CarmenTamayo
closed
6 months ago
6
Update Markdown to recommended best practices
#126
chartgerink
closed
7 months ago
1
Missing reference `Wallinga2007-hw?` in `.bib`
#125
chartgerink
closed
7 months ago
2
Add system dependency instruction
#124
chartgerink
closed
7 months ago
2
Data preparation for episoap pipelines
#123
CarmenTamayo
opened
8 months ago
3
what is the difference between `orderly2` and `episoap`?
#122
avallecam
closed
8 months ago
1
`git-lfs` dependency not documented
#121
chartgerink
opened
8 months ago
1
Changing content of the output of `episoap` templates
#120
CarmenTamayo
closed
5 months ago
12
Add lint-changed-files GHA workflow
#119
Bisaloo
closed
8 months ago
0
Errors with `regional_epinow`
#118
CarmenTamayo
closed
5 months ago
5
Preparing data for {EpiNow2}
#117
CarmenTamayo
closed
4 months ago
2
Do not trigger test report CI more than necessary
#116
Bisaloo
closed
9 months ago
0
Extracting parameters on the transmissibility template
#115
CarmenTamayo
closed
7 months ago
8
What to do if parameterised distributions are not on {epiparameter}?
#114
CarmenTamayo
closed
8 months ago
4
Distributions in Rt estimation using {EpiNow2}
#113
CarmenTamayo
closed
8 months ago
10
Creating epidist objects allowing flexibility for distribution parameters
#112
CarmenTamayo
closed
7 months ago
13
Try adding report testing to CI
#111
Bisaloo
closed
9 months ago
1
Remove deprecated select_tags() function
#110
Bisaloo
closed
10 months ago
0
Distributions for parameters from {epiparameter} vs manual input in transmissibility report
#109
CarmenTamayo
opened
10 months ago
10
Allowing flexibility for probability distributions in transmissibility template
#108
CarmenTamayo
closed
10 months ago
2
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