Very interesting work. Out of interest, do these models factor for population density and how if so?

Enable sensitivity analysis through allowing the user pass several values for e.g. R0 on function call of a model

Some models are built directly on deSolve, whereas other use the EpiModel interface to deSolve. This leads to inconsistent behaviour when e.g. printing the final object

Urgency: medium - high

Add import of cases to all models (rate per day):

• SIR

• SEIR

• Age structured SIR

• Age structured SEIR

• Best approach for models with several infectious compartments e.g. SEIR @timchurches?

Rather than requiring use of functions like x = sir_param(...); y = sir_state0(...) and simulate_sir(...x,y) for every model, add a layer of abstraction allowing use of (say) x = model_param(...); y = model_state0(...) and simulate(model = 'sir',....x,y)

I wish you can help me with this. Since I am in China using this, there are some little bit Chinese, I hope that will not be a problem.

devtools::install_github("cbdrh/covoid",build_vignettes = TRUE)
Downloading GitHub repo cbdrh/covoid@HEAD
√ checking for file 'C:\Users\86158\AppData\Local\Temp\Rtmpq4kWe8\remotes5bc8289b95\CBDRH-covoid-2f2aaad/DESCRIPTION' (1.3s)

• preparing 'covoid': (6.6s)
  √ checking DESCRIPTION meta-information ...
  Warning: C:/Users/86158/AppData/Local/Temp/RtmpWQJdjs/Rbuild4da0201a2a9/covoid/man/create_intervention.Rd:38: unexpected section header '\description'
  Warning: C:/Users/86158/AppData/Local/Temp/RtmpWQJdjs/Rbuild4da0201a2a9/covoid/man/create_intervention.Rd:43: unexpected END_OF_INPUT '
  '

• installing the package to process help pages (447ms)
  E creating vignettes (2m 7.8s)
  --- re-building 'age-structured-mixing-background.Rmd' using rmarkdown
  Scale for 'fill' is already present. Adding another scale for 'fill', which
  will replace the existing scale.
  Scale for 'fill' is already present. Adding another scale for 'fill', which
  will replace the existing scale.
  Scale for 'fill' is already present. Adding another scale for 'fill', which
  will replace the existing scale.
  Scale for 'fill' is already present. Adding another scale for 'fill', which
  will replace the existing scale.
  Warning in is.na(caption) :
  is.na()不适用于类别为'expression'的非串列或非矢量
  Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "age-structured-mixing", and the latter is "Age structured epidemic models". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
  --- finished re-building 'age-structured-mixing-background.Rmd'

  --- re-building 'age-structured-mixing.Rmd' using rmarkdown
  Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "age-structure-mixing", and the latter is "Age structured epidemic models in COVOID". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
  --- finished re-building 'age-structured-mixing.Rmd'

  --- re-building 'available-models.Rmd' using rmarkdown
  Quitting from lines 342-349 (available-models.Rmd)
  Error: processing vignette 'available-models.Rmd' failed with diagnostics:
  Object not found 'Ece'
  --- failed re-building 'available-models.Rmd'

  --- re-building 'covoid-model-usage.Rmd' using rmarkdown
  Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "covoid-model-usage", and the latter is "The COVOID model". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
  --- finished re-building 'covoid-model-usage.Rmd'

  SUMMARY: processing the following file failed:
  'available-models.Rmd'

  错误: Vignette re-building failed.
  此外: Warning message:
  In tools::buildVignettes(dir = ".", tangle = TRUE) :
  Files named as vignettes but with no recognized vignette engine:
  'vignettes/dynamic-vaccination-strategies.Rmd'
  'vignettes/static-vaccination-models.Rmd'
  (Is a VignetteBuilder field missing?)
  停止执行
  错误: Failed to install 'covoid' from GitHub:
  System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
  E> SUMMARY: processing the following file failed:
  E> 'available-models.Rmd'
  E>
  E> 错误: Vignette re-building failed.
  E> 此外: Warning message:
  E> In tools::buildVignettes(dir = ".", tangle = TRUE) :
  E> Files named as vignettes but with no recognized vignette engine:
  E> 'vignettes/dynamic-vaccination-strategies.Rmd'
  E> 'vignettes/static-vaccination-models.Rmd'
  E> (Is a VignetteBuilder

Error?

Contact tracing approach based off https://arxiv.org/pdf/1505.03821.pdf

• Implement SIR model with contact tracing
• Implement SEIR model with contact tracing

• All the contact matrices internally load R objects called cm_all (although the user doesn't see this)
• make the age distribution and contact matrix country names consistent

Urgency: low-medium