update in progress message for docs

epiforecasts · seabbs · Oct 17, 2022 · Oct 17, 2022 · Oct 17, 2022 · 2d8bb0d9f12e99de2011fe15254040d462015f6a
commit 2d8bb0d9f12e99de2011fe15254040d462015f6a
diff --git a/README.Rmd b/README.Rmd
@@ -123,7 +123,7 @@ reported_cases <- example_confirmed[1:60]
 head(reported_cases)
 ```
 
-Estimate cases by date of infection, the time-varying reproduction number, the rate of growth and forecast these estimates into the future by 7 days. Summarise the posterior and return a summary table and plots for reporting purposes. If a `target_folder` is supplied results can be internally saved (with the option to also turn off explicit returning of results).
+Estimate cases by date of infection, the time-varying reproduction number, the rate of growth and forecast these estimates into the future by 7 days. Summarise the posterior and return a summary table and plots for reporting purposes. If a `target_folder` is supplied results can be internally saved (with the option to also turn off explicit returning of results). Here we use the default model parameterisation that priorities real-time performance over run-time or other considerations. For other formulations see the documentation for `estimate_infections()`.
 
 ```{r, message = FALSE, warning = FALSE}
 estimates <- epinow(

diff --git a/vignettes/case-studies.Rmd b/vignettes/case-studies.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-*If aware of other examples please open a PR adding them or open an issue flagging this omission.*
+**This is a work in progress. Please consider submitting a PR to improve it.** 
 
 # Case studies 
 

diff --git a/vignettes/estimate_infections.Rmd b/vignettes/estimate_infections.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-*This is a work in progress.* 
+**This is a work in progress. Please consider submitting a PR to improve it.** 
 
 `estimate_infections()` supports a range of model formulation. Here we describe the most commonly used and highlight other options.
 

diff --git a/vignettes/estimate_secondary.Rmd b/vignettes/estimate_secondary.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-* This documentation is a work in progress.*
+**This is a work in progress. Please consider submitting a PR to improve it.** 
 
 This model is based on a discrete convolution of primary cases, scaled based on the fraction (here described as the secondary fraction but depending on application potentially being the case fatality ratio, case hospitalisation ratio, or the hospitalisation fatality ratio), and a delay distribution that is assumed to follow a discretised daily log normal distribution.
 This model can be thought of as a disrete time ordinary differential equation approximation generalised to log normal, rather than exponential, delay distributions.

diff --git a/vignettes/estimate_truncation.Rmd b/vignettes/estimate_truncation.Rmd
@@ -13,4 +13,4 @@ knitr::opts_chunk$set(
   comment = "#>"
 )
 ```
- *This documentation is a work in progress.*
+**This is a work in progress. Please consider submitting a PR to improve it.**
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,7 +14,7 @@ knitr::opts_chunk$set( @@
     )
     ```
-    *If aware of other examples please open a PR adding them or open an issue flagging this omission.*
+    **This is a work in progress. Please consider submitting a PR to improve it.**
     # Case studies
@@ Expand Down @@