diff --git a/NEWS.md b/NEWS.md index 25e154d64..49245a920 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # EpiNow2 (development version) +## Documentation + +- The installation guide in the README has been updated to provide instructions for configuring the C toolchain of Windows, MacOS, and Linux. By @jamesmbaazam in #707 and reviewed by @. + ## Model changes - `epinow()` now returns the "timing" output in a "time difference"" format that is easier to understand and work with. By @jamesmbaazam in #688 and reviewed by @sbfnk. diff --git a/README.Rmd b/README.Rmd index f70bbc01b..d31fa22f4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -100,7 +100,10 @@ if (!require("remotes")) { remotes::install_github("epiforecasts/EpiNow2") ``` -Windows users will need a working installation of Rtools in order to build the package from source. See [here](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#checking-the-c-toolchain) for a guide to installing Rtools for use with Stan (which is the statistical modelling platform used for the underlying model). For simple deployment/development a prebuilt docker image is also available (see documentation [here](https://github.com/epiforecasts/EpiNow2/wiki/Docker)). +To build `{EpiNow2}` from source, users will need to configure their C toolchain. This is because `{EpiNow2}` implements the underlying models in Stan (a statistical modelling programming language), which is built on C++. + +Each operating system has a different set up procedure. Windows users need to install an appropriate version of [RTools](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows). Mac users can [follow these steps](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac), and Linux users can use [this guide](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux). For +simple deployment/development a prebuilt docker image is also available (see documentation [here](https://github.com/epiforecasts/EpiNow2/wiki/Docker)). ## Resources diff --git a/inst/WORDLIST b/inst/WORDLIST index ae8c83a86..37633c58e 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,4 +1,6 @@ +AndrewRiceMGW BMC +Bisaloo Bracher CMD CMF @@ -16,7 +18,9 @@ ECDC EpiEstim EpiNow Epinow +GauriSaran Gruson +HAKGH HHS Habakuk Hain @@ -24,6 +28,7 @@ HalfNormal Hamada IO Inf +JAllen Jit Kanjilal Kucharski @@ -32,7 +37,10 @@ Lifecycle Linted Lipsitch Lison +LizaHadley +LloydChapman LogNormal +MFZaini Makevars Matern Mayol @@ -45,9 +53,10 @@ PLoS PMF Poisson Quilty +RTools +RichardMN Riutort Rstan -Rtools Runtimes SACEMA SARS @@ -55,17 +64,27 @@ Sanjat Susswein VB Wellcome +adamkucharski +affans +andrjohns +andrybicio ast +athowes +avallecam backcalc backcalculation bp +brynhayder centered cmdstanr codecov com csv +dajmcdon +davidvilanova dd defato +dependabot detectCores discretisation discretise @@ -75,17 +94,32 @@ div doi dt dynamicaltruncation +ellisp epidemia epiforecasts epinow epinowcast epiparameter etc +fabsig filepath +fkrauer frac +furqan github gp +hsbadr intial +jamesmbaazam +jdmunday +jhellewell +joeHickson +johnaponte +joshwlambert +jrcpulliam +kathsherratt +kgostic +krageth laplace ldots lengthscale @@ -93,19 +127,25 @@ leq lineranges linters lintr +lorenzwalthert lt matern mathcal mathrm mc medRxiv +medewitt metacran +munozedg negbin +nikosbosse +nlinton nolint nonmechanistic nowcast nowcasting nowcasts +ntorresd objec obs pak @@ -113,24 +153,38 @@ parallisation parameterisations parameterised params +pcarbo +pearsonca +philturk +pitmonticone pkgdown pmf pngs poisson +raulfernandezn realland +rhamoonga +rp rstan runtimes rw +sbfnk +schiller sd se +seabbs sim +sophie +sophiemeakin st stan stanfit testland th +thlytras tibbles timelimit +tony underreporting varphi vb @@ -138,4 +192,5 @@ vscode warmup wellcomeopenres wil +yungwai yyyy