From b14d1e3e9c08048f5e0dfd8f015fd0e9d1887856 Mon Sep 17 00:00:00 2001
From: James Azam <james.azam@lshtm.ac.uk>
Date: Tue, 2 Jul 2024 14:31:35 +0100
Subject: [PATCH] Update links for configuring c toolchain (#707)

* Update links for configuring c toolchain

* Update WORDLIST

* Add NEWS item

* Revert change to docker statement
---
 NEWS.md       |  4 ++++
 README.Rmd    |  5 ++++-
 inst/WORDLIST | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 64 insertions(+), 2 deletions(-)

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 @<REVIEWER>.
+
 ## 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