Revert README.Rmd changes

README.Rmd

@@ -20,7 +20,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# _epichains_: Methods for simulating and analysing the size and length of transmission chains from branching process models <img src="man/figures/logo.svg" align="right" height="130" />
+# _{{ packagename }}_: Methods for simulating and analysing the size and length of transmission chains from branching process models <img src="man/figures/logo.svg" align="right" height="130" />
 
 <!-- badges: start -->
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
@@ -30,26 +30,26 @@ knitr::opts_chunk$set(
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 
-_epichains_ is an R package to simulate, analyse, and visualize the size 
+_{{ packagename }}_ is an R package to simulate, analyse, and visualize the size 
 and length of branching processes with a given offspring distribution. These 
 models are often used in infectious disease epidemiology, where the chains represent chains of
 transmission, and the offspring distribution represents the distribution of 
 secondary infections caused by an infected individual. 
 
-_epichains_ re-implements [bpmodels](https://github.com/epiverse-trace/bpmodels/)
+_{{ packagename }}_ re-implements [bpmodels](https://github.com/epiverse-trace/bpmodels/)
 by providing bespoke functions and data structures that allow easy
 manipulation and interoperability with other Epiverse-TRACE packages, for example, [superspreading](https://github.com/epiverse-trace/superspreading/) and [epiparameter](https://github.com/epiverse-trace/epiparameter/), and potentially some existing packages for handling transmission chains, for example, [epicontacts](https://github.com/reconhub/epicontacts).
 
-_epichains_ is developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the London School of Hygiene and Tropical Medicine as part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).
+_{{ packagename }}_ is developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the London School of Hygiene and Tropical Medicine as part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).
 
 ## Installation
 
-The latest development version of the _epichains_ package can be installed via
+The latest development version of the _{{ packagename }}_ package can be installed via
 
 ```{r install_pkg, include=TRUE,eval=FALSE}
 # check whether {pak} is installed
 if (!require("pak")) install.packages("pak")
-pak::pak("")
+pak::pak("{{ gh_repo }}")
 ```
 
 To load the package, use
@@ -60,7 +60,7 @@ library("epichains")
 
 ## Quick start
 
-_epichains_ provides two main functions:
+_{{ packagename }}_ provides two main functions:
 
 * `simulate_chains()`: simulates transmission chains using a simple
 branching process model that accepts an index number of cases that seed
@@ -100,7 +100,7 @@ found in the [theory vignette](https://epiverse-trace.github.io/epichains/articl
 We have also collated a bibliography of branching process applications in 
 epidemiology. These can be found in the [literature vignette](https://epiverse-trace.github.io/epichains/articles/branching_process_literature.html).
 
-Specific use cases of _epichains_ can be found in 
+Specific use cases of _{{ packagename }}_ can be found in 
 the [online documentation as package vignettes](https://epiverse-trace.github.io/epichains/), under "Articles".
 
 ## Related R packages
@@ -192,7 +192,7 @@ wish to do so, please follow the [package contributing guide](https://github.com
 
 ## Code of conduct
 
-Please note that the _epichains_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). 
+Please note that the _{{ packagename }}_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). 
 By contributing to this project, you agree to abide by its terms.
 
 ## Citing this package