From 28cbbe2daf41c69ab6b619787f0ea7df7baff3a3 Mon Sep 17 00:00:00 2001
From: James Hay <9113187+jameshay218@users.noreply.github.com>
Date: Thu, 14 Dec 2023 13:46:19 +0000
Subject: [PATCH] Update README
---
README.Rmd | 1 +
README.md | 49 ++--
docs/404.html | 2 +-
docs/LICENSE-text.html | 2 +-
docs/articles/antibody_kinetics_models.html | 2 +-
docs/articles/index.html | 4 +-
docs/articles/serocatalytic_model.html | 212 +++++++++---------
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docs/authors.html | 2 +-
docs/index.html | 2 +-
docs/pkgdown.yml | 2 +-
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docs/reference/boost_function.html | 2 +-
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docs/reference/f_wane.html | 2 +-
docs/reference/index.html | 2 +-
docs/reference/kinetics_ceiling.html | 2 +-
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docs/reference/seroepirecipes-package.html | 2 +-
docs/reference/wane_function.html | 2 +-
docs/reference/wane_function_asymptote.html | 2 +-
docs/search.json | 2 +-
vignettes/antibody_kinetics_models.Rmd | 4 +-
vignettes/serocatalytic_model.Rmd | 5 +-
31 files changed, 167 insertions(+), 152 deletions(-)
diff --git a/README.Rmd b/README.Rmd
index 19c60a6..6f5790d 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -32,6 +32,7 @@ All of the tutorials use either simulated datasets from the [serosim](https://se
* (WIP) Inferring infection histories using _serosolver_
Upcoming vignettes:
+
* (WIP) Estimating the force of infection using antibody acquisition models
* (WIP) Infection times using reversible jump MCMC
* (WIP) Time-since-infection machine learning classifier
diff --git a/README.md b/README.md
index 7618b21..26d8ab0 100644
--- a/README.md
+++ b/README.md
@@ -6,25 +6,48 @@
***seroepirecipes*** implements and links to R packages implementing
commonly used mathematical and statistical models for analyzing
-serological data. We implement a range of methods in R vignettes, from
-fitting antibody kinetics models to longitudinal antibody titer data,
-estimating the force of infection using serocatalytic models, and
-inferring infection histories using time-since-infection methods.
+serological data. The package implements a range of methods in R
+vignettes, from fitting antibody kinetics models to longitudinal
+antibody titer data, estimating the force of infection using
+serocatalytic models, and inferring infection histories using
+time-since-infection methods. This codebase accompanies a [literature
+review](https://osf.io/kqdsn) of analytical methods for
+seroepidemiology.
+
+All of the tutorials use either simulated datasets from the
+[serosim](https://seroanalytics.github.io/serosim/) R-package or
+publicly available datasets.
+
+## DEVELOPER TO DO
+
+- Include Stan models within source code rather than vignette-specific
+ scripts.
+- Attach example datasets
+- Move the jahR antibody kinetics functions here
## Contents
-- Description of datasets included in ***seroepirecipes***
-- Fitting a hierarchical antibody kinetics model to longitudinal
- antibody measurements
-- Using mixture models to classify serostatus
-- Estimating the force of infection using serocatalytic models
-- Infection times using reversible jump MCMC
-- Inferring infection histories using *serosolver*
+- (WIP) Description of datasets included in ***seroepirecipes***
+- (WIP) Common considerations when preparing serological data for
+ analysis
+- (WIP) [Fitting a hierarchical antibody kinetics model to longitudinal
+ antibody
+ measurements]((https://seroanalytics.github.io/seroepirecipes/articles/antibody_kinetics_models.html))
+- (WIP) Using mixture models to classify serostatus
+- [Estimating the force of infection using serocatalytic
+ models](https://seroanalytics.github.io/seroepirecipes/articles/serocatalytic_model.html)
+- (WIP) Inferring infection histories using *serosolver*
+
+Upcoming vignettes:
+
+- (WIP) Estimating the force of infection using antibody acquisition
+ models
+- (WIP) Infection times using reversible jump MCMC
+- (WIP) Time-since-infection machine learning classifier
## Installation
-You can install the development version of ***seroepirecipes*** from
-[GitHub](https://github.com/) with:
+You can install the development version of ***seroepirecipes*** with:
``` r
if(!require("remotes")) install.packages("remotes")
diff --git a/docs/404.html b/docs/404.html
index edd4989..38f9888 100644
--- a/docs/404.html
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@@ -47,7 +47,7 @@
Articles
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 33fd997..4275c5a 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -25,7 +25,7 @@
Articles