First addition of antibody kinetics vignette

DESCRIPTION

@@ -25,6 +25,7 @@ BugReports: https://github.com/seroanalytics/seroepirecipes/issues
 Imports: 
     methods,
     ggplot2,
+    dplyr,
     Rcpp (>= 1.0.11),
     RcppParallel (>= 5.0.1),
     rstan (>= 2.18.1),
@@ -41,8 +42,7 @@ VignetteBuilder: knitr
 Suggests: 
     knitr,
     rmarkdown,
-    cowplot,
-    dplyr,
+    patchwork,
     magrittr,
     tidyr,
     lubridate

README.Rmd

@@ -29,9 +29,11 @@ All of the tutorials use either simulated datasets from the [serosim](https://se
 * (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) Inferring infection histories using _serosolver_
 * (WIP) Time-since-infection machine learning classifier
 
 ## Installation

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   antibody_kinetics_models: antibody_kinetics_models.html
   serocatalytic_model: serocatalytic_model.html
-last_built: 2023-12-14T13:32Z
+last_built: 2023-12-14T13:38Z
 

docs/sitemap.xml

@@ -6,6 +6,9 @@
   <url>
     <loc>/LICENSE-text.html</loc>
   </url>
+  <url>
+    <loc>/articles/antibody_kinetics_models.html</loc>
+  </url>
   <url>
     <loc>/articles/index.html</loc>
   </url>
@@ -18,13 +21,55 @@
   <url>
     <loc>/index.html</loc>
   </url>
+  <url>
+    <loc>/reference/Fast-observation-error-function-continuous.html</loc>
+  </url>
+  <url>
+    <loc>/reference/boost_function.html</loc>
+  </url>
+  <url>
+    <loc>/reference/f_rise.html</loc>
+  </url>
+  <url>
+    <loc>/reference/f_wane.html</loc>
+  </url>
   <url>
     <loc>/reference/hello.html</loc>
   </url>
   <url>
     <loc>/reference/index.html</loc>
   </url>
+  <url>
+    <loc>/reference/kinetics_ceiling.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_gamma.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_piecewise.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_power_function.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_power_function_cpp.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_simple.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kinetics_simple_ode.html</loc>
+  </url>
   <url>
     <loc>/reference/rcpp_hello.html</loc>
   </url>
+  <url>
+    <loc>/reference/seroepirecipes-package.html</loc>
+  </url>
+  <url>
+    <loc>/reference/wane_function.html</loc>
+  </url>
+  <url>
+    <loc>/reference/wane_function_asymptote.html</loc>
+  </url>
 </urlset>

vignettes/antibody_kinetics_models.Rmd

@@ -16,7 +16,9 @@ knitr::opts_chunk$set(
 
 ```{r setup}
 library(seroepirecipes)
-library(cowplot)
+library(ggplot2)
+library(patchwork)
+library(dplyr)
 
 times <- seq(0,365,by=0.1)
 
@@ -28,8 +30,9 @@ y2 <- data.frame(y=kinetics_simple(times,pars_simple),t=times,ver="Simple model
 pars_ranjeva <- c(y0=1,peak=80,k=0,t_peak=28,w=0.008,frac=0.5)
 y3 <- data.frame(y=kinetics_ceiling(times,pars_ranjeva),t=times,ver="Biphasic model (Ranjeva et al. 2019)")
 
-pars_ode <- c("A"=0,"beta"=100,"rho"=0.25,"c_s"=0.15,"c_l"=0.0075,"delta"=0,"r"=0.001)
+pars_ode <- c("A"=0,"beta"=100,"rho"=0.25,"c_s"=0.25,"c_l"=0.1,"delta"=0,"r"=0.001)
 y4 <- data.frame(y=kinetics_simple_ode(times,pars_ode),t=times,ver="ODE model (Pelleau et al. 2021)")
+ggplot(y4) + geom_line(aes(x=t,y=y))
 
 pars_gamma <- c("y0"=0,"peak"=300,"shape"=1.2,"scale"=50)
 y5 <- data.frame(y=kinetics_gamma(times,pars_gamma),t=times,ver="Gamma function (Zhao et al. 2018)")