Draft writeup (#28)

* first draft of writeup

* add authors

* example fixes

* fix figure

* move to docs

* prettier table and move figures

* fix typo and update table

* first draft of writeup

* add authors

* example fixes

* fix figure

* move to docs

* prettier table and move figures

* fix typo

* abstract

* fixes

* add interpretation of biological parameters

* some more references and minor changes

Author: sbfnk

.gitignore

@@ -2,6 +2,7 @@
 stan/model_threads
 figures/additional
 *.pdf       
+!writeup/paper.pdf
 data/cis
 outputs/*.rds
 *.rds

R/model.R

@@ -203,6 +203,8 @@ i2p_inits <- function(dat) {
         beta = array(inv_logit(rnorm(1, -2, 0.4))),
         gamma = array(inv_logit(rnorm(2, -9, 0.4))),
         delta = array(inv_logit(rnorm(1, 3, 0.4))),
+        k = array(exp(rnorm(1, 0, 0.1))),
+        l = array(exp(rnorm(1, 0, 0.1))),
         ab_sigma = array(
           truncnorm::rtruncnorm(1, mean = 0.005, sd = 0.0025, a = 0)
         ),