From 14f259ad21be07b72e72ab1ebfaf4a052052cd1c Mon Sep 17 00:00:00 2001
From: Sam Abbott <s.e.abbott12@gmail.com>
Date: Fri, 4 Oct 2024 19:01:07 +0100
Subject: [PATCH] Issue 109: Add explicit dist and primary arg usage to getting
 started (#122)

* add explicit dist and primary arg usage to getting started

* Update primarycensoreddist.Rmd
---
 NEWS.md                           |  1 +
 vignettes/primarycensoreddist.Rmd | 26 ++++++++++++++------------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index d1bbfbb..0c93319 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,7 @@ This is the development version of `primarycensoreddist` and is not yet ready fo
 
 * Simplified the "Analytic solutions" vignette by removing verbose derivation details.
 * Added links between vignettes to make it easier to navigate the documentation.
+* Added explicit usage of `pdist`, `dprimary`, `rdist`, and `rprimary` arguments in the getting started vignette to make it easier to link to mathematical details.
 
 # primarycensoreddist 0.5.0
 
diff --git a/vignettes/primarycensoreddist.Rmd b/vignettes/primarycensoreddist.Rmd
index bced166..a2ca97a 100644
--- a/vignettes/primarycensoreddist.Rmd
+++ b/vignettes/primarycensoreddist.Rmd
@@ -82,15 +82,17 @@ pwindow <- 1
 
 # Random samples without secondary censoring
 samples <- rprimarycensoreddist(
-  n, rlnorm,
-  meanlog = meanlog, sdlog = sdlog,
-  pwindow = pwindow, swindow = 0, D = obs_time
+  n,
+  rdist = rlnorm, rprimary = runif,
+  pwindow = pwindow, swindow = 0, D = obs_time,
+  meanlog = meanlog, sdlog = sdlog
 )
 # Random samples with secondary censoring
 samples_sc <- rprimarycensoreddist(
-  n, rlnorm,
-  meanlog = meanlog, sdlog = sdlog,
-  pwindow = pwindow, swindow = 1, D = obs_time
+  n,
+  rdist = rlnorm, rprimary = runif,
+  pwindow = pwindow, swindow = 1, D = obs_time,
+  meanlog = meanlog, sdlog = sdlog
 )
 # Calculate the PMF for the samples with secondary censoring
 samples_sc_pmf <- data.frame(
@@ -172,9 +174,9 @@ Let's compare the empirical CDF of our samples without secondary censoring to th
 empirical_cdf <- ecdf(samples)
 theoretical_cdf <- pprimarycensoreddist(
   seq(0, obs_time, length.out = 100),
-  plnorm,
-  meanlog = meanlog, sdlog = sdlog,
-  pwindow = pwindow, D = obs_time
+  pdist = plnorm, dprimary = dunif,
+  pwindow = pwindow, D = obs_time,
+  meanlog = meanlog, sdlog = sdlog
 )
 
 # Create a data frame for plotting
@@ -226,9 +228,9 @@ Let's compare the empirical PMF of our samples with secondary censoring to the t
 # Calculate the theoretical PMF using dprimarycensoreddist
 theoretical_pmf <- dprimarycensoreddist(
   0:(obs_time - 1),
-  plnorm,
-  meanlog = meanlog, sdlog = sdlog,
-  pwindow = pwindow, swindow = 1, D = obs_time
+  pdist = plnorm, dprimary = dunif,
+  pwindow = pwindow, swindow = 1, D = obs_time,
+  meanlog = meanlog, sdlog = sdlog
 )
 
 pmf_df <- data.frame(