Issue 37 draft: Why it works vignette with analytic solutions (#68)

* Add Leung ref * Create why-it-works.Rmd * add cori et al ref * Add analytic solutions: Gamma * slight eq tweak * linting * Add Leung ref * Create why-it-works.Rmd * add cori et al ref * Add analytic solutions: Gamma * slight eq tweak * linting * Update vignettes/why-it-works.Rmd * Update vignettes/why-it-works.Rmd * add self as author * Update vignettes/why-it-works.Rmd Co-authored-by: Sam Abbott <contact@samabbott.co.uk> * Update vignettes/why-it-works.Rmd Co-authored-by: Sam Abbott <contact@samabbott.co.uk> * Update vignettes/why-it-works.Rmd Co-authored-by: Sam Abbott <contact@samabbott.co.uk> * add self as author in DESCRIPTION rather than vignette * change title * changed notation so that window width is lowercase Since not a rv in this treatment * ongoing rewrite * extra ref * seqn updates * reorganise equations * fix lognormal discrete * add note to pkgdown.yml * extra refs * Update WORDLIST * add a "pre-intro" section * Update NEWS.md * Apply suggestions from code review --------- Co-authored-by: Sam Abbott <contact@samabbott.co.uk> Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
epinowcast · Sep 18, 2024 · bffe696 · bffe696
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,6 +7,11 @@ Authors@R:
            role = c("aut", "cre"),
            email = "contact@samabbott.co.uk",
            comment = c(ORCID = "0000-0001-8057-8037")),
+    person(given = "Sam",
+           family = "Brand",
+           role = c("aut"),
+           email = "usi1@cdc.gov",
+           comment = c(ORCID = "0000-0003-0645-5367")),
     person(given = "Adam",
            family = "Howes",
            role = c("ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@ This is the current development version.
 ## Package
 
 * Add `{touchstone}` based benchmarks for benchmarking R utility functions, and fitting the `stan` and `fitdistplus` models.
+* Added a "How it works" vignette.
 
 # primarycensoreddist 0.4.0
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -27,6 +27,8 @@ navbar:
         href: articles/fitting-dists-with-stan.html
       - text: Fitting distributions using primarycensorseddist and fitdistrplus
         href: articles/fitting-dists-with-fitdistrplus.html
+      - text: Why it works
+        href: articles/why-it-works.html
 
 authors:
   Sam Abbott:

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -3,7 +3,9 @@ Charniga
 CmdStan
 CmdStanModel
 Codecov
+Cori
 Dirichlet
+EpiEstim
 Github
 Gumbel
 Inf
@@ -17,31 +19,55 @@ cdot
 cens
 cmdstan
 cmdstanr
+disccensprob
+disccensunifprim
+discretisation
+discretising
 dp
 dprimary
 dprimarycensoreddist
+dy
+dz
+eq
+fcp
 fitdist
 fitdistr
 fitdistrplus
 frac
+gammapartexp
+geq
 hexsticker
 int
 leq
 lfloor
+lim
+ln
+lognormpartexp
+mathbb
 modelhelpers
 modeling
+nF
 obs
+partexp
 pcd
 pdist
 pprimarycensoreddist
 primarycensorseddist
 primaryeventdistributions
+propto
 pwindow
+qquad
 rfloor
+rightarrow
 rprimary
 seabbs
+seccensorprob
 sim
 stan
 stantools
+survgammaunifprim
+survivalfunc
 swindow
+u
+unifprim
 zsusswein
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/vignettes/library.bib b/vignettes/library.bib
@@ -28,3 +28,25 @@ @ARTICLE{Park2024
   year    =  2024,
   doi     = "10.1101/2024.01.12.24301247"
 }
+
+@article{leung1997censoring,
+  title={Censoring issues in survival analysis},
+  author={Leung, Kwan-Moon and Elashoff, Robert M and Afifi, Abdelmonem A},
+  journal={Annual review of public health},
+  volume={18},
+  number={1},
+  pages={83--104},
+  year={1997},
+  publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
+}
+
+@article{cori2013new,
+  title={A new framework and software to estimate time-varying reproduction numbers during epidemics},
+  author={Cori, Anne and Ferguson, Neil M and Fraser, Christophe and Cauchemez, Simon},
+  journal={American journal of epidemiology},
+  volume={178},
+  number={9},
+  pages={1505--1512},
+  year={2013},
+  publisher={Oxford University Press}
+}