Merge branch 'main' into copilot/add-goodness-of-fit-functionality

Author: kristinawlai

.Rbuildignore

@@ -39,5 +39,6 @@ allpopsamples_hlye.csv$
 ^\.lintr\.R$
 ^CLAUDE\.md$
 ^\.claude$
+^_extensions$
 ^macros$
 ^\.gitmodules$

.github/workflows/docs.yaml

@@ -29,8 +29,6 @@ on:
       - reopened
       - ready_for_review
       - closed
-    branches:
-      - main
     paths:
       - "inst/templates/**"
       - "pkgdown/**"
@@ -146,9 +144,9 @@ jobs:
         run: |
           # Set devel = FALSE for version tags, TRUE for everything else
           if [[ "${{ github.ref }}" == refs/tags/v* ]]; then
-            Rscript -e 'pkgdown::build_site(devel = FALSE)'
+            Rscript -e 'pkgdown::build_site(devel = FALSE, quiet = FALSE)'
           else
-            Rscript -e 'pkgdown::build_site(devel = TRUE)'
+            Rscript -e 'pkgdown::build_site(devel = TRUE, quiet = FALSE)'
           fi
         shell: bash
         working-directory: ${{ github.event.repository.name }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.4.0.9016
+Version: 1.4.1.9000
 Authors@R: c(
     person("Kristina", "Lai", , "kwlai@ucdavis.edu", role = c("aut", "cre")),
     person("Chris", "Orwa", role = "aut"),
@@ -51,6 +51,7 @@ Suggests:
     fs,
     ggbeeswarm,
     knitr,
+    maps,
     mixtools,
     pak,
     quarto,
@@ -65,19 +66,21 @@ Suggests:
     forcats,
     snapr (>= 0.0.0.9000),
     rex,
-    readr
+    readr,
+    serodynamics
 LinkingTo: 
     Rcpp
 Config/testthat/edition: 3
 Config/Needs/roxygen2: roxygen2, moodymudskipper/devtag
 Config/Needs/lint: r-lib/lintr
-Config/Needs/website: quarto, lewinfox/foodwebr
+Config/Needs/website: quarto, lewinfox/foodwebr, serodynamics, maps
 Config/Needs/check: readr
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace"))
-Remotes: 
-    d-morrison/snapr
+Remotes:
+    d-morrison/snapr,
+    UCD-SERG/serodynamics
 Config/roxygen2/version: 8.0.0

NEWS.md

@@ -1,5 +1,10 @@
 # serocalculator (development version)
 
+## Documentation
+
+* Added introductory lecture slides to the `methodology` vignette
+  ("Estimating Incidence Rates from Cross-Sectional Serosurveys").
+
 ## Internal
 
 * The `methodology` vignette's LaTeX macros now come from the shared
@@ -23,7 +28,9 @@
   shifted the random-number stream out of sync and made simulated values, and
   their snapshots, differ between macOS, Windows, and Linux). Simulated
   values change slightly as a result of this fix. (#447)
-* Removed lingering terminology discrepancies
+* Corrected default axis labels in `strat_ests_barplot()` (`xlab`) and
+  `strat_ests_scatterplot()` (`ylab`) to say "seroincidence" rather than
+  "seroconversion"/"incidence".
 * `load_noise_params()` and `load_sr_params()` now fail gracefully with informative messages when internet resources are unavailable, complying with CRAN policy (#505)
 * Added Version Crosswalk article to pkgdown website to help users migrate code from v1.3.0 to v1.4.0
   - Provides clear tables comparing old and new function names

R/simresp.tinf.R

@@ -141,8 +141,10 @@ simresp.tinf <- function(# nolint: object_name_linter
 
     t_next <- -log(runif(1, 0, 1)) / lambda
     # Quantize to whole days for cross-platform reproducibility (see the
-    # comment on the first-infection draw above). `t_end` and `t0` are whole
-    # days, so the boundary clamp below stays integer-valued too.
+    # comment on the first-infection draw above). `t0` is always a whole number
+    # of days (accumulated quantized steps); `t_end` may be fractional
+    # (e.g. 10 * 365.25 = 3652.5), so the boundary clamp t_end - t0 can also
+    # be fractional, but that doesn't affect the integer-length time grid.
     t_next <- quantize_t_next(t_next)
     if (t0 <= t_end && t0 + t_next > t_end) {
       t_next <- t_end - t0

_extensions/d-morrison/slidebreak/_extension.yml

@@ -0,0 +1,7 @@
+name: slidebreak
+author: d-morrison
+version: 1.0.0
+quarto-required: ">=1.2.0"
+contributes:
+  shortcodes:
+    - slidebreak.lua

_extensions/d-morrison/slidebreak/slidebreak.lua

@@ -0,0 +1,23 @@
+-- slidebreak.lua
+-- A Quarto shortcode that inserts a slide break in all slide deck formats
+-- (revealjs, pptx, beamer) but does nothing in docx and html formats
+
+function slidebreak()
+  -- Get the current output format
+  -- See: https://quarto.org/docs/extensions/lua-api.html#format-detection
+  local format = quarto.doc.is_format
+
+  -- Insert slide break for all slide/presentation formats (revealjs, pptx, beamer)
+  if format("revealjs") or format("pptx") or format("beamer") then
+    -- Use HorizontalRule which creates a slide separator in presentation formats
+    return pandoc.HorizontalRule()
+  end
+
+  -- Return empty for html and docx formats (and any other non-presentation format)
+  return pandoc.Null()
+end
+
+-- Return the shortcode handler
+return {
+  ['slidebreak'] = slidebreak
+}

inst/WORDLIST

@@ -13,33 +13,44 @@ HlyE
 IgA
 IgG
 IgM
+LMICs
+LPS
 LV
 Lik
 LogLik
 Lotka
 NIAID
 NLL
 Nadu
+Neuzil
 OSF
 Orientia
 PPC
 PRs
+Paratyphi
+Photomicrograph
 RStudio
 Rai
 Readme
 Rmd
 Rtools
 SERG
 SeroEpidemiology
+Seroepidemiology
 Seroincidence
 Serological
+Shigella
+TCVs
 TW
+Trombicula
+Typhi
 UC
 UCD
 Unif
 Vellore
 Volterra
 Wilk
+Wikimedia
 al
 ast
 behaviour
@@ -58,17 +69,23 @@ displaystyle
 dplyr
 dropdown
 dt
+enterica
 eps
+eschar
 estimands
 et
 expf
+flagellar
 forall
 frac
+ge
 geoms
 ggproto
 gh
 hemolysin
+immunocompromised
 infty
+inoculum
 insightsengineering
 invf
 isos
@@ -80,7 +97,9 @@ leq
 linter
 llik
 logf
+macular
 magrittr
+malaise
 mathbb
 mathcal
 mcmc
@@ -89,15 +108,18 @@ mitre
 modelled
 multicohort
 multiversion
+myalgia
 nabla
 nd
 nr
 olds
+operatorname
 overcount
 overcounts
 overline
 param
 params
+pathognomonic
 pipetting
 pkgdown
 pre
@@ -106,6 +128,11 @@ qmd
 qquad
 recombinant
 renamings
+renewcommand
+reproducibly
+rightarrow
+rlang
+roadmap
 se
 sectionally
 sera
@@ -122,16 +149,23 @@ seroresponse
 seroresponses
 serosurvey
 serosurveys
+serotype
+shigella
+slidebreak
 smp
+stylostome
 subfigures
 submodule
+tenesmus
 th
 tibble
 titers
+toxoid
 tsutsugamushi
 undercount
 unstratified
 varepsilon
 vec
 vee
+widehat
 yaml