Fix CI workflows: linting, changelog, and documentation

.lintr.R

@@ -88,6 +88,12 @@ exclusions <- list(
   ),
   "tests/testthat.R" = list(
     undesirable_function_linter = Inf
+  ),
+  "R/t1.R" = list(
+    object_name_linter = Inf
+  ),
+  "R/y1.R" = list(
+    object_name_linter = Inf
   )
 
 )

NEWS.md

@@ -1,5 +1,25 @@
 # serocalculator (development version)
 
+## New features
+
+* Added interactive Shiny app for visualizing antigen-antibody kinetics models
+  - `curve_app()`: Launch interactive Shiny application
+  - `curve_app_ui()`: UI components for the kinetics visualization app
+  - `curve_app_server()`: Server logic for the kinetics visualization app
+  - App allows real-time parameter adjustments via sliders for exploring model behavior
+* Added mathematical functions for modeling antibody and pathogen decay
+  - `antibody_decay_curve()`: Simulate and plot antibody decay over time
+  - `pathogen_decay_curve()`: Simulate and plot pathogen decay over time
+  - `t1f()`: Calculate time to end of active infection
+  - `y1f()`: Calculate peak antibody concentration
+* Added `plot_decay_curve()` for easy plotting of decay functions using ggplot2
+* Added app configuration utilities (`app_sys()`, `get_golem_config()`)
+
+## Improvements
+
+* Improved error messages in `autoplot.seroincidence()` and 
+  `autoplot.seroincidence.by()` to use `cli::cli_abort()` for clearer errors
+
 # serocalculator 1.4.0
 
 ## New features

R/antibody_decay_function.R

@@ -15,36 +15,35 @@
 #' @examples
 #' library(ggplot2)
 #' ggplot() + geom_function(fun = antibody_decay_curve) + xlim(1,100)
-antibody_decay_curve = function(
-    t,
-    y0 = 0.74916052, # taken from simpar run from vignette
-    b0 = 1,
-    mu_b = 0.18432798,
-    mu_y = 0.36853621,
-    gamma = 0.0013040664,
-    alpha = 0.00002192627,
-    rho = 2
-    # rho = 2 # exponential decay?
-)
-{
+antibody_decay_curve <- function(
+  t,
+  y0 = 0.74916052, # taken from simpar run from vignette
+  b0 = 1,
+  mu_b = 0.18432798,
+  mu_y = 0.36853621,
+  gamma = 0.0013040664,
+  alpha = 0.00002192627,
+  rho = 2
+) {
 
-  t1 = t1f(
+  t1 <- t1f(
     b0 = b0,
     y0 = y0,
     mu_y = mu_y,
     mu_b = mu_b,
     gamma = gamma
   )
 
-  y1 = y1f(
+  y1 <- y1f(
     y0 = y0,
     mu_y = mu_y,
-    t1 = t1)
+    t1 = t1
+  )
 
   phase2_rho1 <- y1 * exp(-alpha * (t - t1))
   phase2_default <-
-    y1 * (1+ (rho-1) * (y1 ^ (rho - 1)) * alpha * (t - t1))^(-1/(rho - 1))
-  yt = ifelse(
+    y1 * (1 + (rho - 1) * (y1^(rho - 1)) * alpha * (t - t1))^(-1 / (rho - 1))
+  yt <- ifelse(
     t < t1,
     y0 * exp(mu_y * t),
     ifelse(

R/antigen_decay_curve.R

@@ -14,18 +14,18 @@
 #'   mu_b = 0.18432798,
 #'   mu_y = 0.36853621,
 #'   gamma = 0.0013040664)) + xlim(0, 100)
-pathogen_decay_curve = function(
-    t,
-    y0 = 0.74916052, # taken from simpar run from vignette
-    b0 = 1,
-    mu_b = 0.18432798,
-    mu_y = 0.36853621,
-    gamma = 0.0013040664)
-{
+pathogen_decay_curve <- function(
+  t,
+  y0 = 0.74916052, # taken from simpar run from vignette
+  b0 = 1,
+  mu_b = 0.18432798,
+  mu_y = 0.36853621,
+  gamma = 0.0013040664
+) {
 
-  fraction = gamma * y0 * (exp(mu_y * t) - exp(mu_b*t)) / (mu_y - mu_b)
-  bt_active = (b0 * exp(mu_b * t)) - fraction
+  fraction <- gamma * y0 * (exp(mu_y * t) - exp(mu_b * t)) / (mu_y - mu_b)
+  bt_active <- (b0 * exp(mu_b * t)) - fraction
 
-  bt = pmax(0, bt_active)
+  bt <- pmax(0, bt_active)
   return(bt)
 }

R/app_config.R

@@ -2,7 +2,8 @@
 #'
 #' NOTE: If you manually change your package name in the DESCRIPTION,
 #' don't forget to change it here too, and in the config file.
-#' For a safer name change mechanism, use the `golem::set_golem_name()` function.
+#' For a safer name change mechanism, use the
+#' `golem::set_golem_name()` function.
 #'
 #' @param ... character vectors, specifying subdirectory and file(s)
 #' within your package. The default, none, returns the root of the app.

R/curve_app.R

@@ -6,8 +6,7 @@
 #' \dontrun{
 #' curve_app()
 #' }
-curve_app = function()
-{
+curve_app <- function() {
   shiny::shinyApp(
     ui = curve_app_ui,
     server = curve_app_server

R/curve_app_server.R

@@ -1,34 +1,35 @@
-curve_app_server = function(input, output, session)
-{
-  exp10 = function(x) 10^x
-  derived_params =
-    {
-      tibble(
-        mu_y = input$mu_y |> exp10(),
-        mu_b = input$mu_b |> exp10(),
-        gamma = input$gamma |> exp10(),
-        y0 = input$y0 |> exp10(),
-        b0 = input$b0 |> exp10(),
-        alpha = input$alpha |> exp10(),
-        rho = input$rho,
-        t1 = t1f(
-          mu_y = .data$mu_y,
-          mu_b = .data$mu_b,
-          gamma = .data$gamma,
-          y0 = .data$y0,
-          b0 = .data$b0),
-        y1 = y1f(
-          y0 = .data$y0,
-          mu_y = .data$mu_y,
-          t1 = .data$t1)
-      )
-    }|> reactive()
+curve_app_server <- function(input, output, session) {
+  exp10 <- function(x) {
+    10^x
+  }
+  derived_params <- tibble(
+    mu_y = input$mu_y |> exp10(),
+    mu_b = input$mu_b |> exp10(),
+    gamma = input$gamma |> exp10(),
+    y0 = input$y0 |> exp10(),
+    b0 = input$b0 |> exp10(),
+    alpha = input$alpha |> exp10(),
+    rho = input$rho,
+    t1 = t1f(
+      mu_y = .data$mu_y,
+      mu_b = .data$mu_b,
+      gamma = .data$gamma,
+      y0 = .data$y0,
+      b0 = .data$b0
+    ),
+    y1 = y1f(
+      y0 = .data$y0,
+      mu_y = .data$mu_y,
+      t1 = .data$t1
+    )
+  ) |>
+    reactive()
 
 
-  output$tab1 =
+  output$tab1 <-
     derived_params() |> shiny::renderTable(digits = 4)
 
-  plot1 =
+  plot1 <-
     shiny::eventReactive(
       eventExpr = derived_params() | input$ymax1 | input$alpha | input$rho,
       {
@@ -43,9 +44,11 @@ curve_app_server = function(input, output, session)
           rho = input$rho,
           ymax = input$ymax1 |> exp10()
 
-        )})
+        )
+      }
+    )
 
-  plot2 =
+  plot2 <-
     shiny::eventReactive(
       eventExpr = derived_params() | input$ymax2,
       {
@@ -57,19 +60,15 @@ curve_app_server = function(input, output, session)
           y0 = input$y0 |> exp10(),
           b0 = input$b0 |> exp10(),
           ymax = input$ymax2 |> exp10()
-        )})
+        )
+      }
+    )
 
-  output$plot1 =
+  output$plot1 <-
     plot1() |>
     renderPlot()
-  # plotly::ggplotly()  |>
-  # plotly::layout(legend = list(orientation = 'h')) |>
-  # plotly::renderPlotly()
 
-  output$plot2 =
+  output$plot2 <-
     plot2() |>
     renderPlot()
-  # plotly::ggplotly()  |>
-  # plotly::layout(legend = list(orientation = 'h')) |>
-  # plotly::renderPlotly()
 }

R/curve_app_ui.R

@@ -1,7 +1,6 @@
-curve_app_ui = function(request)
-{
+curve_app_ui <- function(request) {
 
-  sidebar = shiny::sidebarPanel(
+  sidebar <- shiny::sidebarPanel(
     width = 3,
 
     sliderInput(
@@ -10,7 +9,8 @@ curve_app_ui = function(request)
       min = -2,
       max = 2,
       step = .1,
-      value =  0),
+      value =  0
+    ),
 
 
     sliderInput(
@@ -19,45 +19,51 @@ curve_app_ui = function(request)
       min = -2,
       max = 2,
       step = .1,
-      value =  0),
+      value =  0
+    ),
 
     sliderInput(
       inputId = "mu_b",
       label = "log10(mu_b)",
       min = -2,
       max = 2,
       step = .1,
-      value =  log10(0.18432798)),
+      value =  log10(0.18432798)
+    ),
     sliderInput(
       inputId = "mu_y",
       label = "log10(mu_y)",
       min = -2,
       max = 2,
       step = .1,
-      value =  log10(0.36853621)),
+      value =  log10(0.36853621)
+    ),
     sliderInput(
       inputId = "gamma",
       label = "log10(gamma)",
       min = -10,
       max = 10,
       step = .1,
-      value =  log10(0.0013040664)),
+      value =  log10(0.0013040664)
+    ),
 
     sliderInput(
       inputId = "rho",
       label = "rho",
       min = 1,
       max = 3,
       step = .1,
-      value =  2),
+      value =  2
+    ),
 
     sliderInput(
       inputId = "alpha",
       label = "log10(alpha)",
       min = -8,
       max = -1,
       step = .1,
-      value =  log10(0.00002192627))
+      value =  log10(0.00002192627)
+    )
   )
 
 
@@ -73,28 +79,26 @@ curve_app_ui = function(request)
         shiny::column(
           width = 12,
           h2("pathogens"),
-          # plotly::plotlyOutput("plot2")),
           shiny::plotOutput(height = "300px", "plot2"),
           shiny::sliderInput(
             inputId = "ymax2",
             label = "log10(ymax)",
             min = 0,
             max = 5,
             step = .1,
-            value = 1),
-          # shiny::column(
-          # width = 6,
+            value = 1
+          ),
           h2("antibodies"),
-          # plotly::plotlyOutput("plot1"))
-          shiny::plotOutput(height = "300px", 'plot1'),
+          shiny::plotOutput(height = "300px", "plot1"),
           shiny::sliderInput(
             inputId = "ymax1",
             label = "log10(ymax)",
             min = 2,
             max = 10,
             step = .1,
-            value = 4.5)
+            value = 4.5
           )
+        )
 
 
       )