Merge branch 'main' into error-on-test-warning

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

R/add_point_to_graph.R

@@ -5,7 +5,7 @@ add_point_to_graph <- function(
     point_data =
       tibble(
         x = fit$estimate %>% exp(),
-        y = llik(.data$x, ...),
+        y = log_likelihood(.data$x, ...),
         label = "est.incidence"
       ),
     ...) {

R/build_likelihood_function.R

@@ -10,7 +10,7 @@ build_likelihood_function <- function(
     for (cur_antigen in antigen_isos)
     {
       res <- res +
-        fdev(
+        f_dev(
           lambda = lambda,
           csdata = cross_sectional_data[[cur_antigen]],
           lnpars = longitudinal_parameter_samples[[cur_antigen]],

R/graph.loglik.R

@@ -68,7 +68,7 @@ graph.loglik = function(
   plot_data <-
     tibble(
       x = x %>% sort(),
-      y = llik(
+      y = log_likelihood(
         pop_data = pop_data,
         curve_params = curve_params,
         noise_params = noise_params,
@@ -94,7 +94,7 @@ graph.loglik = function(
         ggplot2::geom_point(
           data = tibble(
             x = highlight_points,
-            y = llik(
+            y = log_likelihood(
               pop_data = pop_data,
               curve_params = curve_params,
               noise_params = noise_params,

R/llik.R

@@ -68,7 +68,7 @@ llik <- function(
 #' ) # high cutoff (y.high)
 #'
 #' # Calculate log-likelihood
-#' ll_AG <- llik(
+#' ll_AG <- log_likelihood(
 #'   pop_data = xs_data,
 #'   curve_params = dmcmc,
 #'   noise_params = cond,
@@ -120,14 +120,14 @@ log_likelihood <- function(
     }
 
     nllSingle <-
-      fdev(
+      f_dev(
         lambda = lambda,
         csdata = cur_data,
         lnpars = cur_curve_params,
         cond = cur_noise_params
       )
 
-    # if (!is.na(nllSingle))  # not meaningful for vectorized fdev()
+    # if (!is.na(nllSingle))  # not meaningful for vectorized f_dev()
     {
       nllTotal <- nllTotal + nllSingle # DEM note: summing log likelihoods represents an independence assumption for multiple Antibodies, given time since seroconversion
     }

R/nll.R

@@ -1,11 +1,11 @@
 #' Calculate negative log-likelihood
 #' @description
-#' Same as [llik()], except negated and requiring lambda on log scale (used in combination with `nlm()`, to ensure that the optimization search doesn't stray into negative values of `lambda`).
+#' Same as [log_likelihood()], except negated and requiring lambda on log scale (used in combination with `nlm()`, to ensure that the optimization search doesn't stray into negative values of `lambda`).
 #' @param log.lambda natural logarithm of incidence rate
-#' @inheritDotParams llik -lambda
+#' @inheritDotParams log_likelihood -lambda
 
 #' @return the negative log-likelihood of the data with the current parameter values
 #' @keywords internal
 .nll <- function(log.lambda, ...) {
-  -llik(lambda = exp(log.lambda), ...)
+  -log_likelihood(lambda = exp(log.lambda), ...)
 }

R/sim.cs.R

@@ -94,7 +94,7 @@ sim.cs <- function(
     filter(.data$antigen_iso %in% antigen_isos) %>%
     droplevels() %>%
     prep_curve_params_for_array() %>%
-    df.to.array(dim_var_names = c("antigen_iso", "parameter"))
+    df_to_array(dim_var_names = c("antigen_iso", "parameter"))
 
   stopifnot(length(lambda) == 1)
 

codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  status:
+    project: #add everything under here, more options at https://docs.codecov.com/docs/commit-status
+      default:
+        # basic
+        target: auto #default
+        threshold: 1%
+        base: auto
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

data-raw/typhoid_results.qmd

@@ -70,7 +70,7 @@ log.lmax <- log(10 * lambda)
 
 
 objfunc <- function(llam) {
-  return(res <- fdev(llam, p.hlye.IgG, c.hlye.IgG, cond.hlye.IgG))
+  return(res <- f_dev(llam, p.hlye.IgG, c.hlye.IgG, cond.hlye.IgG))
 }