Merge pull request #229 from mrc-ide/gh-226

Implement str for pmcmc_samples objects

.github/workflows/R-CMD-check.yaml

@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 

.github/workflows/make-release.yaml

@@ -27,7 +27,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 

.github/workflows/pkgdown.yaml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1
 

.github/workflows/test-coverage.yaml

@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mcstate
 Title: Monte Carlo Methods for State Space Models
-Version: 0.9.15
+Version: 0.9.16
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Marc", "Baguelin", role = "aut"),

NAMESPACE

@@ -7,6 +7,7 @@ S3method(format,mcstate_pmcmc)
 S3method(predict,mcstate_pmcmc)
 S3method(predict,smc2_result)
 S3method(print,mcstate_pmcmc)
+S3method(str,mcstate_pmcmc)
 export(adaptive_proposal_control)
 export(array_bind)
 export(array_drop)

R/pmcmc_utils.R

@@ -126,6 +126,13 @@ print.mcstate_pmcmc <- function(x, ...) {
 }
 
 
+##' @export
+str.mcstate_pmcmc <- function(object, ...) {
+  object <- unclass(object)
+  NextMethod("str")
+}
+
+
 ## NOTE: we need to expose a 'force' argument here for testing, as
 ## otherwise under R CMD check the progress bar does not run.
 pmcmc_progress <- function(n_steps, progress, simple = FALSE, force = FALSE) {

tests/testthat/test-pmcmc.R

@@ -785,3 +785,14 @@ test_that("can run pmcmc for ode models", {
   expect_equal(results1$predict$model_time, results1$predict$time)
   expect_identical(results1$predict$filter, p1$inputs())
 })
+
+
+test_that("can use str() without error on samples object", {
+  dat <- example_uniform()
+  control <- pmcmc_control(10, save_state = FALSE, save_trajectories = FALSE)
+  res <- pmcmc(dat$pars, dat$filter, control = control)
+  cmp <- structure(res, class = NULL)
+  expect_output(str(res),
+                paste(capture.output(str(cmp)), collapse = "\n"),
+                fixed = TRUE)
+})