Merge pull request #139 from mrc-ide/mrc-6058

Get coefficients from likelihood objects

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dust2
 Title: Next Generation dust
-Version: 0.3.7
+Version: 0.3.8
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Imperial College of Science, Technology and Medicine",

NAMESPACE

@@ -9,6 +9,7 @@ S3method("[<-",dust_system_generator)
 S3method("[[<-",dust_likelihood)
 S3method("[[<-",dust_system)
 S3method("[[<-",dust_system_generator)
+S3method(coef,dust_likelihood)
 S3method(coef,dust_system)
 S3method(coef,dust_system_generator)
 S3method(dim,dust_system)
@@ -50,4 +51,5 @@ export(dust_system_update_pars)
 export(dust_unfilter_create)
 export(dust_unpack_index)
 export(dust_unpack_state)
+importFrom(stats,coef)
 useDynLib(dust2, .registration = TRUE)

R/interface-likelihood.R

@@ -295,5 +295,13 @@ print.dust_likelihood <- function(x, ...) {
   time_type <- attr(x$generator, "properties")$time_type
   cli::cli_bullets(
     c(i = describe_time(time_type, NULL, x$time_control$dt)))
+  cli::cli_alert_info(
+    "Use {.help [coef()](stats::coef)} to get more information on parameters")
   invisible(x)
 }
+
+
+##' @export
+coef.dust_likelihood <- function(object, ...) {
+  coef(object$generator)
+}

R/interface.R

@@ -621,6 +621,7 @@ describe_time <- function(time_type, default_dt, dt) {
   }
 }
 
+##' @importFrom stats coef
 ##' @export
 coef.dust_system_generator <- function(object, ...) {
   attr(object, "parameters")
@@ -635,8 +636,8 @@ dim.dust_system <- function(x, ...) {
 }
 
 ##' @export
-coef.dust_system <- function(x, ...) {
-  x$parameters
+coef.dust_system <- function(object, ...) {
+  object$parameters
 }
 
 

tests/testthat/test-filter.R

@@ -800,3 +800,16 @@ test_that("prevent access to the filter after serialisation", {
     "Pointer has been serialised, cannot continue safely (filter_rng_state)",
     fixed = TRUE)
 })
+
+
+test_that("can get coefficients from filter", {
+  pars <- list(beta = 0.1, gamma = 0.2, N = 1000, I0 = 10, exp_noise = 1e6)
+  time_start <- 0
+  data <- data.frame(time = c(4, 8, 12, 16), incidence = 1:4)
+  dt <- 1
+  n_particles <- 100
+  seed <- 42
+  obj <- dust_filter_create(sir(), time_start, data, dt = dt,
+                            n_particles = n_particles, seed = seed)
+  expect_equal(coef(obj), coef(sir))
+})