update tests

kingaa · Jun 3, 2024 · e54664e · e54664e
1 parent c784574
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.13.1.1
-Date: 2024-05-28
+Version: 0.13.1.2
+Date: 2024-06-03
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )

diff --git a/NAMESPACE b/NAMESPACE
@@ -115,7 +115,6 @@ importFrom(grid,upViewport)
 importFrom(grid,viewport)
 importFrom(pomp,bake)
 importFrom(pomp,covariate_table)
-importFrom(pomp,euler)
 importFrom(pomp,freeze)
 importFrom(pomp,onestep)
 importFrom(pomp,pomp)

diff --git a/R/lbdp.R b/R/lbdp.R
@@ -158,7 +158,7 @@ lbdp_exact <- function (x, lambda, mu, psi, n0 = 1) {
 ##' @rdname lbdp
 ##' @details
 ##' \code{lbdp_pomp} constructs a \pkg{pomp} object containing a given set of data and a linear birth-death-sampling process.
-##' @importFrom pomp pomp onestep euler covariate_table
+##' @importFrom pomp pomp onestep covariate_table
 ##' @inheritParams lbdp_exact
 ##' @export
 lbdp_pomp <- function (x, lambda, mu, psi, n0 = 1, t0 = 0)

diff --git a/src/seirs_pomp.c b/src/seirs_pomp.c
@@ -2,7 +2,7 @@
 #include "internal.h"
 
 static inline int random_choice (double n) {
-  return (int) floor(R_unif_index(n));
+  return random_integer((int) nearbyint(n));
 }
 
 static void change_color (double *color, int nsample,

diff --git a/tests/gendat.Rout.save b/tests/gendat.Rout.save
@@ -7,6 +7,8 @@ R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 
+  Natural language support but running in an English locale
+
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

diff --git a/tests/seir2-04.png b/tests/seir2-04.png
diff --git a/tests/seir2-05.png b/tests/seir2-05.png
diff --git a/tests/seir2.Rout.save b/tests/seir2.Rout.save
@@ -59,47 +59,47 @@ Error : in 'seirs_pomp': 'S0','E0','I0','R0' must be nonnegative integers.
 > 
 > po |> rinit(nsim=5)
        .id
-name    [,1] [,2] [,3] [,4] [,5]
-  S      100  100  100  100  100
-  E        3    3    3    3    3
-  I        5    5    5    5    5
-  R      100  100  100  100  100
-  ll       0    0    0    0    0
-  node     5    5    5    5    5
-  ellE     3    3    3    3    2
-  ellI     3    3    3    3    4
-  color    1    0    1    1    1
-           0    1    1    1    0
-           1    0    0    0    1
-          NA   NA   NA   NA   NA
-           0    1    1    0    1
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-          NA   NA   NA   NA   NA
-           1    0    0    0    1
-           0    1    0    1    0
+name       [,1]   [,2]   [,3]   [,4]    [,5]
+  S     100.000 100.00 100.00 100.00 100.000
+  E       3.000   3.00   3.00   3.00   3.000
+  I       5.000   5.00   5.00   5.00   5.000
+  R     100.000 100.00 100.00 100.00 100.000
+  ll      0.624   1.03   1.03   1.03   0.624
+  node    5.000   5.00   5.00   5.00   5.000
+  ellE    2.000   3.00   3.00   3.00   2.000
+  ellI    4.000   3.00   3.00   3.00   4.000
+  color   1.000   0.00   1.00   1.00   1.000
+          0.000   1.00   1.00   1.00   0.000
+          1.000   0.00   0.00   0.00   1.000
+             NA     NA     NA     NA      NA
+          0.000   1.00   1.00   0.00   1.000
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+             NA     NA     NA     NA      NA
+          1.000   0.00   0.00   0.00   1.000
+          1.000   1.00   0.00   1.00   0.000
 > 
 > po |> pfilter(Np=1000) |> replicate(n=20) |> concat() -> pf
 > pf |> logLik()
- [1] -33.0 -32.8 -33.1 -33.9 -33.6 -33.4 -33.0 -32.6 -34.5 -32.8 -33.3 -33.5
-[13] -33.4 -33.6 -34.4 -32.7 -33.5 -31.5 -34.3 -32.8
+ [1] -32.4 -32.0 -30.2 -30.2 -28.9 -28.7 -31.7 -31.4 -31.5 -30.1 -30.6 -31.2
+[13] -30.9 -30.8 -28.4 -29.9 -31.5 -30.8 -32.1 -30.3
 > pf |> logLik() |> logmeanexp(se=TRUE,ess=TRUE)
-   est     se    ess 
--33.01   0.23  10.80 
+    est      se     ess 
+-30.041   0.325   7.337 
 > 
 > pf |> plot(type="s")
 >