update coverage; fix bug

Author: kingaa

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.14.8.0
-Date: 2024-11-15
+Version: 0.14.8.1
+Date: 2024-11-25
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )

R/getinfo.R

@@ -57,8 +57,6 @@ getInfo <- function (
   )
   if (!is.null(x$lineages))
     x$lineages |> reshape_lineages() -> x$lineages
-  if (!is.null(x$gendat))
-    x$gendat |> as_tibble() -> x$gendat
   x
 }
 

tests/gendat.R

@@ -15,6 +15,8 @@ x |>
 
 g
 
+stopifnot(identical(g,getInfo(x,gendat=TRUE)$gendat))
+
 g |>
   with({
     stopifnot(

tests/gendat.Rout.save

@@ -75,6 +75,8 @@ $nsample
 $nnode
 [1] 28
 
+> 
+> stopifnot(identical(g,getInfo(x,gendat=TRUE)$gendat))
 > 
 > g |>
 +   with({

tests/seir2.R

@@ -2,14 +2,14 @@ png(filename="seir2-%02d.png",res=100)
 
 suppressPackageStartupMessages({
   library(tidyverse)
-  library(phylopomp)
   library(pomp)
+  library(phylopomp)
 })
 theme_set(theme_bw())
 set.seed(842110120)
 options(digits=3)
 
-runSEIR(
+simulate("SEIRS",
   Beta=4,sigma=1,gamma=1,psi=1,omega=1,
   S0=100,E0=3,I0=5,R0=100,
   time=5

tests/seir2.Rout.save

@@ -21,14 +21,14 @@ Type 'q()' to quit R.
 > 
 > suppressPackageStartupMessages({
 +   library(tidyverse)
-+   library(phylopomp)
 +   library(pomp)
++   library(phylopomp)
 + })
 > theme_set(theme_bw())
 > set.seed(842110120)
 > options(digits=3)
 > 
-> runSEIR(
+> simulate("SEIRS",
 +   Beta=4,sigma=1,gamma=1,psi=1,omega=1,
 +   S0=100,E0=3,I0=5,R0=100,
 +   time=5

tests/simulate.R

@@ -1,3 +1,4 @@
 library(phylopomp)
-simulate()
+try(simulate("billyjoe"))
 try(simulate(22))
+simulate()

tests/simulate.Rout.save

@@ -25,6 +25,12 @@ The following object is masked from 'package:stats':
 
     simulate
 
+> try(simulate("billyjoe"))
+Error : unrecognized model: 'billyjoe'.
+Do 'simulate()' to view available models.
+> try(simulate(22))
+Error : in 'simulate.default': 'object' must be specified as either the name of a model or the result of a previous simulation.
+Do 'simulate()' to view available models.
 > simulate()
 Available phylopomp models:
 - LBDP: Linear birth-death-sampling model
@@ -39,7 +45,4 @@ Available phylopomp models:
 - SEIRS: synonymous with SEIR
 
 
-> try(simulate(22))
-Error : in 'simulate.default': 'object' must be specified as either the name of a model or the result of a previous simulation.
-Do 'simulate()' to view available models.
 >