update for R 4.3.3

kingaa · Mar 27, 2024 · 59c16b7 · 59c16b7
1 parent 88c5a2a
commit 59c16b7
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Showing 91 changed files with 212 additions and 614 deletions.
diff --git a/R/objfun.R b/R/objfun.R
@@ -73,7 +73,7 @@ setIs(
     as(from@env$object,"pomp")
   },
   replace= function (from, to, value) {
-    pStop(who=-2L,"cannot replace the pomp object in a stateful objective function.")
+    pStop(who=-4L,"cannot replace the pomp object in a stateful objective function.")
   }
 )
 

diff --git a/inst/doc/index.html b/inst/doc/index.html
diff --git a/tests/R_v_C.Rout b/tests/R_v_C.Rout
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -109,16 +109,16 @@ Type 'q()' to quit R.
 > ## ----comparison----------------------------------------------------------
 > system.time(simulate(gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  7.361   0.042   7.403 
+  6.806   0.114   6.921 
 > system.time(simulate(Gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  0.160   0.004   0.165 
+  0.161   0.001   0.162 
 > system.time(pfilter(gompertz,Np=1000))
    user  system elapsed 
-  0.660   0.012   0.671 
+  0.642   0.013   0.655 
 > system.time(pfilter(Gompertz,Np=1000))
    user  system elapsed 
-  0.029   0.000   0.029 
+  0.029   0.001   0.029 
 > 
 > dev.off()
 null device 

diff --git a/tests/abc.Rout.save b/tests/abc.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/baddm.Rout.save b/tests/baddm.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bake.Rout.save b/tests/bake.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/basic_probes.Rout.save b/tests/basic_probes.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/betabinom.Rout.save b/tests/betabinom.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/blowflies.Rout.save b/tests/blowflies.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bsmc2.Rout.save b/tests/bsmc2.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bsplines1.Rout.save b/tests/bsplines1.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bsplines2.Rout.save b/tests/bsplines2.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/concat.Rout.save b/tests/concat.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/covmat.Rout.save b/tests/covmat.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/csnippet.Rout.save b/tests/csnippet.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/dacca.Rout.save b/tests/dacca.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/defunct.Rout.save b/tests/defunct.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/dinit.Rout.save b/tests/dinit.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/dp-01.png b/tests/dp-01.png
diff --git a/tests/dp-02.png b/tests/dp-02.png
diff --git a/tests/dp-03.png b/tests/dp-03.png
diff --git a/tests/dp.Rout.save b/tests/dp.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/dprocess.Rout.save b/tests/dprocess.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/ebola.Rout.save b/tests/ebola.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/emeasure.Rout.save b/tests/emeasure.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/eulermultinom.Rout.save b/tests/eulermultinom.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/flow.Rout.save b/tests/flow.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/gillespie.R b/tests/gillespie.R
@@ -133,7 +133,11 @@ bind_rows(
   ggplot(aes(x=time,y=value,color=model))+
   labs(color="",y="reports",title="comparison of implementations")+
   geom_line()+
-  theme_bw()+theme(legend.position=c(0.2,0.8))
+  theme_bw()+
+  theme(
+    legend.position="inside",
+    legend.position.inside=c(0.2,0.8)
+  )
 
 try(gillespie(rate.fun=rate.fun,v=as.numeric(Vmatrix)))
 w <- Vmatrix

diff --git a/tests/gillespie.Rout.save b/tests/gillespie.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -153,7 +153,11 @@ NOTE: The provided object 'nbasis' is available for use by POMP basic components
 +   ggplot(aes(x=time,y=value,color=model))+
 +   labs(color="",y="reports",title="comparison of implementations")+
 +   geom_line()+
-+   theme_bw()+theme(legend.position=c(0.2,0.8))
++   theme_bw()+
++   theme(
++     legend.position="inside",
++     legend.position.inside=c(0.2,0.8)
++   )
 > 
 > try(gillespie(rate.fun=rate.fun,v=as.numeric(Vmatrix)))
 Error : in 'gillespie': 'v' must be a matrix.

diff --git a/tests/gompertz.Rout.save b/tests/gompertz.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/helpers.Rout.save b/tests/helpers.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/hitch.Rout.save b/tests/hitch.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/issue109.Rout.save b/tests/issue109.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/issue56.Rout.save b/tests/issue56.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/kalman.Rout.save b/tests/kalman.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/kalman2.Rout.save b/tests/kalman2.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/link.Rout.save b/tests/link.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/load.Rout.save b/tests/load.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/logmeanexp.Rout.save b/tests/logmeanexp.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/lookup.Rout.save b/tests/lookup.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/map.Rout.save b/tests/map.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/mcap.Rout.save b/tests/mcap.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/measure.Rout.save b/tests/measure.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/mif2.Rout.save b/tests/mif2.Rout.save
@@ -1,6 +1,6 @@
 
-R version 4.3.2 (2023-10-31) -- "Eye Holes"
-Copyright (C) 2023 The R Foundation for Statistical Computing
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.