[Pomp-commits] r377 - in pkg: R tests

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2010-10-11 17:26:01 +0200 (Mon, 11 Oct 2010)
New Revision: 377

Added:
   pkg/tests/ricker-spect.Rout.save
Modified:
   pkg/R/simulate-pomp.R
   pkg/tests/ricker-probe.R
   pkg/tests/ricker-spect.R
Log:

- fix bug in 'simulate' as applied to objects inheriting from 'pomp'
- add 'tests/ricker-spect.Rout.save'


Modified: pkg/R/simulate-pomp.R
===================================================================
--- pkg/R/simulate-pomp.R	2010-10-10 22:10:01 UTC (rev 376)
+++ pkg/R/simulate-pomp.R	2010-10-11 15:26:01 UTC (rev 377)
@@ -13,6 +13,8 @@
             call.=FALSE
             )
 
+  object <- as(object,"pomp")
+
   if (missing(times))
     times <- time(object,t0=FALSE)
   else
@@ -38,7 +40,16 @@
   }
   
   retval <- try(
-                .Call(simulation_computations,object,params,times,t0,nsim,obs,states),
+                .Call(
+                      simulation_computations,
+                      object,
+                      params,
+                      times,
+                      t0,
+                      nsim,
+                      obs,
+                      states
+                      ),
                 silent=FALSE
                 )
 

Modified: pkg/tests/ricker-probe.R
===================================================================
--- pkg/tests/ricker-probe.R	2010-10-10 22:10:01 UTC (rev 376)
+++ pkg/tests/ricker-probe.R	2010-10-11 15:26:01 UTC (rev 377)
@@ -146,6 +146,8 @@
                               )
             )
 plot(pm)
+plot(as(pm,"pomp"),variables="y")
+plot(simulate(pm),variables="y")
 
 cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
 

Modified: pkg/tests/ricker-spect.R
===================================================================
--- pkg/tests/ricker-spect.R	2010-10-10 22:10:01 UTC (rev 376)
+++ pkg/tests/ricker-spect.R	2010-10-11 15:26:01 UTC (rev 377)
@@ -37,4 +37,6 @@
 plot(sp)
 summary(sp)
 
+plot(simulate(sp),variables="y")
+
 dev.off()

Added: pkg/tests/ricker-spect.Rout.save
===================================================================
--- pkg/tests/ricker-spect.Rout.save	                        (rev 0)
+++ pkg/tests/ricker-spect.Rout.save	2010-10-11 15:26:01 UTC (rev 377)
@@ -0,0 +1,95 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+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.
+
+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.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(pomp)
+> 
+> data(ricker)
+> 
+> pdf(file="ricker-spect.pdf")
+> 
+> set.seed(6457673L)
+> 
+> sp <- spect(
++             ricker,
++             kernel.width=3,
++             nsim=1000,
++             seed=838775L
++             )
+> plot(sp)
+> summary(sp)
+$coef
+    log.r log.sigma   log.phi       N.0       e.0 
+ 3.800000 -1.203973  2.302585  7.000000  0.000000 
+
+$nsim
+[1] 1000
+
+$pvals
+        y       all 
+0.6113886 0.6113886 
+
+> 
+> po <- ricker
+> coef(po,"log.r") <- log(5)
+> sp <- spect(
++             po,
++             kernel.width=3,
++             nsim=1000,
++             seed=838775L
++             )
+> plot(sp)
+> summary(sp)
+$coef
+    log.r log.sigma   log.phi       N.0       e.0 
+ 1.609438 -1.203973  2.302585  7.000000  0.000000 
+
+$nsim
+[1] 1000
+
+$pvals
+          y         all 
+0.000999001 0.000999001 
+
+> 
+> po <- ricker
+> coef(po,"log.phi") <- log(30)
+> sp <- spect(
++             po,
++             kernel.width=3,
++             nsim=1000,
++             seed=838775L
++             )
+> plot(sp)
+> summary(sp)
+$coef
+    log.r log.sigma   log.phi       N.0       e.0 
+ 3.800000 -1.203973  3.401197  7.000000  0.000000 
+
+$nsim
+[1] 1000
+
+$pvals
+          y         all 
+0.000999001 0.000999001 
+
+> 
+> plot(simulate(sp),variables="y")
+> 
+> dev.off()
+null device 
+          1 
+>