[Pomp-commits] r1198 - pkg/pomp/inst/examples

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

Author: kingaa
Date: 2015-06-11 13:55:58 +0200 (Thu, 11 Jun 2015)
New Revision: 1198

Modified:
   pkg/pomp/inst/examples/bbs.R
   pkg/pomp/inst/examples/euler.sir.R
   pkg/pomp/inst/examples/gillespie.sir.R
Log:
- fix error in paramnames alignment with SIR models

Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R	2015-06-11 11:55:53 UTC (rev 1197)
+++ pkg/pomp/inst/examples/bbs.R	2015-06-11 11:55:58 UTC (rev 1198)
@@ -42,7 +42,7 @@
      statenames=c("S","I","R","cases","W"),
      paramnames=c(
        "gamma","mu","iota",
-       "beta","beta.sd","pop","rho","sigma",
+       "beta","beta.sd","pop","rho",
        "S.0","I.0","R.0"
        ),
      zeronames=c("cases"),

Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R	2015-06-11 11:55:53 UTC (rev 1197)
+++ pkg/pomp/inst/examples/euler.sir.R	2015-06-11 11:55:58 UTC (rev 1198)
@@ -220,7 +220,7 @@
        beta1=400,beta2=480,beta3=320,
        beta.sd=1e-3,
        pop=2.1e6,
-       rho=0.6,overdisp=1,
+       rho=0.6,
        S.0=26/400,I.0=0.001,R.0=1-26/400
        ),
      rprocess=euler.sim(
@@ -236,7 +236,7 @@
      statenames=c("S","I","R","cases","W"),
      paramnames=c(
        "gamma","mu","iota",
-       "beta1","beta.sd","pop","rho","overdisp",
+       "beta1","beta.sd","pop","rho",
        "S.0","I.0","R.0"
        ),
      zeronames=c("cases"),

Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R	2015-06-11 11:55:53 UTC (rev 1197)
+++ pkg/pomp/inst/examples/gillespie.sir.R	2015-06-11 11:55:58 UTC (rev 1198)
@@ -575,8 +575,7 @@
      degree=3L,
      period=1.0,
      initializer=function(params, t0, comp.names, ic.names, ...) {
-       x0 <- numeric(5)
-       names(x0) <- c("S","I","R","N","cases")
+       x0 <- setNames(numeric(5),c("S","I","R","N","cases"))
        fracs <- params[ic.names]
        x0["N"] <- params["pop"]
        x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))