fixed error in RMG

dd-harp · Mar 15, 2024 · 84fe891 · 84fe891
1 parent da859bb
commit 84fe891
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Showing 6 changed files with 38 additions and 94 deletions.
diff --git a/R/MYZmod-RMG.R b/R/MYZmod-RMG.R
@@ -10,7 +10,7 @@ MBionomics.RMG <- function(t, y, pars, s) {
     pars$MYZpar[[s]]$f <- f0
     pars$MYZpar[[s]]$q <- q0
     pars$MYZpar[[s]]$g <- g0
-    pars$MYZpar[[s]]$phi <- 1/phi0
+    pars$MYZpar[[s]]$phi <- phi0
     pars$MYZpar[[s]]$sigma <- sigma0
     pars$MYZpar[[s]]$nu <- nu0
 
@@ -111,7 +111,7 @@ setup_MYZpar.RMG = function(MYZname, pars, s, MYZopts=list(), EIPmod, calK){
 #' @return a [list]
 #' @export
 make_MYZpar_RMG = function(nPatches, MYZopts=list(), EIPmod, calK,
-                          g=1/12, sigma=1/8, f=0.3, q=0.95,
+                          g=1/12, sigma=1/8, f=0.5, q=0.95,
                           nu=1, eggsPerBatch=60){
 
   stopifnot(is.matrix(calK))
@@ -131,6 +131,7 @@ make_MYZpar_RMG = function(nPatches, MYZopts=list(), EIPmod, calK,
     MYZpar$q      <- checkIt(q, nPatches)
     MYZpar$nu     <- checkIt(nu, nPatches)
     MYZpar$eggsPerBatch <- eggsPerBatch
+    MYZpar$phi <- 1/MYZpar$eip
 
     # Store as baseline values
     MYZpar$g0      <- MYZpar$g

diff --git a/man/make_MYZpar_RMG.Rd b/man/make_MYZpar_RMG.Rd
diff --git a/vignettes/MYZmod-RMG.R b/vignettes/MYZmod-RMG.R
@@ -14,3 +14,6 @@ xde_plot_M(model)
 xde_plot_YZ(model, add_axes = F)
 xde_plot_YZ_fracs(model)
 
+## -----------------------------------------------------------------------------
+xde_plot_YZ_fracs(model)
+
diff --git a/vignettes/MYZmod-RMG.Rmd b/vignettes/MYZmod-RMG.Rmd
@@ -129,5 +129,9 @@ xde_plot_YZ(model, add_axes = F)
 xde_plot_YZ_fracs(model)
 ```
 
+```{r}
+xde_plot_YZ_fracs(model)
+```
+
 
 
diff --git a/vignettes/MYZmod-RMG.html b/vignettes/MYZmod-RMG.html
diff --git a/vignettes/Scaling.html b/vignettes/Scaling.html