Merge pull request #15 from dd-harp/dev

reorganization

Author: smitdave

NAMESPACE

@@ -5,6 +5,10 @@ S3method(adult_dynamics,BQS)
 S3method(aquatic_dynamics,basicL)
 S3method(compute_G,BQ)
 S3method(compute_G,BQS)
+S3method(compute_Kbq,BQ)
+S3method(compute_Kbq,BQS)
+S3method(compute_Kqb,BQ)
+S3method(compute_Kqb,BQS)
 S3method(compute_V,BQ)
 S3method(compute_V,BQS)
 S3method(compute_diffs_L,basicL)
@@ -16,10 +20,6 @@ S3method(init_aquatic_model,basicL)
 S3method(init_states_L,basicL)
 S3method(init_states_M,BQ)
 S3method(init_states_M,BQS)
-S3method(make_Kbq,BQ)
-S3method(make_Kbq,BQS)
-S3method(make_Kqb,BQ)
-S3method(make_Kqb,BQS)
 S3method(make_all_graphs,BQ)
 S3method(make_all_graphs,BQS)
 S3method(make_movie,BQ)
@@ -41,6 +41,7 @@ export(add_arrows_xx)
 export(add_arrows_xy)
 export(add_bent_arrows_xx)
 export(add_bent_arrows_xy)
+export(add_convex_hulls)
 export(add_nth_arrow_xx)
 export(add_nth_arrow_xy)
 export(add_nth_segment)
@@ -58,6 +59,11 @@ export(clusters_nm)
 export(clusters_xy)
 export(compute_G)
 export(compute_GG)
+export(compute_KGV)
+export(compute_Kbb)
+export(compute_Kbq)
+export(compute_Kqb)
+export(compute_Kqq)
 export(compute_V)
 export(compute_VC)
 export(compute_diffs_L)
@@ -79,11 +85,6 @@ export(init_aquatic_model_basicL)
 export(init_states_L)
 export(init_states_M)
 export(lattice)
-export(makeKGV)
-export(make_Kbb)
-export(make_Kbq)
-export(make_Kqb)
-export(make_Kqq)
 export(make_Psi_BQ)
 export(make_Psi_BQS)
 export(make_Psi_xx)
@@ -102,7 +103,11 @@ export(make_model_squareLattice)
 export(make_model_unif)
 export(make_movie)
 export(make_tiles)
-export(net2meta)
+export(mod_convex_hulls)
+export(mod_convex_hulls.i)
+export(net2patches)
+export(outline_points_b)
+export(outline_points_q)
 export(plotDDcmf)
 export(plotDDpmf)
 export(plot_Kbb)
@@ -126,9 +131,10 @@ export(plot_dispersal_G)
 export(plot_dispersal_GG)
 export(plot_dispersal_V)
 export(plot_dispersal_VV)
+export(plot_graph)
 export(plot_matrix_xx)
 export(plot_matrix_xy)
-export(plot_meta)
+export(plot_patches)
 export(plot_points)
 export(plot_points_bq)
 export(plot_points_bqs)

R/K_matrices.R

@@ -1,5 +1,5 @@
 
-#' Simulate adult dynamics for the `BQ` model
+#' Update States for the `BQ` model
 #'
 #' @inheritParams adult_dynamics
 #'
@@ -184,12 +184,12 @@ make_demography_BQ = function(model){
     model$Mpar$Mbl = Psi_bq %*% diag(pQ, nq)
     # the "hardened adult" mosquito population dispersal matrix
     model$Mpar$bigM = with(model$Mpar,
-      rbind(
-        cbind(Mbb, Mbq),
-        cbind(Mqb, Mqq))
-      )
+                           rbind(
+                             cbind(Mbb, Mbq),
+                             cbind(Mqb, Mqq))
+    )
     return(model)
-})})})}
+  })})})}
 
 #' Setup a BQ model for adult mosquitoes
 #'