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dd-harp · Mar 18, 2024 · 8ebef1d · 8ebef1d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: motrap.micro
+Package: ramp.micro
 Type: Package
 Title: *Mo*squito *Tr*ansmitted *P*athogen *Micro*simulation with Behavioral States 
 Version: 0.1.0
@@ -11,8 +11,8 @@ Description: A set of algorithms to setup, simulate, and analyze systems of equa
 License: GPL-3 
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
-URL: https://dd-harp.github.io/motrap.micro/
+RoxygenNote: 7.3.1
+URL: https://dd-harp.github.io/ramp.micro/
 Imports: 
   stats, 
   deldir,

diff --git a/vignettes/landscapes.R b/vignettes/landscapes.R
@@ -2,7 +2,7 @@
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 
 ## -----------------------------------------------------------------------------
 dd = seq(0, 5, by = 0.01)

diff --git a/vignettes/landscapes.Rmd b/vignettes/landscapes.Rmd
@@ -11,7 +11,7 @@ vignette: >
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 ```
 
 

diff --git a/vignettes/landscapes.html b/vignettes/landscapes.html
diff --git a/vignettes/point_sets.R b/vignettes/point_sets.R
@@ -2,7 +2,7 @@
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 
 ## ----fig.height=5, fig.width=5------------------------------------------------
 par(bty = "o")

diff --git a/vignettes/point_sets.Rmd b/vignettes/point_sets.Rmd
@@ -11,7 +11,7 @@ vignette: >
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 ```
 
 

diff --git a/vignettes/point_sets.html b/vignettes/point_sets.html
diff --git a/vignettes/simulation.R b/vignettes/simulation.R
@@ -2,15 +2,16 @@
 library(viridisLite)
 library(knitr)
 library(viridis)
-#library(motrap.micro)
-devtools::load_all()
+library(ramp.micro)
+#devtools::load_all()
 
 ## -----------------------------------------------------------------------------
 set.seed(24328)
 bb = unif_xy(256, -17, 17) 
 qq = unif_xy(289, -17, 17) 
 
-## ----fig.height=7, fig.width=7------------------------------------------------
+## ----fig.height=6, fig.width=6------------------------------------------------
+par(mar = c(1,1,1,1))
 plot_points_bq(bb, qq)
 
 ## -----------------------------------------------------------------------------
@@ -52,5 +53,11 @@ model <- SIM(model)
 #  devtools::load_all()
 
 ## ----fig.height=6, fig.width=6, echo=F----------------------------------------
-plot_points(model, bwts = model$states$M$B_t[[201]], qwts= model$states$M$B_t[[201]])
+par(mar = c(1,1,1,1))
+plot_points(model, bwts = model$states$M$B_t[[201]], qwts= model$states$M$B_t[[201]], max_pt_sz=2)
+
+## ----eval=F, echo=F-----------------------------------------------------------
+#  model1 <- model
+#  model1$Lpar$xi = .1
+#  model1 <- SIM(model1)
 
diff --git a/vignettes/simulation.Rmd b/vignettes/simulation.Rmd
@@ -11,7 +11,7 @@ vignette: >
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 #devtools::load_all()
 ```
 

diff --git a/vignettes/simulation.html b/vignettes/simulation.html
diff --git a/vignettes/test_plots.R b/vignettes/test_plots.R
@@ -2,7 +2,7 @@
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 #suppressWarnings(devtools::load_all() )
 set.seed(25)
 

diff --git a/vignettes/test_plots.Rmd b/vignettes/test_plots.Rmd
@@ -11,7 +11,7 @@ vignette: >
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 #suppressWarnings(devtools::load_all() )
 set.seed(25)
 ```

diff --git a/vignettes/test_plots.html b/vignettes/test_plots.html
@@ -343,7 +343,7 @@ <h1 class="title toc-ignore">On Dispersal Matrices</h1>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(viridisLite)</span>
 <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>
 <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">library</span>(viridis)</span>
-<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">library</span>(motrap.micro)</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">library</span>(ramp.micro)</span>
 <span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co">#suppressWarnings(devtools::load_all() )</span></span>
 <span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">25</span>)</span></code></pre></div>
 <div id="introduction" class="section level2">

diff --git a/vignettes/visualizing_dispersal.R b/vignettes/visualizing_dispersal.R
@@ -2,7 +2,7 @@
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 set.seed(25)
 
 ## ----echo=F, eval=F-----------------------------------------------------------

diff --git a/vignettes/visualizing_dispersal.Rmd b/vignettes/visualizing_dispersal.Rmd
@@ -12,7 +12,7 @@ vignette: >
 library(viridisLite)
 library(knitr)
 library(viridis)
-library(motrap.micro)
+library(ramp.micro)
 set.seed(25)
 ```
 

diff --git a/vignettes/visualizing_dispersal.html b/vignettes/visualizing_dispersal.html
@@ -343,7 +343,7 @@ <h1 class="title toc-ignore">Visualizing Micro-Dispersal</h1>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(viridisLite)</span>
 <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>
 <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">library</span>(viridis)</span>
-<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">library</span>(motrap.micro)</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">library</span>(ramp.micro)</span>
 <span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">25</span>)</span></code></pre></div>
 <div id="introduction" class="section level2">
 <h2>Introduction</h2>