Boreal_LBMRDataPrep.Rmd bugfixes for stand alone

Boreal_LBMRDataPrep.Rmd

@@ -62,11 +62,10 @@ paths <- getPaths()
 
 ```{r get-study-area}
 library(raster)
-cachePath <- file.path("Boreal_LBMRDataPrep", "cache")
-modulePath <- Cache(readline, paste0("Where is the module path? (e.g., ~/module, with no quotes).\n",
-                                     "Press Enter to accept the path in getPaths()$modulePath: "),
-                    cacheRepo = cachePath)
-setPaths(cachePath = cachePath, modulePath = modulePath)
+# modulePath <- Cache(readline, paste0("Where is the module path? (e.g., ~/module, with no quotes).\n",
+#                                      "Press Enter to accept the path in getPaths()$modulePath: "),
+#                     cacheRepo = cachePath)
+# setPaths(cachePath = cachePath, modulePath = modulePath)
 
 ## do you want to hand-draw a map or use defaults?
 # - note that large areas will take longer to compute
@@ -89,16 +88,17 @@ if (handDrawMap) {
     shpStudyAreaLarge <- SpatialPolygons(list(Polygons(list(Polygon(severalrandompoints$coords)), ID = 1)),
                                           proj4string = crs(canadaMap))
   }
+  Plot(shpStudyAreaLarge, addTo = "canadaMap", col = "red")
 }
-Plot(shpStudyAreaLarge, addTo = "canadaMap", col = "red")
 
 times <- list(start = 0, end = 10)
 modules <- list("Boreal_LBMRDataPrep")
 objects <- if (handDrawMap) list("shpStudyAreaLarge" = shpStudyAreaLarge,
                                  "shpStudyArea" = shpStudyAreaLarge) else list()
 
-mySim <- simInit(times = times, params = parameters, modules = modules,
-                 objects = objects)
+mySim <- simInit(times = times, #params = parameters, 
+                 modules = append(modules, "LBMR"),
+                 objects = objects, paths = getPaths())
 ```
 
 # Run `spades`