New option to adjust smoothness of kernel density estimator in Kernel…

…R and KernelTimeR (#245)

* Add smoothness option to kde

* update docu

---------

Co-authored-by: Antonia Runge <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DSSM
 Title: Pandora & IsoMemo spatiotemporal modeling
-Version: 24.09.0
+Version: 24.09.1
 Authors@R: c(
             person("Marcus", "Gross", email = "[email protected]", role = c("cre", "aut")),
             person("Antonia", "Runge", email = "[email protected]", role = c("aut"))

NEWS.md

@@ -1,3 +1,8 @@
+# DSSM 24.09.1
+
+## New Features
+- _KernelR_ + _KernelTimeR_: New option to adjust smoothness of kernel density estimator
+
 # DSSM 24.09.0
 
 ## Bug Fixes

R/01-estimateMap.R

@@ -1999,6 +1999,7 @@ invLogit <- function(x){
 #' @param nClustRange numeric: range of potential mclust cluster
 #' @param restriction numeric vector: spatially restricts model data 4 entries for latitude (min/max) and longitude(min/max)
 #' @param nSim numeric: number of bootstrap samples
+#' @param smoothness numeric: smoothness adjustment
 #' @param kdeType character: "1" for correlated bandwidth, "2" for diagonal bandwidth, "3" for diagonal, equal long/lat bandwidth
 #' @inheritParams centerData
 #' @examples
@@ -2030,6 +2031,7 @@ estimateMapKernel <- function(data,
                               trimRatio = 0.05,
                               restriction = c(-90, 90, -180, 180),
                               nSim = 10,
+                              smoothness = 1,
                               kdeType = "1"){
   center <- match.arg(center)
 
@@ -2099,7 +2101,8 @@ estimateMapKernel <- function(data,
         H = Hpi.diag(cbind(data3$Longitude, data3$Latitude))
         diag(H) <- prod(diag(H)^0.5)
       }
-
+      #smoothness adjustment
+      H = H*smoothness
       kde(cbind(data3$Longitude, data3$Latitude), w = data3[,Weighting], H=H)
     }),
     silent = TRUE)
@@ -2116,7 +2119,8 @@ estimateMapKernel <- function(data,
         H = Hpi.diag(cbind(data3$Longitude, data3$Latitude))
         diag(H) <- prod(diag(H)^0.5)
       }
-
+      #smoothness adjustment
+      H = H*smoothness
       kde(cbind(data3$Longitude, data3$Latitude), H=H)
     }), silent = TRUE)
   }
@@ -2186,6 +2190,7 @@ estimateMapKernelWrapper <- function(data, input) {
                 kMeansAlgo = input$kMeansAlgo,
                 restriction = restriction,
                 nSim = input$nSim,
+
                 kdeType = input$kdeType)
 }
 
@@ -2212,6 +2217,7 @@ estimateMapKernelWrapper <- function(data, input) {
 #' @param dateUnc character: one of "uniform", "normal", "point"
 #' @param restriction numeric vector: spatially restricts model data 4 entries for latitude (min/max) and longitude(min/max)
 #' @param nSim numeric: number of bootstrap samples
+#' @param smoothness numeric: smoothness adjustment
 #' @param kdeType character: "1" for correlated bandwidth, "2" for diagonal bandwidth, "3" for diagonal, equal long/lat bandwidth
 #' @inheritParams centerData
 #' @examples
@@ -2245,6 +2251,7 @@ estimateMap3DKernel <- function(data,
                                 dateUnc = "point",
                                 restriction = c(-90, 90, -180, 180),
                                 nSim = 10,
+                                smoothness = 1,
                                 kdeType = "1") {
   center <- match.arg(center)
 
@@ -2377,7 +2384,8 @@ estimateMap3DKernel <- function(data,
         H = Hpi.diag(cbind(data3$Longitude, data3$Latitude, data3$Date2))
         diag(H)[1:2] <- prod(diag(H)[1:2]^0.5)
       }
-
+      #smoothness adjustment
+      H = H*smoothness
       kde(cbind(data3$Longitude, data3$Latitude, data3$Date2), H= H, w = data3[,Weighting])
     }), silent = TRUE)
   } else {
@@ -2400,6 +2408,8 @@ estimateMap3DKernel <- function(data,
         H = Hpi.diag(cbind(data3$Longitude, data3$Latitude, data3$Date2))
         diag(H) <- prod(diag(H)^0.5)
       }
+      #smoothness adjustment
+      H = H*smoothness
       kde(cbind(data3$Longitude, data3$Latitude, data3$Date2), H = H)}), silent = TRUE)
   }
 

R/03-modelResults2DKernel.R

@@ -91,6 +91,7 @@ modelResults2DKernelUI <- function(id, title = "", asFruitsTab = FALSE){
             ns = ns
           )
         ),
+        sliderInput(ns("smoothParam"), value = 1.0, min = 0.1, max = 5.0, step = 0.1, label = "Adjust smoothness (optional)"),
         radioButtons(ns("kdeType"), "Bandwidth matrix type",
                      choices = c("Correlated" = "1", "Diagonal" = "2", "Diagonal + equal in longitudes and latitudes" = "3")),
         actionButton( ns("start"), "Start"),
@@ -515,6 +516,7 @@ modelResults2DKernel <- function(input, output, session, isoData, savedMaps, fru
                   trimRatio = input$trimRatio,
                   restriction = restriction,
                   nSim = input$nSim,
+                  smoothness = input$smoothParam,
                   kdeType = input$kdeType) %>%
         tryCatchWithWarningsAndErrors()
       },

R/03-modelResults3DKernel.R

@@ -117,6 +117,7 @@ modelResults3DKernelUI <- function(id, title = ""){
             ns = ns
           )
         ),
+        sliderInput(ns("smoothParam"), value = 1.0, min = 0.1, max = 5.0, step = 0.1, label = "Adjust smoothness (optional)"),
         radioButtons(ns("kdeType"), "Bandwidth matrix type",
                      choices = c("Correlated" = "1", "Diagonal" = "2", "Diagonal + equal in longitudes and latitudes" = "3")),
         actionButton( ns("start"), "Start"),
@@ -627,6 +628,7 @@ modelResults3DKernel <- function(input, output, session, isoData, savedMaps, fru
                       modelUnc = input$modelUnc,
                       restriction = restriction,
                       nSim = input$nSim,
+                      smoothness = input$smoothParam,
                       kdeType = input$kdeType) %>%
           tryCatchWithWarningsAndErrors()
         },