Merge pull request #1 from rubak/master

Adapt to new spatstat.random package.
machiela-lab · Feb 2, 2022 · 4df5d85 · 4df5d85
2 parents 3ee98b0 + 6bbdea5
commit 4df5d85
Show file tree

Hide file tree

Showing 12 changed files with 45 additions and 50 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,10 +38,6 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Depends: 
     R (>= 3.5.0),
-    spatstat.geom,
-    spatstat.core,
-    spatstat.linnet,
-    spatstat (>= 2.0-0)
 Imports: 
     doFuture,
     doRNG,
@@ -55,8 +51,12 @@ Imports:
     raster,
     sp,
     sparr,
+    spatstat.geom,
+    spatstat.random,
     stats
 Suggests: 
+    spatstat.data,
+    spatstat (>= 2.0-0),
     testthat,
     spelling,
     R.rsp

diff --git a/NAMESPACE b/NAMESPACE
@@ -5,10 +5,7 @@ export(pval_correct)
 export(spatial_data)
 export(spatial_plots)
 export(spatial_power)
-import(spatstat)
-import(spatstat.core)
 import(spatstat.geom)
-import(spatstat.linnet)
 importFrom(doFuture,registerDoFuture)
 importFrom(doRNG,"%dorng%")
 importFrom(fields,image.plot)
@@ -33,10 +30,6 @@ importFrom(raster,values)
 importFrom(sp,coordinates)
 importFrom(sp,gridded)
 importFrom(sparr,risk)
-importFrom(spatstat.core,rNeymanScott)
-importFrom(spatstat.core,rpoispp)
-importFrom(spatstat.core,runifdisc)
-importFrom(spatstat.core,runifpoint)
 importFrom(spatstat.geom,as.solist)
 importFrom(spatstat.geom,disc)
 importFrom(spatstat.geom,marks)
@@ -47,6 +40,10 @@ importFrom(spatstat.geom,rsyst)
 importFrom(spatstat.geom,shift)
 importFrom(spatstat.geom,superimpose)
 importFrom(spatstat.geom,unit.square)
+importFrom(spatstat.random,rNeymanScott)
+importFrom(spatstat.random,rpoispp)
+importFrom(spatstat.random,runifdisc)
+importFrom(spatstat.random,runifpoint)
 importFrom(stats,na.omit)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
diff --git a/R/jitter_power.R b/R/jitter_power.R
@@ -56,7 +56,7 @@
 #' @importFrom future multisession plan
 #' @importFrom lifecycle badge deprecate_warn deprecated is_present
 #' @importFrom sparr risk
-#' @importFrom spatstat.core rpoispp runifpoint
+#' @importFrom spatstat.random rpoispp runifpoint
 #' @importFrom spatstat.geom marks ppp superimpose
 #' @importFrom stats sd
 #' @export
@@ -65,7 +65,7 @@
 #'
 #' @examples
 #' # Using the 'chorley' data set from 'spatstat.data' package
-#'  data(chorley)
+#'  data(chorley, package="spatstat.data")
 #'  f1 <- jitter_power(obs_data = unique(chorley),
 #'                     samp_control = "CSR",
 #'                     verbose = FALSE)
@@ -107,13 +107,13 @@ jitter_power <- function(obs_data,
   rcluster_control <- function(n, l, win, s, types = "control", ...) {
     if (samp_control == "uniform") {
       repeat {  
-        x <- spatstat.core::runifpoint(n = n, win = win, ...)
+        x <- spatstat.random::runifpoint(n = n, win = win, ...)
         if (x$n == n) break
       }
     }
 
     if (samp_control == "CSR") {
-      x <- spatstat.core::rpoispp(lambda = l, win = win, ...)
+      x <- spatstat.random::rpoispp(lambda = l, win = win, ...)
     }
 
     if (samp_control == "MVN") {

diff --git a/R/package.R b/R/package.R
@@ -26,7 +26,7 @@
 #' @aliases sparrpowR-package sparrpowR
 #' @docType package
 #' 
-#' @section Dependencies: The 'sparrpowR' package relies heavily upon \code{\link{sparr}}, \code{\link{spatstat.core}}, \code{\link{spatstat.geom}}, and \code{\link{raster}} for computing the statistical power and visualizing the output. Computation can be performed in parallel using \code{\link{doFuture}}, \code{\link[future]{multisession}}, \code{\link{doRNG}}, and \code{\link[foreach]{foreach}}. Basic visualizations rely on the \code{\link[spatstat.geom]{plot.ppp}} and \code{\link[fields]{image.plot}} functions.
+#' @section Dependencies: The 'sparrpowR' package relies heavily upon \code{\link{sparr}}, \code{\link{spatstat.random}}, \code{\link{spatstat.geom}}, and \code{\link{raster}} for computing the statistical power and visualizing the output. Computation can be performed in parallel using \code{\link{doFuture}}, \code{\link[future]{multisession}}, \code{\link{doRNG}}, and \code{\link[foreach]{foreach}}. Basic visualizations rely on the \code{\link[spatstat.geom]{plot.ppp}} and \code{\link[fields]{image.plot}} functions.
 #' 
 #' @author Ian D. Buller\cr \emph{Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.} \cr\cr
 #' Derek W. Brown\cr \emph{Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.}
@@ -50,7 +50,4 @@ NULL
 #' @importFrom sparr risk
 #' @importFrom stats na.omit rnorm sd
 #' @import spatstat.geom
-#' @import spatstat.core
-#' @import spatstat.linnet
-#' @import spatstat
 NULL
diff --git a/R/spatial_data.R b/R/spatial_data.R
@@ -20,9 +20,9 @@
 #' @param l_case Optional. A single positive number, a vector of positive numbers, a function(x,y, ...), or a pixel image. Intensity of the Poisson process for case clusters. Ignored if \code{samp_control != "IPP"}.
 #' @param l_control Optional. A single positive number, a vector of positive numbers, a function(x,y, ...), or a pixel image. Intensity of the Poisson process for control clusters. Ignored if \code{samp_control = "uniform"}, \code{samp_control = "systematic"}, \code{samp_control = "MVN"}, or \code{samp_control = "CSR"}.
 #' @param e_control Optional. A single non-negative number for the size of the expansion of the simulation window for generating parent points. Ignored if \code{samp_control != "clustered"}.
-#' @param ... Arguments passed to \code{\link[spatstat.core]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.core]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.core]{rNeymanScott}} depending on \code{samp_control} or \code{samp_control}.
+#' @param ... Arguments passed to \code{\link[spatstat.random]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.random]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.random]{rNeymanScott}} depending on \code{samp_control} or \code{samp_control}.
 #' 
-#' @details This function generates random data for a spatial relative risk function (nonparametric estimate of relative risk by kernel smoothing) using various random point pattern generators from the \code{\link{spatstat.core}} package to generate data.
+#' @details This function generates random data for a spatial relative risk function (nonparametric estimate of relative risk by kernel smoothing) using various random point pattern generators from the \code{\link{spatstat.random}} package to generate data.
 #' 
 #' If \code{samp_case = "uniform"} the case locations are randomly generated uniformly within a disc of radius \code{r_case} (or discs of radii \code{r_case}) centered at coordinates (\code{x_case}, \code{y_case}). 
 #' 
@@ -47,11 +47,11 @@
 #' @return An object of class "ppplist". This is a list of marked point patterns that have a single mark with two levels: case and control.
 #' 
 #' @importFrom stats rnorm
-#' @importFrom spatstat.core rNeymanScott rpoispp runifdisc runifpoint
+#' @importFrom spatstat.random rNeymanScott rpoispp runifdisc runifpoint
 #' @importFrom spatstat.geom as.solist disc marks ppp rsyst shift superimpose unit.square
 #' @export
 #'
-#' @seealso \code{\link[spatstat.core]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.core]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.core]{rNeymanScott}} for additional arguments for random point pattern generation.
+#' @seealso \code{\link[spatstat.random]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.random]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.random]{rNeymanScott}} for additional arguments for random point pattern generation.
 #'
 #' @examples
 #'  spatial_data(x_case = c(0.25, 0.5, 0.75),
@@ -139,7 +139,7 @@ spatial_data <- function(win = spatstat.geom::unit.square(),
   rcluster_case <- function(x0, y0, rad, n, scalar, lamb, wind, types = "case", ...) {
 
     if (samp_case == "uniform"){
-      x <- spatstat.core::runifdisc(n = n, radius = rad, centre = c(x0, y0), win = wind, ...)
+      x <- spatstat.random::runifdisc(n = n, radius = rad, centre = c(x0, y0), win = wind, ...)
     }  
 
     if (samp_case == "MVN"){
@@ -153,7 +153,7 @@ spatial_data <- function(win = spatstat.geom::unit.square(),
     if (samp_case == "CSR"){
       win_case <- spatstat.geom::disc(radius = rad, centre = c(0.5, 0.5), ...)
       l <- n / (diff(win_case$xrange)*diff(win_case$yrange))
-      x <- spatstat.core::rpoispp(lambda = l, win = win_case, ...)
+      x <- spatstat.random::rpoispp(lambda = l, win = win_case, ...)
       x <- spatstat.geom::shift(x, c(x0 - 0.5, y0 - 0.5))
     }
 
@@ -162,7 +162,7 @@ spatial_data <- function(win = spatstat.geom::unit.square(),
         stop("The argument 'l_case' should be an intensity function")
       }
       win_case <- spatstat.geom::disc(radius = rad, centre = c(0.5, 0.5), ...)
-      x <- spatstat.core::rpoispp(lambda = lamb, win = win_case, ...)
+      x <- spatstat.random::rpoispp(lambda = lamb, win = win_case, ...)
       x <- spatstat.geom::shift(x, c(x0 - 0.5, y0 - 0.5))
     }
 
@@ -173,7 +173,7 @@ spatial_data <- function(win = spatstat.geom::unit.square(),
   # marked uniform ppp for controls
   rcluster_control <- function(x0, y0, scalar, n, lamb, ex, nclust, rad, types = "control", wind, ...) {
     if (samp_control == "uniform"){ 
-      x <- spatstat.core::runifpoint(n, win = wind, ...) 
+      x <- spatstat.random::runifpoint(n, win = wind, ...) 
     }
 
     if (samp_control == "systematic") {
@@ -190,22 +190,22 @@ spatial_data <- function(win = spatstat.geom::unit.square(),
 
     if (samp_control == "CSR") {
       l <- n / (diff(wind$xrange)*diff(wind$yrange))
-      x <- spatstat.core::rpoispp(lambda = l, win = wind, ...)
+      x <- spatstat.random::rpoispp(lambda = l, win = wind, ...)
     }
 
     if (samp_control == "IPP") {
       if (class(lamb) != "function") {
         stop("The argument 'l_control' should be an intensity function")
       }
-      x <- spatstat.core::rpoispp(lambda = lamb, win = wind, ...)
+      x <- spatstat.random::rpoispp(lambda = lamb, win = wind, ...)
     }
 
     if (samp_control == "clustered") {
       control_clustering <- function(x0, y0, radius, n) {
-        X <- spatstat.core::runifdisc(n, radius, centre = c(x0, y0))
+        X <- spatstat.random::runifdisc(n, radius, centre = c(x0, y0))
         return(X)
       }
-      x <- spatstat.core::rNeymanScott(kappa = lamb,
+      x <- spatstat.random::rNeymanScott(kappa = lamb,
                                   expand = ex,
                                   rcluster = control_clustering, 
                                   n = nclust,

diff --git a/R/spatial_power.R b/R/spatial_power.R
@@ -25,12 +25,12 @@
 #' @param parallel Logical. If TRUE, will execute the function in parallel. If FALSE (the default), will not execute the function in parallel.
 #' @param n_core Optional. Integer specifying the number of CPU cores on current host to use for parallelization (the default is 2 cores).
 #' @param verbose Logical. If TRUE (the default), will print function progress during execution. If FALSE, will not print.
-#' @param ... Arguments passed to \code{\link[spatstat.core]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.core]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.core]{rNeymanScott}} depending on \code{samp_control} or \code{samp_control}. Arguments also passed to \code{\link[sparr]{risk}} to select bandwidth, edge correction, and resolution.
+#' @param ... Arguments passed to \code{\link[spatstat.random]{runifdisc}}, \code{\link[spatstat.geom]{disc}}, \code{\link[spatstat.random]{rpoispp}}, \code{\link[spatstat.geom]{rsyst}}, or \code{\link[spatstat.random]{rNeymanScott}} depending on \code{samp_control} or \code{samp_control}. Arguments also passed to \code{\link[sparr]{risk}} to select bandwidth, edge correction, and resolution.
 #' @param cascon `r lifecycle::badge("deprecated")` \code{cascon} is no longer supported and this function will output power for case-only and case/control clustering. This argument has been moved to \code{spatial_plots} function.
 #' @param lower_tail `r lifecycle::badge("deprecated")` \code{lower_tail} is no longer supported; this function uses \code{alpha} to set the critical p-value. 
 #' @param upper_tail `r lifecycle::badge("deprecated")` \code{lupper_tail} is no longer supported; this function uses \code{alpha} to set the critical p-value. 
 #'
-#' @details This function computes the statistical power of the spatial relative risk function (nonparametric estimate of relative risk by kernel smoothing) for randomly generated data using various random point pattern generators from the \code{\link{spatstat.core}} package.
+#' @details This function computes the statistical power of the spatial relative risk function (nonparametric estimate of relative risk by kernel smoothing) for randomly generated data using various random point pattern generators from the \code{\link{spatstat.random}} package.
 #' 
 #' The function uses the \code{\link[sparr]{risk}} function to estimate the spatial relative risk function and forces the \code{tolerate} argument to be TRUE in order to calculate asymptotic p-values.
 #' 
@@ -86,7 +86,7 @@
 #' @importFrom iterators icount
 #' @importFrom lifecycle badge deprecate_warn deprecated is_present
 #' @importFrom sparr risk
-#' @importFrom spatstat.core rNeymanScott rpoispp runifdisc runifpoint
+#' @importFrom spatstat.random rNeymanScott rpoispp runifdisc runifpoint
 #' @importFrom spatstat.geom as.solist disc marks ppp rsyst shift superimpose unit.square
 #' @importFrom stats rnorm sd
 #' @export
@@ -198,7 +198,7 @@ spatial_power <- function(win = spatstat.geom::unit.square(),
   rcluster_case <- function(x0, y0, rad, n, scalar, lamb, win, types = "case", ...) {
 
     if (samp_case == "uniform") {
-      x <- spatstat.core::runifdisc(n = n, radius = rad, centre = c(x0, y0), win = win, ...)
+      x <- spatstat.random::runifdisc(n = n, radius = rad, centre = c(x0, y0), win = win, ...)
     }  
 
     if (samp_case == "MVN") {
@@ -212,7 +212,7 @@ spatial_power <- function(win = spatstat.geom::unit.square(),
     if (samp_case == "CSR") {
       win_case <- spatstat.geom::disc(radius = rad, centre = c(0.5, 0.5), ...)
       l <- n/(diff(win_case$xrange)*diff(win_case$yrange))
-      x <- spatstat.core::rpoispp(lambda = l, win = win_case, ...)
+      x <- spatstat.random::rpoispp(lambda = l, win = win_case, ...)
       x <- spatstat.geom::shift(x, c(x0 - 0.5, y0 - 0.5))
      }
 
@@ -221,7 +221,7 @@ spatial_power <- function(win = spatstat.geom::unit.square(),
         stop("The argument 'l_case' should be an intensity function")
        }
       win_case <- spatstat.geom::disc(radius = rad, centre = c(0.5, 0.5), ...)
-      x <- spatstat.core::rpoispp(lambda = lamb, win = win_case, ...)
+      x <- spatstat.random::rpoispp(lambda = lamb, win = win_case, ...)
       x <- spatstat.geom::shift(x, c(x0 - 0.5, y0 - 0.5))
      }
 
@@ -232,7 +232,7 @@ spatial_power <- function(win = spatstat.geom::unit.square(),
   # marked uniform ppp for controls
   rcluster_control <- function(x0, y0, scalar, n, lamb, ex, nclust, rad, types = "control", win, ...) {
     if (samp_control == "uniform") { 
-      x <- spatstat.core::runifpoint(n, win = win, ...) 
+      x <- spatstat.random::runifpoint(n, win = win, ...) 
      }
 
     if (samp_control == "systematic") {
@@ -249,22 +249,22 @@ spatial_power <- function(win = spatstat.geom::unit.square(),
 
     if (samp_control == "CSR") {
       l <- n / (diff(win$xrange) * diff(win$yrange))
-      x <- spatstat.core::rpoispp(lambda = l, win = win, ...)
+      x <- spatstat.random::rpoispp(lambda = l, win = win, ...)
      }
 
     if (samp_control == "IPP") {
       if (class(lamb) != "function") {
         stop("The argument 'l_control' should be an intensity function")
       }
-      x <- spatstat.core::rpoispp(lambda = lamb, win = win, ...)
+      x <- spatstat.random::rpoispp(lambda = lamb, win = win, ...)
     }
 
     if (samp_control == "clustered") {
       control_clustering <- function(x0, y0, radius, n) {
-        X <- spatstat.core::runifdisc(n, radius, centre = c(x0, y0))
+        X <- spatstat.random::runifdisc(n, radius, centre = c(x0, y0))
         return(X)
        }
-      x <- spatstat.core::rNeymanScott(kappa = lamb,
+      x <- spatstat.random::rNeymanScott(kappa = lamb,
                                        expand = ex,
                                        rcluster = control_clustering, 
                                        n = nclust,

diff --git a/dev/build.R b/dev/build.R
@@ -169,7 +169,7 @@ t2 <- Sys.time()
 t2-t1
 spatial_plots(tttt)
 
-data(chorley)
+data(chorley, package="spatstat.data")
 t1 <- Sys.time()
 f1 <- jitter_power(obs_data = unique(chorley),
                   samp_control = "CSR",

diff --git a/man/jitter_power.Rd b/man/jitter_power.Rd
diff --git a/man/sparrpowR-package.Rd b/man/sparrpowR-package.Rd