From bef7dd540344b196282b34d87dd441528d0bc97f Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 13:55:39 +0800
Subject: [PATCH 1/9] update parallel computing settomh up

---
 R/spc.R                | 32 +++++++++++++++-----------------
 R/ssh_marginalcontri.R |  8 ++++----
 2 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/R/spc.R b/R/spc.R
index 94a352e..a155e0d 100644
--- a/R/spc.R
+++ b/R/spc.R
@@ -3,13 +3,9 @@
 #' @param data A `data.frame`, `tibble` or `sf` object of observation data.
 #' @param overlay (optional) Spatial overlay method. One of `and`, `or`, `intersection`.
 #' Default is `and`.
-#' @param discnum A numeric vector of discretized classes of columns that need to be discretized.
-#' Default all `discvar` use `3:8`.
-#' @param minsize (optional) The min size of each discretization group. Default all use `1`.
-#' @param strategy (optional) Optimal discretization strategy. When `strategy` is `1L`, choose the highest
-#' q-statistics to determinate optimal spatial data discretization parameters. When `strategy` is `2L`,
-#' The optimal discrete parameters of spatial data are selected by combining LOESS model.
-#' @param increase_rate (optional) The critical increase rate of the number of discretization. Default is `5%`.
+#' @param discnum (optional) A vector of number of classes for discretization. Default is `3:8`.
+#' @param discmethod (optional) A vector of methods for discretization, default is using
+#' `c("sd","equal","geometric","quantile","natural")` by invoking `sdsfun`.
 #' @param cores (optional) Positive integer (default is 1). When cores are greater than 1, use
 #' multi-core parallel computing.
 #'
@@ -28,25 +24,27 @@
 #' g
 #' }
 #'
-spc = \(data, overlay = 'and', discnum = 3:8, minsize = 1,
-        strategy = 2L, increase_rate = 0.05, cores = 1){
+spc = \(data, overlay = 'and', discnum = 3:8,
+        discmethod = c("sd","equal","geometric","quantile","natural"),
+        cores = 1){
   if (inherits(data,'sf')) {
     data = sf::st_drop_geometry(data)
   }
   xsname = names(data)
-  calcul_spcv = \(yname,data,overlay,discnum,minsize,strategy,increase_rate,cores){
-    rgd_res = gdverse::rgd(paste0(yname," ~ ."), data = data, discnum = discnum,
-                           minsize = minsize, strategy = strategy,
-                           increase_rate = increase_rate, cores = cores)
-    dti = dplyr::bind_cols(dplyr::select(data,dplyr::all_of(yname)),rgd_res$opt_disc)
+  calcul_spcv = \(yname,data,overlay,discn,discm,cores){
+    opgd_res = gdverse::gd_optunidisc(
+      paste0(yname," ~ ."), data = data, discnum = discn,
+      discmethod = discm, cores = cores
+    )
+    dti = dplyr::bind_cols(dplyr::select(data,dplyr::all_of(yname)),opgd_res$disc)
     sshmcv = cisp::ssh_marginalcontri(paste0(yname," ~ ."), data = dti,
                                       overlay = overlay, cores = cores)
     return(sshmcv$spd)
   }
   res = purrr::map_dfr(xsname,
-                       \(.x) calcul_spcv(.x,data = data,overlay = overlay,
-                              discnum = discnum,minsize = minsize,strategy = strategy,
-                              increase_rate = increase_rate, cores = cores) |>
+                       \(.x) calcul_spcv(.x, data = data, overlay = overlay,
+                                         discn = discnum, discm = discmethod,
+                                         cores = cores) |>
                      dplyr::mutate(yv = .x) |>
                      dplyr::rename(xv = variable,
                                    correlation = spd) |>
diff --git a/R/ssh_marginalcontri.R b/R/ssh_marginalcontri.R
index 07bb2af..c9b9344 100644
--- a/R/ssh_marginalcontri.R
+++ b/R/ssh_marginalcontri.R
@@ -64,12 +64,12 @@ ssh_marginalcontri = \(formula, data, overlay = 'and', cores = 1){
   doclust = FALSE
   if (cores > 1) {
     doclust = TRUE
-    cores = parallel::makeCluster(cores)
-    on.exit(parallel::stopCluster(cores), add=TRUE)
+    cl = parallel::makeCluster(cores)
+    on.exit(parallel::stopCluster(cl), add=TRUE)
   }
 
   if (doclust) {
-    out_pdv = parallel::parLapply(cores, xs, calcul_pd,
+    out_pdv = parallel::parLapply(cl, xs, calcul_pd,
                                   dti = data, overlay = overlay)
     out_pdv = tibble::as_tibble(do.call(rbind, out_pdv))
   } else {
@@ -110,7 +110,7 @@ ssh_marginalcontri = \(formula, data, overlay = 'and', cores = 1){
   }
 
   if (doclust) {
-    out_g = parallel::parLapply(cores,xname,calcul_shap)
+    out_g = parallel::parLapply(cl,xname,calcul_shap)
     out_g = tibble::as_tibble(do.call(rbind, out_g))
   } else {
     out_g = purrr::map_dfr(xname,calcul_shap)

From 6288f85ff5d6c1d19de78b4f246c13c799c9b7c8 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 14:16:41 +0800
Subject: [PATCH 2/9] update `gdverse` dependence version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7b84ed5..e6201d1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,7 @@ Depends:
 Imports: 
     dplyr,
     forcats,
-    gdverse (>= 1.3-1),
+    gdverse (>= 1.3-2),
     ggplot2,
     ggraph,
     igraph,

From 39a45209bc5c631aab038206f7d8cfe63a2ebedc Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 14:54:31 +0800
Subject: [PATCH 3/9] update `spc` docs

---
 R/spc.R    |  1 -
 man/spc.Rd | 17 ++++-------------
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/R/spc.R b/R/spc.R
index a155e0d..286831d 100644
--- a/R/spc.R
+++ b/R/spc.R
@@ -23,7 +23,6 @@
 #' g = spc(sim1, discnum = 3:6, cores = 1)
 #' g
 #' }
-#'
 spc = \(data, overlay = 'and', discnum = 3:8,
         discmethod = c("sd","equal","geometric","quantile","natural"),
         cores = 1){
diff --git a/man/spc.Rd b/man/spc.Rd
index a348c1f..8437eaf 100644
--- a/man/spc.Rd
+++ b/man/spc.Rd
@@ -8,9 +8,7 @@ spc(
   data,
   overlay = "and",
   discnum = 3:8,
-  minsize = 1,
-  strategy = 2L,
-  increase_rate = 0.05,
+  discmethod = c("sd", "equal", "geometric", "quantile", "natural"),
   cores = 1
 )
 }
@@ -20,16 +18,10 @@ spc(
 \item{overlay}{(optional) Spatial overlay method. One of \code{and}, \code{or}, \code{intersection}.
 Default is \code{and}.}
 
-\item{discnum}{A numeric vector of discretized classes of columns that need to be discretized.
-Default all \code{discvar} use \code{3:8}.}
+\item{discnum}{(optional) A vector of number of classes for discretization. Default is \code{3:8}.}
 
-\item{minsize}{(optional) The min size of each discretization group. Default all use \code{1}.}
-
-\item{strategy}{(optional) Optimal discretization strategy. When \code{strategy} is \code{1L}, choose the highest
-q-statistics to determinate optimal spatial data discretization parameters. When \code{strategy} is \code{2L},
-The optimal discrete parameters of spatial data are selected by combining LOESS model.}
-
-\item{increase_rate}{(optional) The critical increase rate of the number of discretization. Default is \verb{5\%}.}
+\item{discmethod}{(optional) A vector of methods for discretization, default is using
+\code{c("sd","equal","geometric","quantile","natural")} by invoking \code{sdsfun}.}
 
 \item{cores}{(optional) Positive integer (default is 1). When cores are greater than 1, use
 multi-core parallel computing.}
@@ -51,5 +43,4 @@ sim1 = sf::st_as_sf(gdverse::sim,coords = c('lo','la'))
 g = spc(sim1, discnum = 3:6, cores = 1)
 g
 }
-
 }

From bc9ec43dd85faa8cf4fe1e6eedbdc80f92ed4149 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:17:04 +0800
Subject: [PATCH 4/9] update `spc` result name

---
 R/spc.R    | 12 ++++++------
 man/spc.Rd |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/spc.R b/R/spc.R
index 286831d..e4463f3 100644
--- a/R/spc.R
+++ b/R/spc.R
@@ -11,8 +11,8 @@
 #'
 #' @return A list.
 #' \describe{
-#' \item{\code{correlation_tbl}}{A tibble with power of spatial pattern correlation}
-#' \item{\code{correlation_mat}}{A matrix with power of spatial pattern correlation}
+#' \item{\code{cor_tbl}}{A tibble with power of spatial pattern correlation}
+#' \item{\code{cor_mat}}{A matrix with power of spatial pattern correlation}
 #' }
 #' @export
 #'
@@ -53,7 +53,7 @@ spc = \(data, overlay = 'and', discnum = 3:8,
     tibble::column_to_rownames(var = 'xv') |>
     as.matrix()
   res_mat[is.na(res_mat)] = 1
-  res = list("correlation_tbl" = res,"correlation_mat" = res_mat)
+  res = list("cor_tbl" = res,"cor_mat" = res_mat)
   class(res) = 'spc_result'
   return(res)
 }
@@ -64,7 +64,7 @@ spc = \(data, overlay = 'and', discnum = 3:8,
 #'
 print.spc_result = \(x, ...) {
   cat("***   Spatial Pattern Correlation    ")
-  print(knitr::kable(x$correlation_tbl, format = "markdown", digits = 5, align = 'c', ...))
+  print(knitr::kable(x$cor_tbl, format = "markdown", digits = 5, align = 'c', ...))
 }
 
 #' @title plot spc result
@@ -75,7 +75,7 @@ plot.spc_result = \(x, style = c("network","matrix"), ...) {
   style = match.arg(style)
   switch(style,
          "network" = {
-           g = igraph::graph_from_data_frame(x$correlation_tbl, directed = TRUE)
+           g = igraph::graph_from_data_frame(x$cor_tbl, directed = TRUE)
            fig_g = ggraph::ggraph(g, layout = "circle") +
              ggraph::geom_edge_arc(ggplot2::aes(width = abs(correlation), color = correlation),
                                    arrow = grid::arrow(type = "closed", length = grid::unit(3, "mm")),
@@ -96,7 +96,7 @@ plot.spc_result = \(x, style = c("network","matrix"), ...) {
              ggplot2::labs(edge_color = "Strength")
          },
          "matrix" = {
-           g = x$correlation_tbl
+           g = x$cor_tbl
            fig_g = ggplot2::ggplot(data = g,
                                    ggplot2::aes(x = yv, y = xv, fill = correlation)) +
              ggplot2::geom_tile(color = "white") +
diff --git a/man/spc.Rd b/man/spc.Rd
index 8437eaf..25f58a0 100644
--- a/man/spc.Rd
+++ b/man/spc.Rd
@@ -29,8 +29,8 @@ multi-core parallel computing.}
 \value{
 A list.
 \describe{
-\item{\code{correlation_tbl}}{A tibble with power of spatial pattern correlation}
-\item{\code{correlation_mat}}{A matrix with power of spatial pattern correlation}
+\item{\code{cor_tbl}}{A tibble with power of spatial pattern correlation}
+\item{\code{cor_mat}}{A matrix with power of spatial pattern correlation}
 }
 }
 \description{

From c772681992c3ecc09a474fba701721cc6521e7c4 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:21:23 +0800
Subject: [PATCH 5/9] update `spc` docs

---
 R/spc.R    | 8 ++++----
 man/spc.Rd | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/spc.R b/R/spc.R
index e4463f3..9df606e 100644
--- a/R/spc.R
+++ b/R/spc.R
@@ -6,8 +6,8 @@
 #' @param discnum (optional) A vector of number of classes for discretization. Default is `3:8`.
 #' @param discmethod (optional) A vector of methods for discretization, default is using
 #' `c("sd","equal","geometric","quantile","natural")` by invoking `sdsfun`.
-#' @param cores (optional) Positive integer (default is 1). When cores are greater than 1, use
-#' multi-core parallel computing.
+#' @param cores (optional) Positive integer (default is 1). When cores are greater than 1,
+#' use parallel computing.
 #'
 #' @return A list.
 #' \describe{
@@ -17,9 +17,9 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' ## The following code needs to configure the Python environment to run:
 #' sim1 = sf::st_as_sf(gdverse::sim,coords = c('lo','la'))
+#' sim1
+#' \donttest{
 #' g = spc(sim1, discnum = 3:6, cores = 1)
 #' g
 #' }
diff --git a/man/spc.Rd b/man/spc.Rd
index 25f58a0..e55d25b 100644
--- a/man/spc.Rd
+++ b/man/spc.Rd
@@ -23,8 +23,8 @@ Default is \code{and}.}
 \item{discmethod}{(optional) A vector of methods for discretization, default is using
 \code{c("sd","equal","geometric","quantile","natural")} by invoking \code{sdsfun}.}
 
-\item{cores}{(optional) Positive integer (default is 1). When cores are greater than 1, use
-multi-core parallel computing.}
+\item{cores}{(optional) Positive integer (default is 1). When cores are greater than 1,
+use parallel computing.}
 }
 \value{
 A list.
@@ -37,9 +37,9 @@ A list.
 spatial pattern correlation
 }
 \examples{
-\dontrun{
-## The following code needs to configure the Python environment to run:
 sim1 = sf::st_as_sf(gdverse::sim,coords = c('lo','la'))
+sim1
+\donttest{
 g = spc(sim1, discnum = 3:6, cores = 1)
 g
 }

From 556407d164a09a0f4cef14b466484e6475c76eb0 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:24:19 +0800
Subject: [PATCH 6/9] =?UTF-8?q?Temporarily=20use=20the=20development=20ver?=
 =?UTF-8?q?sion=20of=20gdverse,=20waiting=20for=20its=20release=20on=20CRA?=
 =?UTF-8?q?N=E2=80=98?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index e6201d1..553d990 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -42,4 +42,6 @@ Imports:
 Suggests: 
     knitr,
     rmarkdown
+Remotes:
+    stscl/sdsfun
 VignetteBuilder: knitr

From d72285a1da2d33e6d187532d12fb032204101f44 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:27:34 +0800
Subject: [PATCH 7/9] update docs

---
 R/spc.R                   | 3 +--
 R/ssh_marginalcontri.R    | 6 ++----
 man/spc.Rd                | 1 +
 man/ssh_marginalcontri.Rd | 4 ++--
 4 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/R/spc.R b/R/spc.R
index 9df606e..cdaac3c 100644
--- a/R/spc.R
+++ b/R/spc.R
@@ -22,6 +22,7 @@
 #' \donttest{
 #' g = spc(sim1, discnum = 3:6, cores = 1)
 #' g
+#' plot(g,"matrix")
 #' }
 spc = \(data, overlay = 'and', discnum = 3:8,
         discmethod = c("sd","equal","geometric","quantile","natural"),
@@ -61,7 +62,6 @@ spc = \(data, overlay = 'and', discnum = 3:8,
 #' @title print spc result
 #' @export
 #' @noRd
-#'
 print.spc_result = \(x, ...) {
   cat("***   Spatial Pattern Correlation    ")
   print(knitr::kable(x$cor_tbl, format = "markdown", digits = 5, align = 'c', ...))
@@ -70,7 +70,6 @@ print.spc_result = \(x, ...) {
 #' @title plot spc result
 #' @export
 #' @noRd
-#'
 plot.spc_result = \(x, style = c("network","matrix"), ...) {
   style = match.arg(style)
   switch(style,
diff --git a/R/ssh_marginalcontri.R b/R/ssh_marginalcontri.R
index c9b9344..d0521b4 100644
--- a/R/ssh_marginalcontri.R
+++ b/R/ssh_marginalcontri.R
@@ -4,8 +4,8 @@
 #' @param data A `data.frame`, `tibble` or `sf` object of observation data.
 #' @param overlay (optional) Spatial overlay method. One of `and`, `or`, `intersection`.
 #' Default is `and`.
-#' @param cores (optional) Positive integer (default is 1). When cores are greater than 1, use
-#' multi-core parallel computing.
+#' @param cores (optional) Positive integer (default is 1). When cores are greater than 1,
+#' use parallel computing.
 #'
 #' @return A list.
 #' \describe{
@@ -166,7 +166,6 @@ ssh_marginalcontri = \(formula, data, overlay = 'and', cores = 1){
 #' @title print ssh_marginalcontri result
 #' @export
 #' @noRd
-#'
 print.sshmc_result = \(x, ...) {
   cat("***   SSH Marginal Contributions    ")
   print(knitr::kable(x$spd, format = "markdown", digits = 12, align = 'c', ...))
@@ -175,7 +174,6 @@ print.sshmc_result = \(x, ...) {
 #' @title plot ssh_marginalcontri result
 #' @export
 #' @noRd
-#'
 plot.sshmc_result = \(x, low_color = "#6600CC",
                       high_color = "#FFCC33", ...){
   g = x$determination
diff --git a/man/spc.Rd b/man/spc.Rd
index e55d25b..86353c4 100644
--- a/man/spc.Rd
+++ b/man/spc.Rd
@@ -42,5 +42,6 @@ sim1
 \donttest{
 g = spc(sim1, discnum = 3:6, cores = 1)
 g
+plot(g,"matrix")
 }
 }
diff --git a/man/ssh_marginalcontri.Rd b/man/ssh_marginalcontri.Rd
index c1237ab..1355de0 100644
--- a/man/ssh_marginalcontri.Rd
+++ b/man/ssh_marginalcontri.Rd
@@ -14,8 +14,8 @@ ssh_marginalcontri(formula, data, overlay = "and", cores = 1)
 \item{overlay}{(optional) Spatial overlay method. One of \code{and}, \code{or}, \code{intersection}.
 Default is \code{and}.}
 
-\item{cores}{(optional) Positive integer (default is 1). When cores are greater than 1, use
-multi-core parallel computing.}
+\item{cores}{(optional) Positive integer (default is 1). When cores are greater than 1,
+use parallel computing.}
 }
 \value{
 A list.

From 3093556ad135dfb43029f3116a44b5f7ba82abc2 Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:31:57 +0800
Subject: [PATCH 8/9] update examples

---
 R/ssh_marginalcontri.R    | 1 +
 man/ssh_marginalcontri.Rd | 1 +
 2 files changed, 2 insertions(+)

diff --git a/R/ssh_marginalcontri.R b/R/ssh_marginalcontri.R
index d0521b4..b8fc78e 100644
--- a/R/ssh_marginalcontri.R
+++ b/R/ssh_marginalcontri.R
@@ -19,6 +19,7 @@
 #' NTDs1 = sf::st_as_sf(gdverse::NTDs, coords = c('X','Y'))
 #' g = ssh_marginalcontri(incidence ~ ., data = NTDs1, cores = 1)
 #' g
+#' plot(g)
 #'
 ssh_marginalcontri = \(formula, data, overlay = 'and', cores = 1){
   formula = stats::as.formula(formula)
diff --git a/man/ssh_marginalcontri.Rd b/man/ssh_marginalcontri.Rd
index 1355de0..9f086ab 100644
--- a/man/ssh_marginalcontri.Rd
+++ b/man/ssh_marginalcontri.Rd
@@ -32,5 +32,6 @@ spatial association marginal contributions derived from spatial stratified heter
 NTDs1 = sf::st_as_sf(gdverse::NTDs, coords = c('X','Y'))
 g = ssh_marginalcontri(incidence ~ ., data = NTDs1, cores = 1)
 g
+plot(g)
 
 }

From 467205a70e09685389c93347cbe65a358f06c41f Mon Sep 17 00:00:00 2001
From: SpatLyu <lyu.geosocial@gmail.com>
Date: Thu, 23 Jan 2025 16:38:50 +0800
Subject: [PATCH 9/9] fix installation error

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 553d990..57c4759 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,5 +43,5 @@ Suggests:
     knitr,
     rmarkdown
 Remotes:
-    stscl/sdsfun
+    stscl/gdverse
 VignetteBuilder: knitr