Version 0.1.4. Add locked_in and locked_out arguments.

cadam00 · Jan 19, 2025 · bfe0ac5 · bfe0ac5
1 parent 74fbbe7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: priorCON
 Type: Package
 Title: Graph Community Detection Methods into Systematic Conservation Planning
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: c(person("Christos", "Adam", role = c("aut", "cre"),
              email = "[email protected]",
              comment = c(ORCID = "0009-0003-3244-7034")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,16 +4,17 @@ importFrom("brainGraph", "s_core")
 importFrom("grDevices", "terrain.colors")
 importFrom("stats", "complete.cases")
 importFrom("utils", "read.csv")
-importFrom("igraph", "graph_from_data_frame", "as.undirected", "simplify",
+importFrom("igraph", "graph_from_data_frame", "as_undirected", "simplify",
            "igraph_opt", "cluster_louvain", "sizes", "membership",
            "cluster_walktrap", "eigen_centrality", "betweenness", "strength",
            "as_data_frame", "E", "V", "delete_vertices", "page_rank")
 importFrom("sf", "st_sfc", "st_crs", "st_as_sf", "st_cast", "st_combine",
            "st_crs<-")
 importFrom("tmap", "tm_shape", "tm_raster", "tm_lines")
 importFrom("prioritizr", "problem", "add_max_utility_objective",
-       "add_binary_decisions", "add_relative_targets", "add_default_solver",
-       "eval_target_coverage_summary")
+           "add_binary_decisions", "add_relative_targets", "add_default_solver",
+           "eval_target_coverage_summary", "add_locked_in_constraints",
+           "add_locked_out_constraints")
 
 
 export("basic_scenario")

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# priorCON 0.1.4
+
+## Major changes
+
+- Add `locked_in` and `locked_out` arguments in `priorCON::basic_scenario` and
+`priorCON::connectivity_scenario`.
+
 # priorCON 0.1.3
 
 ## Minor changes

diff --git a/R/functions_connect.R b/R/functions_connect.R
@@ -99,7 +99,7 @@ get_metrics <- function(connect_mat, which_community="s_core"){
   colnames(edge_list_i) <- c("from","to","weight")
 
   directed_graph_wgt <- graph_from_data_frame(edge_list_i, directed = TRUE)
-  net_result <- as.undirected(directed_graph_wgt, mode = "collapse",
+  net_result <- as_undirected(directed_graph_wgt, mode = "collapse",
                               edge.attr.comb = "sum")
 
   # Simplifying graph
@@ -276,7 +276,7 @@ get_metrics <- function(connect_mat, which_community="s_core"){
     el        <- el[stats::complete.cases(el),]
 
     directed_graph_wgt       <- graph_from_data_frame(el, directed = TRUE)
-    net_result               <- as.undirected(directed_graph_wgt,
+    net_result               <- as_undirected(directed_graph_wgt,
                                               mode = "collapse",
                                               edge.attr.comb = "sum")
     net_result               <- simplify(net_result, remove.multiple = TRUE,
@@ -310,7 +310,8 @@ get_metrics <- function(connect_mat, which_community="s_core"){
 
 }
 
-basic_scenario <- function(cost_raster, features_rasters, budget_perc){
+basic_scenario <- function(cost_raster, features_rasters, budget_perc,
+                           locked_in = NULL, locked_out = NULL){
 
   if ((budget_perc < 0) || (budget_perc > 1))
     stop("budget_perc must be a numeric value between 0 and 1")
@@ -331,6 +332,14 @@ basic_scenario <- function(cost_raster, features_rasters, budget_perc){
     add_relative_targets(0.17) |>
     add_default_solver(verbose=FALSE)
 
+  if (!is.null(locked_in)){
+    p0 <- p0 |> add_locked_in_constraints(locked_in)
+  }
+
+  if (!is.null(locked_out)){
+    p0 <- p0 |> add_locked_out_constraints(locked_out)
+  }
+
   solution <- NULL
   solution$solution <- suppressWarnings(solve(p0, force = TRUE))
   names(solution$solution) <- "basic scenario"
@@ -347,7 +356,8 @@ basic_scenario <- function(cost_raster, features_rasters, budget_perc){
 }
 
 connectivity_scenario <- function(cost_raster, features_rasters=NULL,
-                                  budget_perc, pre_graphs){
+                                  budget_perc, pre_graphs,
+                                  locked_in = NULL, locked_out = NULL){
 
   if ((budget_perc < 0) || (budget_perc > 1))
     stop("budget_perc must be a numeric value between 0 and 1")
@@ -444,6 +454,14 @@ connectivity_scenario <- function(cost_raster, features_rasters=NULL,
     add_relative_targets(0.17) |>
     add_default_solver(verbose=FALSE)
 
+  if (!is.null(locked_in)){
+    p_cluster <- p_cluster |> add_locked_in_constraints(locked_in)
+  }
+
+  if (!is.null(locked_out)){
+    p_cluster <- p_cluster |> add_locked_out_constraints(locked_out)
+  }
+
   solution <- NULL
   solution$solution <- suppressWarnings(solve(p_cluster, force=TRUE))
   names(solution$solution) <- "connectivity scenario"

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/priorCON)](https://CRAN.R-project.org/package=priorCON)
-[![Developmental version](https://img.shields.io/badge/devel%20version-0.1.3-blue.svg)](https://CRAN.R-project.org/package=priorCON)
+[![Developmental version](https://img.shields.io/badge/devel%20version-0.1.4-blue.svg)](https://CRAN.R-project.org/package=priorCON)
 [![R-CMD-check](https://github.com/cadam00/priorCON/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cadam00/priorCON/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/cadam00/priorCON/branch/main/graph/badge.svg)](https://app.codecov.io/gh/cadam00/priorCON?branch=main)
 <!-- badges: end -->

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,7 +1,6 @@
 url: https://cadam00.github.io/priorCON/
 template:
   bootstrap: 5
-
 navbar:
   left:
     - icon: fa-home

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,19 +1,9 @@
-# priorCON 0.1.3
+# priorCON 0.1.4
 
-## Minor changes
+## Major changes
 
-- Update package authors in DESCRIPTION.
-
-# priorCON 0.1.2
-
-## Minor changes
-
-- Remove redundant `r` SpatRaster object at `terra::rasterize` use (we care only
-for the "geometry" of the `r`, so no need for new object).
-
-- Update Introduction.Rmd, README and DESCRIPTION text.
-
-- Add pkgdown website.
+- Add `locked_in` and `locked_out` arguments in `priorCON::basic_scenario` and
+`priorCON::connectivity_scenario`.
 
 ## R CMD check results
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html
diff --git a/docs/articles/index.html b/docs/articles/index.html