Replaced purrr::transpose() with purrr::list_transpose(), which super…

…sedes it.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ergm
-Version: 4.7.5-7458
-Date: 2024-11-04
+Version: 4.7.5-7485
+Date: 2024-11-24
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(
              person(c("Mark", "S."), "Handcock", role=c("aut"), email="[email protected]"),

R/InitErgmConstraint.R

@@ -319,8 +319,9 @@ InitErgmConstraint.blocks <- function(nw, arglist, ...) {
     offset <- 0L
   }
 
-  levels2_list <- transpose(expand.grid(row = row_levels,
-                                        col = col_levels, stringsAsFactors = FALSE))
+  levels2_list <- list_transpose(expand.grid(row = row_levels,
+                                             col = col_levels, stringsAsFactors = FALSE),
+                                 simplify = FALSE)
   indices2_grid <- expand.grid(row = seq_along(row_levels),
                                col = offset + seq_along(col_levels))
 

R/InitErgmTerm.R

@@ -1298,10 +1298,10 @@ InitErgmTerm.b1twostar <- function(nw, arglist, ..., version=packageVersion("erg
   nr <- length(b1u)
   nc <- length(b2u)
 
-  levels2.grid <- expand.grid(row = b1u, col = b2u, col2 = b2u, stringsAsFactors=FALSE)
-  indices2.grid <- expand.grid(row = 1:nr, col = 1:nc, col2 = 1:nc)
+  levels2.grid <- expand.grid(row = b1u, col = b2u, col2 = b2u, stringsAsFactors=FALSE) %>% unclass()
+  indices2.grid <- expand.grid(row = 1:nr, col = 1:nc, col2 = 1:nc) %>% unclass()
 
-  levels2.list <- transpose(levels2.grid[indices2.grid$col <= indices2.grid$col2,])
+  levels2.list <- list_transpose(levels2.grid[indices2.grid$col <= indices2.grid$col2,], simplify = FALSE)
   indices2.grid <- indices2.grid[indices2.grid$col <= indices2.grid$col2,]
 
   levels2.sel <- if((!hasName(attr(a,"missing"), "levels2") || attr(a,"missing")["levels2"]) && any(a$base != 0)) levels2.list[-a$base]
@@ -1873,10 +1873,10 @@ InitErgmTerm.b2twostar <- function(nw, arglist, ..., version=packageVersion("erg
   nr <- length(b1u)
   nc <- length(b2u)
 
-  levels2.grid <- expand.grid(row = b2u, col = b1u, col2 = b1u, stringsAsFactors=FALSE)
-  indices2.grid <- expand.grid(row = 1:nc, col = 1:nr, col2 = 1:nr)
+  levels2.grid <- expand.grid(row = b2u, col = b1u, col2 = b1u, stringsAsFactors=FALSE) %>% unclass()
+  indices2.grid <- expand.grid(row = 1:nc, col = 1:nr, col2 = 1:nr) %>% unclass()
 
-  levels2.list <- transpose(levels2.grid[indices2.grid$col <= indices2.grid$col2,])
+  levels2.list <- list_transpose(levels2.grid[indices2.grid$col <= indices2.grid$col2,], simplify = FALSE)
   indices2.grid <- indices2.grid[indices2.grid$col <= indices2.grid$col2,]
 
   levels2.sel <- if((!hasName(attr(a,"missing"), "levels2") || attr(a,"missing")["levels2"]) && any(NVL(a$base,0)!=0)) levels2.list[-a$base]
@@ -2946,8 +2946,8 @@ InitErgmTerm.hammingmix<-function (nw, arglist, ..., version=packageVersion("erg
   nr <- length(u)
   nc <- length(u)
 
-  levels2.list <- transpose(expand.grid(row = u, col = u, stringsAsFactors=FALSE))
-  indices2.grid <- expand.grid(row = 1:nr, col = 1:nc)
+  levels2.list <- list_transpose(expand.grid(row = u, col = u, stringsAsFactors=FALSE), simplify = FALSE)
+  indices2.grid <- expand.grid(row = 1:nr, col = 1:nc) %>% unclass()
 
   levels2.sel <- if((!hasName(attr(a,"missing"), "levels2") || attr(a,"missing")["levels2"]) && any(NVL(a$base,0)!=0)) levels2.list[-a$base]
                  else ergm_attr_levels(a$levels2, list(row = nodecov, col = nodecov), nw, levels2.list)
@@ -3495,18 +3495,18 @@ InitErgmTerm.mm<-function (nw, arglist, ..., version=packageVersion("ergm")) {
     map_if(~length(.)==2, ~call("~", .[[2]], .[[2]])) %>% # Convert ~X to X~X.
     map(as.list) %>% map(~.[-1]) %>% # Convert to list(X,X).
     map(set_names, c("row", "col")) %>% # Name elements rowspec and colspec.
-    transpose() %>%
+    list_transpose(simplify = FALSE) %>%
     unlist(recursive=FALSE) %>% # Convert into a flat list.
     map_if(~is.name(.)&&.==".", ~NULL) %>% # If it's just a dot, convert to NULL.
     map_if(~is.call(.)||(is.name(.)&&.!="."), ~as.formula(call("~", .))) %>% # If it's a call or a symbol, embed in formula.
     relist(skeleton=list(row=c(attrs=NA, levels=NA), col=c(attrs=NA, levels=NA))) %>% # Reconstruct list.
-    transpose()
+    list_transpose(simplify = FALSE)
 
   if(is(a$attrs, "formula"))
     spec[["attrs"]] <- lapply(spec[["attrs"]], function(x){if(is(x,"formula")) environment(x) <- environment(a$attrs); x})
   if(is(a$levels, "formula"))
     spec[["levels"]] <- lapply(spec[["levels"]], function(x){if(is(x,"formula")) environment(x) <- environment(a$levels); x})
-  spec <- transpose(spec)
+  spec <- list_transpose(spec, simplify = FALSE)
 
   # Extract attribute values.
   attrval <-
@@ -3547,8 +3547,8 @@ InitErgmTerm.mm<-function (nw, arglist, ..., version=packageVersion("ergm")) {
     })
 
   # Construct all pairwise level combinations (table cells) and their numeric codes.
-  levels2codes <- expand.grid(row=attrval$row$levelcodes, col=attrval$col$levelcodes) %>% transpose()
-  levels2 <- expand.grid(row=attrval$row$levels, col=attrval$col$levels, stringsAsFactors=FALSE) %>% transpose()
+  levels2codes <- expand.grid(row=attrval$row$levelcodes, col=attrval$col$levelcodes) %>% unclass() %>% list_transpose(simplify = FALSE)
+  levels2 <- expand.grid(row=attrval$row$levels, col=attrval$col$levels, stringsAsFactors=FALSE) %>% unclass() %>% list_transpose(simplify = FALSE)
 
   # Drop redundant table cells if symmetrising.
   if(symm){
@@ -3575,7 +3575,7 @@ InitErgmTerm.mm<-function (nw, arglist, ..., version=packageVersion("ergm")) {
   # Construct the level names
   levels2names <-
     levels2 %>%
-    transpose() %>%
+    list_transpose(simplify = FALSE) %>%
     map(unlist) %>%
     with(paste0(
       "[",
@@ -4181,8 +4181,8 @@ InitErgmTerm.nodemix<-function (nw, arglist, ..., version=packageVersion("ergm")
     nr <- length(b1namescov)
     nc <- length(b2namescov)
 
-    levels2.list <- transpose(expand.grid(row = b1namescov, col = b2namescov, stringsAsFactors=FALSE))
-    indices2.grid <- expand.grid(row = 1:nr, col = nr + 1:nc)
+    levels2.list <- expand.grid(row = b1namescov, col = b2namescov, stringsAsFactors=FALSE) %>% unclass() %>% list_transpose(simplify = FALSE)
+    indices2.grid <- expand.grid(row = 1:nr, col = nr + 1:nc) %>% unclass()
 
     if ((!hasName(attr(a,"missing"), "levels2") || attr(a,"missing")["levels2"]) && any(NVL(a$base,0)!=0)) {
       levels2.sel <- levels2.list[-a$base]
@@ -4240,8 +4240,8 @@ InitErgmTerm.nodemix<-function (nw, arglist, ..., version=packageVersion("ergm")
     nr <- length(u)
     nc <- length(u)
 
-    levels2.list <- transpose(expand.grid(row = u, col = u, stringsAsFactors=FALSE))
-    indices2.grid <- expand.grid(row = 1:nr, col = 1:nc)
+    levels2.list <- expand.grid(row = u, col = u, stringsAsFactors=FALSE) %>% unclass() %>% list_transpose(simplify = FALSE)
+    indices2.grid <- expand.grid(row = 1:nr, col = 1:nc) %>% unclass()
     uun <- as.vector(outer(u,u,paste,sep="."))
 
     if (!is.directed(nw)) {

R/InitErgmTerm.coincidence.R

@@ -38,7 +38,7 @@ InitErgmTerm.coincidence<-function(nw, arglist, ..., version=packageVersion("erg
                         vartypes = c("matrix","numeric"),
                         defaultvalues = list(NULL,0),
                         required = c(FALSE,FALSE))
-	levels <- if(!is.null(a$d)) I(transpose(data.frame(node1 = a$d[,1], node2 = a$d[,2]))) else NULL
+	levels <- if(!is.null(a$d)) I(list_transpose(list(node1 = a$d[,1], node2 = a$d[,2]), simplify = FALSE)) else NULL
   }else{
     a <- check.ErgmTerm(nw, arglist, directed=FALSE, bipartite=TRUE,
                         varnames = c("levels","active"),
@@ -54,10 +54,10 @@ InitErgmTerm.coincidence<-function(nw, arglist, ..., version=packageVersion("erg
   # this behavior is preserved here, although it violates the convention used by other terms
   levels2.grid <- expand.grid(node2 = 1:nb2, node1 = 1:nb2)
   levels2.grid <- levels2.grid[,c(2,1)] # make the second column vary fastest
-  levels2.grid <- levels2.grid[levels2.grid$node1 < levels2.grid$node2,]
+  levels2.grid <- levels2.grid[levels2.grid$node1 < levels2.grid$node2,] %>% unclass()
 
   if(!is.null(levels)) {
-	levels2.list <- transpose(levels2.grid)
+	levels2.list <- list_transpose(levels2.grid, simplify = FALSE)
     levels2.sel <- ergm_attr_levels(levels, list(node1 = 1:nb2, node2 = 1:nb2), nw, levels2.list)
 
 	active <- !is.na(match(levels2.list, levels2.sel))