Merge pull request #245 from snlab-ch/develop

v0.11.3
stocnet · Sep 13, 2022 · a916526 · a916526
2 parents 20939df + 9b0d233
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: migraph
 Title: Tools for Multimodal Network Analysis
-Version: 0.11.2
-Date: 2022-09-10
+Version: 0.11.3
+Date: 2022-09-13
 Description: A set of tools for analysing multimodal networks.
    All functions operate with matrices, edge lists, 
    and 'igraph', 'network', and 'tidygraph' objects,
@@ -53,7 +53,7 @@ Suggests:
 Authors@R: 
     c(person(given = "James",
              family = "Hollway",
-             role = c("cph", "cre", "aut", "ctb"),
+             role = c("cre", "aut", "ctb"),
              email = "james.hollway@graduateinstitute.ch",
              comment = c("IHEID", ORCID = "0000-0002-8361-9647")),
       person(given = "Jael",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+# migraph 0.11.3
+
+## Package
+
+- Fixed CRAN LaTeX issue relating to underscores in manual figures
+
+## Mapping
+
+- Fixed bug in plotting space coordinates for named two-mode networks
+- Suppressed messages relating to 'graph' class being defined by multiple packages
+
 # migraph 0.11.2
 
 ## Package

diff --git a/R/data_ison.R b/R/data_ison.R
@@ -53,11 +53,11 @@
 #'   (autographr(ison_bb) | autographr(ison_bm) | autographr(ison_mm) | autographr(ison_mb))/
 #'   (autographr(to_mode1(ison_mm)) | autographr(to_mode1(ison_mm)) | 
 #'     autographr(to_mode1(ison_mm)) | autographr(to_mode1(ison_mm)))
-#'   ggsave("man/figures/ison_proj.png", width = 7, height = 3.5, dpi = "screen")
-#'   ggsave("man/figures/ison_proj.pdf", width = 7, height = 3.5)
+#'   ggsave("man/figures/isonproj.png", width = 7, height = 3.5, dpi = "screen")
+#'   ggsave("man/figures/isonproj.pdf", width = 7, height = 3.5)
 #'   ```
-#' \if{html}{\figure{ison_proj.png}{options: width="100\%" alt="Figure: ison_proj"}}
-#' \if{latex}{\figure{ison_proj.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonproj.png}{options: width="100\%" alt="Figure: ison_proj"}}
+#' \if{latex}{\figure{isonproj.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_projection
@@ -94,11 +94,11 @@
 #' 
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_algebra, labels = FALSE) + ggtitle("ison_algebra")
-#'   ggsave("man/figures/ison_algebra.png", width = 5, height = 5, dpi = "screen")
-#'   ggsave("man/figures/ison_algebra.pdf", width = 5, height = 5)
+#'   ggsave("man/figures/isonalgebra.png", width = 5, height = 5, dpi = "screen")
+#'   ggsave("man/figures/isonalgebra.pdf", width = 5, height = 5)
 #'   ```
-#' \if{html}{\figure{ison_algebra.png}{options: width="75\%" alt="Figure: ison_algebra"}}
-#' \if{latex}{\figure{ison_algebra.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonalgebra.png}{options: width="75\%" alt="Figure: ison_algebra"}}
+#' \if{latex}{\figure{isonalgebra.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_algebra
@@ -121,11 +121,11 @@
 #'
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_adolescents, labels = FALSE) + ggtitle("ison_adolescents")
-#'   ggsave("man/figures/ison_adolescents.png", width = 5, height = 5, dpi = "screen")
-#'   ggsave("man/figures/ison_adolescents.pdf", width = 5, height = 5)
+#'   ggsave("man/figures/isonadolescents.png", width = 5, height = 5, dpi = "screen")
+#'   ggsave("man/figures/isonadolescents.pdf", width = 5, height = 5)
 #'   ```
-#' \if{html}{\figure{ison_adolescents.png}{options: width="75\%" alt="Figure: ison_adolescents"}}
-#' \if{latex}{\figure{ison_adolescents.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonadolescents.png}{options: width="75\%" alt="Figure: ison_adolescents"}}
+#' \if{latex}{\figure{isonadolescents.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_adolescents
@@ -159,11 +159,11 @@
 #' 
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_karateka) + ggtitle("ison_karateka")
-#'   ggsave("man/figures/ison_karateka.png", width = 7, height = 3.5, dpi = "screen")
-#'   ggsave("man/figures/ison_karateka.pdf", width = 7, height = 3.5)
+#'   ggsave("man/figures/isonkarateka.png", width = 7, height = 3.5, dpi = "screen")
+#'   ggsave("man/figures/isonkarateka.pdf", width = 7, height = 3.5)
 #'   ```
-#' \if{html}{\figure{ison_karateka.png}{options: width="75\%" alt="Figure: ison_karateka"}}
-#' \if{latex}{\figure{ison_karateka.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonkarateka.png}{options: width="75\%" alt="Figure: ison_karateka"}}
+#' \if{latex}{\figure{isonkarateka.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_karateka
@@ -191,10 +191,10 @@
 #' 
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_networkers, labels = FALSE) + ggtitle("ison_networkers")
-#'   ggsave("man/figures/ison_networkers.png", width = 5, height = 5, dpi = "screen")
-#'   ggsave("man/figures/ison_networkers.pdf", width = 5, height = 5)
+#'   ggsave("man/figures/isonnetworkers.png", width = 5, height = 5, dpi = "screen")
+#'   ggsave("man/figures/isonnetworkers.pdf", width = 5, height = 5)
 #'   ```
-#' \if{latex}{\figure{ison_networkers.pdf}{options: width=7cm}}
+#' \if{latex}{\figure{isonnetworkers.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_networkers
@@ -223,11 +223,11 @@
 #'
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_brandes) + ggtitle("ison_brandes") + autographr(ison_brandes2)
-#'   ggsave("man/figures/ison_brandes.png", width = 7, height = 3.5, dpi = "screen")
-#'   ggsave("man/figures/ison_brandes.pdf", width = 7, height = 3.5)
+#'   ggsave("man/figures/isonbrandes.png", width = 7, height = 3.5, dpi = "screen")
+#'   ggsave("man/figures/isonbrandes.pdf", width = 7, height = 3.5)
 #'   ```
-#' \if{html}{\figure{ison_brandes.png}{options: width="100\%" alt="Figure: ison_brandes"}}
-#' \if{latex}{\figure{ison_brandes.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonbrandes.png}{options: width="100\%" alt="Figure: ison_brandes"}}
+#' \if{latex}{\figure{isonbrandes.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_brandes
@@ -257,11 +257,11 @@
 #'
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(ison_southern_women, "hierarchy", labels = FALSE) + ggtitle("ison_southern_women")
-#'   ggsave("man/figures/ison_southern_women.png", width = 7, height = 3.5, dpi = "screen")
-#'   ggsave("man/figures/ison_southern_women.pdf", width = 7, height = 3.5)
+#'   ggsave("man/figures/isonsouthernwomen.png", width = 7, height = 3.5, dpi = "screen")
+#'   ggsave("man/figures/isonsouthernwomen.pdf", width = 7, height = 3.5)
 #'   ```
-#' \if{html}{\figure{ison_southern_women.png}{options: width="75\%" alt="Figure: ison_southern_women"}}
-#' \if{latex}{\figure{ison_southern_women.pdf}{options: width=7cm}}
+#' \if{html}{\figure{isonsouthernwomen.png}{options: width="75\%" alt="Figure: ison_southern_women"}}
+#' \if{latex}{\figure{isonsouthernwomen.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_southern_women

diff --git a/R/data_mpn.R b/R/data_mpn.R
@@ -20,11 +20,11 @@
 #'
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(mpn_elite_mex, labels = FALSE) + ggtitle("mpn_elite_mex")
-#'   ggsave("man/figures/mpn_elite_mex.png", width = 5, height = 5, dpi = "screen")
-#'   ggsave("man/figures/mpn_elite_mex.pdf", width = 5, height = 5)
+#'   ggsave("man/figures/mpnelitemex.png", width = 5, height = 5, dpi = "screen")
+#'   ggsave("man/figures/mpnelitemex.pdf", width = 5, height = 5)
 #'   ```
-#' \if{html}{\figure{mpn_elite_mex.png}{options: width="100\%" alt="Figure: mpn_elite_mex"}}
-#' \if{latex}{\figure{mpn_elite_mex.pdf}{options: width=7cm}}
+#' \if{html}{\figure{mpnelitemex.png}{options: width="100\%" alt="Figure: mpn_elite_mex"}}
+#' \if{latex}{\figure{mpnelitemex.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name mpn_elite_mex
@@ -63,11 +63,11 @@
 #'   ```{r, eval = FALSE, echo = FALSE, include = FALSE}
 #'   autographr(mpn_elite_usa_advice, labels = FALSE) + ggtitle("mpn_elite_usa_advice") +
 #'     autographr(mpn_elite_usa_money, labels = FALSE) + ggtitle("mpn_elite_usa_money")
-#'   ggsave("man/figures/mpn_elite_usa.png", width = 7, height = 3.5, dpi = "screen")
-#'   ggsave("man/figures/mpn_elite_usa.pdf", width = 7, height = 3.5)
+#'   ggsave("man/figures/mpneliteusa.png", width = 7, height = 3.5, dpi = "screen")
+#'   ggsave("man/figures/mpneliteusa.pdf", width = 7, height = 3.5)
 #'   ```
-#' \if{html}{\figure{mpn_elite_usa.png}{options: width="100\%" alt="Figure: mpn_elite_usa"}}
-#' \if{latex}{\figure{mpn_elite_usa.pdf}{options: width=7cm}}
+#' \if{html}{\figure{mpneliteusa.png}{options: width="100\%" alt="Figure: mpn_elite_usa"}}
+#' \if{latex}{\figure{mpneliteusa.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name mpn_elite_usa

diff --git a/R/measure_diversity.R b/R/measure_diversity.R
@@ -20,7 +20,7 @@ NULL
 #'    Gibbs-Martin index, and probability of interspecific encounter (PIE)): 
 #'    \deqn{1 - \sum\limits_{i = 1}^k {p_i^2 }}, 
 #'    where \eqn{p_i} is the proportion of group members in \eqn{i}th category 
-#'    and _k_ is the number of categories for an attribute of interest. 
+#'    and \eqn{k} is the number of categories for an attribute of interest. 
 #'    This index can be interpreted as the probability that two members 
 #'    randomly selected from a group would be from different categories. 
 #'    This index finds its minimum value (0) when there is no variety, 

diff --git a/R/viz_autographr.R b/R/viz_autographr.R
@@ -122,10 +122,10 @@ autographr <- auto_graph <- function(object,
                                        repel = TRUE)
     } else { # Plot two modes
       p <- p + ggraph::geom_node_text(ggplot2::aes(label = name),
-                                       size = 2,
-                                       hjust = "outward",
-                                      nudge_x = ifelse(lo[,1] == 1, 0.05, -0.05)) +
-        ggplot2::coord_cartesian(xlim=c(-0.2,1.2))
+                                      repel = TRUE,
+                                      size = 2,
+                                      hjust = "outward",
+                                      nudge_x = ifelse(lo[,1] == 1, 0.05, -0.05))
     }
   }
 

diff --git a/R/viz_layout_partition.R b/R/viz_layout_partition.R
@@ -38,8 +38,8 @@ layout_tbl_graph_hierarchy <- function(object,
   }
   if(any(prep<0)) prep[prep<0] <- 0
   out <- as_graphAM(prep)
-  out <- Rgraphviz::layoutGraph(out, layoutType = 'dot', 
-                                attrs = list(graph = list(rankdir = "BT")))
+  out <- suppressMessages(Rgraphviz::layoutGraph(out, layoutType = 'dot', 
+                                attrs = list(graph = list(rankdir = "BT"))))
   nodeX <- .rescale(out@renderInfo@nodes$nodeX)
   nodeY <- .rescale(out@renderInfo@nodes$nodeY)
   # nodeY <- abs(nodeY - max(nodeY))
@@ -61,8 +61,8 @@ layout_tbl_graph_alluvial <- function(object,
   }
   if(any(prep<0)) prep[prep<0] <- 0
   out <- as_graphAM(prep)
-  out <- Rgraphviz::layoutGraph(out, layoutType = 'dot', 
-                                attrs = list(graph = list(rankdir = "LR")))
+  out <- suppressMessages(Rgraphviz::layoutGraph(out, layoutType = 'dot', 
+                                attrs = list(graph = list(rankdir = "LR"))))
   nodeX <- .rescale(out@renderInfo@nodes$nodeX)
   nodeY <- .rescale(out@renderInfo@nodes$nodeY)
   # nodeY <- abs(nodeY - max(nodeY))

diff --git a/README.Rmd b/README.Rmd
@@ -71,7 +71,12 @@ as well as with objects constructed from the following packages:
 `{migraph}`'s `as_*()` functions can be used to translate objects 
 from one of the above classes into any other, and include:
 
-- `r list_functions("^as_")`
+```{r coercion-graph, echo = FALSE}
+autographr(igraph::graph_from_literal(edgelist:matrix:igraph:network:tidygraph+--+edgelist:matrix:igraph:network:tidygraph,
+                                      edgelist:matrix:igraph:network:tidygraph--+graphAM,
+                                      siena:goldfish--+edgelist:matrix:igraph:network:tidygraph:graphAM),
+           "circle", node_size = 2)
+```
 
 These functions are designed to be as intuitive and lossless as possible,
 outperforming many other class-coercion packages.

diff --git a/README.md b/README.md
@@ -61,8 +61,7 @@ as well as with objects constructed from the following packages:
 `{migraph}`’s `as_*()` functions can be used to translate objects from
 one of the above classes into any other, and include:
 
--   `as_edgelist()`, `as_graphAM()`, `as_igraph()`, `as_matrix()`,
-    `as_network()`, `as_tidygraph()`
+<img src="man/figures/README-coercion-graph-1.png" width="100%" />
 
 These functions are designed to be as intuitive and lossless as
 possible, outperforming many other class-coercion packages.

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
 ## Test environments
 
-* local R installation, x86_64-apple-darwin17.0, R 4.2.0
+* local R installation, x86_64-apple-darwin17.0, R 4.2.1
 * Mac OS X 11.6.5 (on Github), R 4.2.1
 * Microsoft Windows Server 2022 10.0.20348 (on Github), R 4.2.1
 * Ubuntu 20.04.4 (on Github), R 4.2.1
@@ -9,4 +9,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-- Fixed documentation issues
+- Renamed figures for the PDF manual
diff --git a/man/diversity.Rd b/man/diversity.Rd
diff --git a/man/figures/README-coercion-graph-1.png b/man/figures/README-coercion-graph-1.png
diff --git a/man/figures/ison_algebra.png b/man/figures/ison_algebra.png
diff --git a/man/figures/ison_brandes.png b/man/figures/ison_brandes.png
diff --git a/man/figures/ison_karateka.png b/man/figures/ison_karateka.png
diff --git a/man/figures/ison_networkers.png b/man/figures/ison_networkers.png
diff --git a/man/figures/ison_proj.pdf b/man/figures/ison_proj.pdf
diff --git a/man/figures/ison_proj.png b/man/figures/ison_proj.png
diff --git a/man/figures/ison_southern_women.png b/man/figures/ison_southern_women.png
diff --git a/man/figures/ison_adolescents.pdf → man/figures/isonadolescents.pdf b/man/figures/ison_adolescents.pdf → man/figures/isonadolescents.pdf
diff --git a/man/figures/ison_adolescents.png → man/figures/isonadolescents.png b/man/figures/ison_adolescents.png → man/figures/isonadolescents.png
diff --git a/man/figures/ison_algebra.pdf → man/figures/isonalgebra.pdf b/man/figures/ison_algebra.pdf → man/figures/isonalgebra.pdf
diff --git a/man/figures/isonalgebra.png b/man/figures/isonalgebra.png
diff --git a/man/figures/ison_brandes.pdf → man/figures/isonbrandes.pdf b/man/figures/ison_brandes.pdf → man/figures/isonbrandes.pdf
diff --git a/man/figures/isonbrandes.png b/man/figures/isonbrandes.png
diff --git a/man/figures/ison_karateka.pdf → man/figures/isonkarateka.pdf b/man/figures/ison_karateka.pdf → man/figures/isonkarateka.pdf
diff --git a/man/figures/isonkarateka.png b/man/figures/isonkarateka.png
diff --git a/man/figures/ison_networkers.pdf → man/figures/isonnetworkers.pdf b/man/figures/ison_networkers.pdf → man/figures/isonnetworkers.pdf
diff --git a/man/figures/isonnetworkers.png b/man/figures/isonnetworkers.png
diff --git a/man/figures/isonproj.pdf b/man/figures/isonproj.pdf
diff --git a/man/figures/isonproj.png b/man/figures/isonproj.png
diff --git a/man/figures/ison_southern_women.pdf → man/figures/isonsouthernwomen.pdf b/man/figures/ison_southern_women.pdf → man/figures/isonsouthernwomen.pdf
diff --git a/man/figures/isonsouthernwomen.png b/man/figures/isonsouthernwomen.png
diff --git a/man/figures/mpn_elite_mex.png b/man/figures/mpn_elite_mex.png
diff --git a/man/figures/mpn_elite_usa.png b/man/figures/mpn_elite_usa.png
diff --git a/man/figures/mpn_elite_mex.pdf → man/figures/mpnelitemex.pdf b/man/figures/mpn_elite_mex.pdf → man/figures/mpnelitemex.pdf
diff --git a/man/figures/mpnelitemex.png b/man/figures/mpnelitemex.png
diff --git a/man/figures/mpn_elite_usa.pdf → man/figures/mpneliteusa.pdf b/man/figures/mpn_elite_usa.pdf → man/figures/mpneliteusa.pdf
diff --git a/man/figures/mpneliteusa.png b/man/figures/mpneliteusa.png
diff --git a/man/ison_adolescents.Rd b/man/ison_adolescents.Rd
diff --git a/man/ison_algebra.Rd b/man/ison_algebra.Rd
diff --git a/man/ison_brandes.Rd b/man/ison_brandes.Rd
diff --git a/man/ison_karateka.Rd b/man/ison_karateka.Rd
diff --git a/man/ison_networkers.Rd b/man/ison_networkers.Rd
diff --git a/man/ison_projection.Rd b/man/ison_projection.Rd
diff --git a/man/ison_southern_women.Rd b/man/ison_southern_women.Rd
diff --git a/man/mpn_elite_mex.Rd b/man/mpn_elite_mex.Rd
diff --git a/man/mpn_elite_usa.Rd b/man/mpn_elite_usa.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/tests/testthat/test-viz_autographr.R b/tests/testthat/test-viz_autographr.R
@@ -124,3 +124,11 @@ test_that("edge colours graph correctly", {
   test_brandes2 <- autographr(ison_brandes2, edge_color = "tiecolour")
   expect_false(is.null(test_brandes2$layers[[1]]$mapping$edge_colour))
 })
+
+# Named networks
+test_that("named networks plot correctly", {
+  onemode <- autographr(ison_adolescents)
+  twomode <- autographr(ison_southern_women)
+  expect_equal(onemode[["data"]][["name"]], node_names(ison_adolescents))
+  expect_equal(twomode[["data"]][["name"]], node_names(ison_southern_women))
+})