1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749
|
#' @importFrom statnet.common once
.warn_bipartite_vertex_reorder <- once(
function() {
warning(
"`vertices` were not provided in the order required for bipartite networks. Reordering.",
"\n\nThis is the first and last time you will be warned during this session.",
call. = FALSE
)
}
)
.head <- function(x, n = 6) {
n <- min(length(x), n)
x[seq_len(n)]
}
.validate_edge_df <- function(edges, directed, hyper, loops, multiple, bipartite, ...) {
# confirm edge data frame has valid dimensions
if (ncol(edges) < 2L || nrow(edges) == 0L) {
stop(
"`x` should be a data frame with at least two columns and one row.",
call. = FALSE
)
}
el <- edges[, 1:2]
sources <- edges[[1L]]
targets <- edges[[2L]]
# validate edge column types
if (hyper) {
# confirm that hyper-edges are list columns
if (!is.list(sources) || !is.list(targets)) {
stop(
"If `hyper` is `TRUE`, the first two columns of `x` should be list columns.",
call. = FALSE
)
}
# first edge type is the `target_type`, against which all other values are tested
target_type <- typeof(sources[[1L]])
# confirm that target_type is itself valid
if (any(is.na(sources[[1L]])) || target_type %in% c("NULL", "list")) {
stop(
"`x`'s first two columns contain invalid values.",
"\n\t- `x[[1]][[1]]` is `NULL`, recursive, or it contains `NA` values.",
call. = FALSE
)
}
# Iterate through edge columns, testing that they're not `NA` and are of the same type
# as `target_type`. `incompat_types` is a logical matrix of the test results.
incompat_types <- vapply(
el, function(.x) {
vapply(.x, function(.y) any(is.na(.y)) || typeof(.y) != target_type, logical(1L))
},
logical(nrow(el))
)
# if any values are incompatible, throw error pointing user to the problem values
if (any(incompat_types)) {
incompat_rows <- row(incompat_types)[incompat_types]
incompat_cols <- col(incompat_types)[incompat_types]
stop(
"The values in the first two columns of `x` must be of the same type and cannot be `NULL`, `NA`, or recursive values.",
"\nThe following values are incompatible:",
paste(
"\n\t-",
sprintf("`x[%d, %d]`", .head(incompat_rows), .head(incompat_cols))
),
call. = FALSE
)
}
} else { # for non-hyper edges...
# ... confirm edge columns are atomic vectors
if (!is.atomic(sources) || !is.atomic(targets)) {
stop(
"If `hyper` is `FALSE`, the first two columns of `x` should be atomic vectors.",
call. = FALSE
)
}
# confirm that edge columns are of the same type
if (typeof(sources) != typeof(targets)) {
stop(
"The first two columns of `x` must be of the same type.",
call. = FALSE
)
}
# confirm edge columns don't contain `NA`s
if (any(is.na(el))) {
stop(
"The first two columns of `x` cannot contain `NA` values.",
call. = FALSE
)
}
}
# if `loops` is `FALSE`, confirm that edge columns don't contain loops
if (!loops) {
# if hyper, test if each intersection's length is not 0
if (hyper) {
loop_rows <- which(
mapply(
function(.x, .y) length(intersect(.x, .y)) != 0L,
sources, targets,
USE.NAMES = FALSE
)
)
} else { # if not hyper...
# ... test via simple vector comparison
loop_rows <- which(sources == targets)
}
# if loops are found, throw error pointing user to the edge rows that contain them
if (length(loop_rows) > 0L) {
stop(
"`loops` is `FALSE`, but `x` contains loops.",
"\nThe following values are affected:",
paste("\n\t-", sprintf("`x[%d, 1:2]`", .head(loop_rows))),
call. = FALSE
)
}
}
# TODO does network support bipartite hypergraphs?
if (!hyper && bipartite) {
# check for intersection between edge columns
confused_nodes <- intersect(sources, targets)
# if there's an intersection, throw error informing users which nodes are in both columns
if (length(confused_nodes) > 0L) {
stop(
"`bipartite` is `TRUE`, but there are vertices that appear in both of the",
" first two columns of `x`.\n",
"The following vertices appear in both columns:",
paste("\n\t-", .head(confused_nodes)),
call. = FALSE
)
}
}
# TODO does network support multiplex hypergraphs?
if (!hyper && !multiple) {
if (directed) {
test_el <- el
} else {
test_el <- t(apply(el, 1L, sort))
}
if (anyDuplicated(test_el) != 0L) {
parallel_edges <- which(duplicated(test_el))
stop(
"`multiple` is `FALSE`, but `x` contains parallel edges.\n",
"The following rows in `x` are duplicated:",
paste("\n\t-", sprintf("`x[%d, ]`", .head(parallel_edges))),
call. = FALSE
)
}
}
}
.validate_vertex_df <- function(vertices, el_vert_ids) {
# confirm `vertices` is a data frame
if (!is.data.frame(vertices)) {
stop(
"If provided, `vertices` should be a data frame.",
call. = FALSE
)
}
# confirm `vertices` has valid dimensions
if (nrow(vertices) == 0L || ncol(vertices) == 0L) {
stop(
"`vertices` should contain at least one column and row.",
call. = FALSE
)
}
vertex_ids <- vertices[[1L]]
if (!is.atomic(vertex_ids)) {
stop(
"The first column of `vertices` must be an atomic vector.",
call. = FALSE
)
}
# confirm vertex IDs match type used in edges
if (typeof(vertex_ids) != typeof(el_vert_ids)) {
stop(
"The first column of `vertices` must be the same type as the value with which",
" they are referenced in `x`'s first two columns.",
call. = FALSE
)
}
# check for vertex names that are in the edges, but are missing from `vertices`
missing_vertex_names <- setdiff(el_vert_ids, vertex_ids)
if (length(missing_vertex_names) != 0L) {
stop(
"The following vertices are in `x`, but not in `vertices`:",
paste("\n\t-", .head(missing_vertex_names)),
call. = FALSE
)
}
# check if any of the `vertices` have duplicate names
if (anyDuplicated(vertex_ids) != 0L) {
stop(
"The following vertex names are duplicated in `vertices`:",
paste("\n\t-", .head(vertex_ids[duplicated(vertex_ids)])),
call. = FALSE
)
}
}
.prep_bipartite_vertices <- function(vertices, el_vert_ids, bipartite_col) {
# use "is_actor" column if provided
if (bipartite_col %in% names(vertices)) {
# check if `"is_actor"` column is valid
if (!is.logical(vertices[[bipartite_col]]) || any(is.na(vertices[[bipartite_col]]))) {
stop(
sprintf(
paste0(
'`bipartite` is `TRUE` and vertex types are specified via a column in `vertices` named `"%s"`.',
'\n\t- If provided, all values in `vertices[["%s"]]` must be `TRUE` or `FALSE`.'
),
bipartite_col, bipartite_col
)
)
}
# actors (`TRUE`) go before non-actors (`FALSE`)
vertex_order <- order(vertices[[bipartite_col]], decreasing = TRUE)
} else { # if no "is_actor" column is provided...
vertex_ids <- vertices[[1L]]
# ... check for isolates...
isolates <- setdiff(vertex_ids, el_vert_ids)
# ... and throw error informing user of which vertices are isolates
if (length(isolates) > 0L) {
stop(
sprintf(
"`bipartite` is `TRUE`, but the `vertices` you provided contain names that are not present in `x` (i.e. you have isolates).",
"\nIf you have isolates, `vertices` must have a `logical` column named \"%s\" indicating each vertex's type.",
"\nThe following vertex names are in `vertices`, but not in `x`:",
bipartite_col
),
paste("\n\t-", .head(isolates))
)
}
# if there are no isolates, follow order of vertices as they appear in the edges
vertex_order <- match(el_vert_ids, vertex_ids)
}
if (!identical(vertices[[1L]], vertices[[1L]][vertex_order])) {
.warn_bipartite_vertex_reorder()
}
# reorder the vertex rows to match the actor/non-actor order of the final network
vertices[vertex_order, ]
}
.distribute_vec_attrs <- function(x) {
lapply(x, function(.x) {
if (is.atomic(.x)) {
lapply(.x, `attributes<-`, attributes(.x))
} else {
.x
}
})
}
.prep_edge_attrs <- function(edges) {
edge_attr_names <- names(edges)[-(1:2)]
init_vals_eval <- .distribute_vec_attrs(edges[, edge_attr_names, drop = FALSE])
list(
names_eval = rep(list(as.list(edge_attr_names)), times = nrow(edges)),
vals_eval = .mapply(list, init_vals_eval, NULL)
)
}
.prep_vertex_attrs <- function(vertices) {
vertices[-1L] <- .distribute_vec_attrs(vertices[-1L])
vertices
}
#' @rdname network
#'
#' @param vertices If \code{x} is a \code{data.frame}, \code{vertices} is an optional
#' \code{data.frame} containing the vertex attributes. The first column is assigned
#' to the \code{"vertex.names"} and additional columns are used to set vertex attributes
#' using their column names. If \code{bipartite} is \code{TRUE}, a \code{logical} column
#' named \code{"is_actor"} (or the name of a column specified using the
#' \code{bipartite_col} parameter) can be provided indicating which vertices
#' should be considered as actors. If not provided, vertices referenced in the
#' first column of \code{x} are assumed to be the network's actors. If your
#' network has isolates (i.e. there are vertices referenced in \code{vertices}
#' that are not referenced in \code{x}), the \code{"is_actor"} column is required.
#'
#' @param bipartite_col \code{character(1L)}, default: \code{"is_actor"}.
#' The name of the \code{logical} column indicating which vertices should be
#' considered as actors in bipartite networks.
#'
#' @examples
#' # networks from data frames ===========================================================
#' #* simple networks ====================================================================
#' simple_edge_df <- data.frame(
#' from = c("b", "c", "c", "d", "a"),
#' to = c("a", "b", "a", "a", "b"),
#' weight = c(1, 1, 2, 2, 3),
#' stringsAsFactors = FALSE
#' )
#' simple_edge_df
#'
#' as.network(simple_edge_df)
#'
#' # simple networks with vertices =======================================================
#' simple_vertex_df <- data.frame(
#' name = letters[1:5],
#' residence = c("urban", "rural", "suburban", "suburban", "rural"),
#' stringsAsFactors = FALSE
#' )
#' simple_vertex_df
#'
#' as.network(simple_edge_df, vertices = simple_vertex_df)
#'
#' as.network(simple_edge_df,
#' directed = FALSE, vertices = simple_vertex_df,
#' multiple = TRUE
#' )
#'
#' #* splitting multiplex data frames into multiple networks =============================
#' simple_edge_df$relationship <- c(rep("friends", 3), rep("colleagues", 2))
#' simple_edge_df
#'
#' lapply(split(simple_edge_df, f = simple_edge_df$relationship),
#' as.network,
#' vertices = simple_vertex_df
#' )
#'
#' #* bipartite networks without isolates ================================================
#' bip_edge_df <- data.frame(
#' actor = c("a", "a", "b", "b", "c", "d", "d", "e"),
#' event = c("e1", "e2", "e1", "e3", "e3", "e2", "e3", "e1"),
#' actor_enjoyed_event = rep(c(TRUE, FALSE), 4),
#' stringsAsFactors = FALSE
#' )
#' bip_edge_df
#'
#' bip_node_df <- data.frame(
#' node_id = c("a", "e1", "b", "e2", "c", "e3", "d", "e"),
#' node_type = c(
#' "person", "event", "person", "event", "person",
#' "event", "person", "person"
#' ),
#' color = c(
#' "red", "blue", "red", "blue", "red", "blue",
#' "red", "red"
#' ),
#' stringsAsFactors = FALSE
#' )
#' bip_node_df
#'
#' as.network(bip_edge_df, directed = FALSE, bipartite = TRUE)
#' as.network(bip_edge_df, directed = FALSE, vertices = bip_node_df, bipartite = TRUE)
#'
#' #* bipartite networks with isolates ===================================================
#' bip_nodes_with_isolates <- rbind(
#' bip_node_df,
#' data.frame(
#' node_id = c("f", "e4"),
#' node_type = c("person", "event"),
#' color = c("red", "blue"),
#' stringsAsFactors = FALSE
#' )
#' )
#' # indicate which vertices are actors via a column named `"is_actor"`
#' bip_nodes_with_isolates$is_actor <- bip_nodes_with_isolates$node_type == "person"
#' bip_nodes_with_isolates
#'
#' as.network(bip_edge_df,
#' directed = FALSE, vertices = bip_nodes_with_isolates,
#' bipartite = TRUE
#' )
#'
#' #* hyper networks from data frames ====================================================
#' hyper_edge_df <- data.frame(
#' from = c("a/b", "b/c", "c/d/e", "d/e"),
#' to = c("c/d", "a/b/e/d", "a/b", "d/e"),
#' time = 1:4,
#' stringsAsFactors = FALSE
#' )
#' tibble::as_tibble(hyper_edge_df)
#'
#' # split "from" and "to" at `"/"`, coercing them to list columns
#' hyper_edge_df$from <- strsplit(hyper_edge_df$from, split = "/")
#' hyper_edge_df$to <- strsplit(hyper_edge_df$to, split = "/")
#' tibble::as_tibble(hyper_edge_df)
#'
#' as.network(hyper_edge_df,
#' directed = FALSE, vertices = simple_vertex_df,
#' hyper = TRUE, loops = TRUE
#' )
#'
#' # convert network objects back to data frames =========================================
#' simple_g <- as.network(simple_edge_df, vertices = simple_vertex_df)
#' as.data.frame(simple_g)
#' as.data.frame(simple_g, unit = "vertices")
#'
#' bip_g <- as.network(bip_edge_df,
#' directed = FALSE, vertices = bip_node_df,
#' bipartite = TRUE
#' )
#' as.data.frame(bip_g)
#' as.data.frame(bip_g, unit = "vertices")
#'
#' hyper_g <- as.network(hyper_edge_df,
#' directed = FALSE, vertices = simple_vertex_df,
#' hyper = TRUE, loops = TRUE
#' )
#' as.data.frame(hyper_g)
#' as.data.frame(hyper_g, unit = "vertices")
#' @export as.network.data.frame
#' @export
as.network.data.frame <- function(x,
directed = TRUE,
vertices = NULL,
hyper = FALSE,
loops = FALSE,
multiple = FALSE,
bipartite = FALSE,
bipartite_col = "is_actor",
...) {
# validate network type args
invalid_network_args <- vapply(
list(
directed = directed, hyper = hyper, loops = loops,
multiple = multiple, bipartite = bipartite
),
function(.x) is.na(.x) || !is.logical(.x),
logical(1L)
)
if (any(invalid_network_args)) {
stop(
"The following arguments must be either `TRUE` or `FALSE`:",
paste("\n\t-", names(invalid_network_args)[invalid_network_args])
)
}
if (length(bipartite_col) != 1L || !is.character(bipartite_col) || is.na(bipartite_col)) {
stop("`bipartite_col` must be a single, non-`NA` `character` value.")
}
# handle incompatible network type args
if (bipartite && directed) {
warning("If `bipartite` is `TRUE`, edges are interpreted as undirected.")
directed <- FALSE
}
if (bipartite && loops) {
warning("If `bipartite` is `TRUE`, `loops` must be `FALSE`.")
loops <- FALSE
}
if (hyper && !directed && !loops) {
warning("If `hyper` is `TRUE` and `directed` is `FALSE`, `loops` must be `TRUE`.")
loops <- TRUE
}
if (hyper && bipartite) {
stop("Both `hyper` and `bipartite` are `TRUE`, but bipartite hypergraphs are not supported.")
}
# validate edges
.validate_edge_df(
edges = x, directed = directed, hyper = hyper, loops = loops,
multiple = multiple, bipartite = bipartite
)
# create variable containing vertex IDs in the order they appear in the edges
vertex_ids_in_el <- unique(unlist(x[, 1:2], use.names = FALSE))
# create reference variables to minimize bracket spam
sources <- x[[1L]]
targets <- x[[2L]]
# validate vertices
if (!is.null(vertices)) {
.validate_vertex_df(vertices, el_vert_ids = vertex_ids_in_el)
}
# if vertices aren't provided, use the order in which they appear in the edges
if (is.null(vertices)) {
vertex_names <- vertex_ids_in_el
} else { # if vertices are provided, use that order
if (bipartite) {
# if bipartite, first reorder vertices so actors come before non-actors
vertices <- .prep_bipartite_vertices(vertices,
el_vert_ids = vertex_ids_in_el,
bipartite_col = bipartite_col)
}
vertex_names <- vertices[[1L]]
}
# out_sources/out_targets consist of the numerical indices to add to the final network
out_sources <- lapply(sources, match, vertex_names)
out_targets <- lapply(targets, match, vertex_names)
# prep edge attributes
if (ncol(x) == 2L) {
edge_attrs <- list(names_eval = NULL, vals_eval = NULL)
} else {
edge_attrs <- .prep_edge_attrs(x)
}
# start building the network to return
out <- network.initialize(
n = length(vertex_names),
directed = directed,
hyper = hyper,
loops = loops,
multiple = multiple,
bipartite = if (bipartite) length(unique(sources)) else FALSE
)
# add edges (and any edge attributes)
out <- add.edges.network(
x = out,
tail = out_sources,
head = out_targets,
names.eval = edge_attrs[["names_eval"]],
vals.eval = edge_attrs[["vals_eval"]],
...
)
# set vertex attributes
if (is.null(vertices)) {
# if vertices aren't provided, set "vertex.names" as the values used in edges
out <- set.vertex.attribute(out, attrname = "vertex.names", value = vertex_names)
} else if (ncol(vertices) == 1L) {
out <- set.vertex.attribute(out, attrname = "vertex.names", value = vertices[[1L]])
} else {
out <- set.vertex.attribute(
x = out,
attrname = c(
"vertex.names", # first column is always "vertex.names"
names(vertices)[-1L]
),
value = .prep_vertex_attrs(vertices)
)
}
out
}
.is_atomic_scalar <- function(x) {
is.atomic(x) && length(x) == 1L
}
.all_are_atomic_scalars <- function(x) {
all(vapply(x, .is_atomic_scalar, logical(1L), USE.NAMES = FALSE))
}
.is_vectorizable <- function(x) {
vapply(x, .all_are_atomic_scalars, logical(1L), USE.NAMES = FALSE)
}
.vectorize_safely <- function(x) {
to_vectorize <- .is_vectorizable(x)
x[to_vectorize] <- lapply(x[to_vectorize], function(.x) {
`attributes<-`(unlist(.x, use.names = FALSE), attributes(.x[[1L]]))
})
x
}
.as_edge_df <- function(x, attrs_to_ignore, na.rm, name_vertices, sort_attrs, store_eid, ...) {
if (network.edgecount(x, na.omit = FALSE) == 0L) {
empty_edge_df <- structure(
list(.tail = logical(), .head = logical(), .na = logical()),
row.names = integer(),
class = "data.frame"
)
if ("na" %in% attrs_to_ignore) {
empty_edge_df <- empty_edge_df[, c(".tail", ".head")]
}
return(empty_edge_df)
}
vertex_names <- network.vertex.names(x)
deleted <- vapply(x[["mel"]], is.null, logical(1))
if (name_vertices) {
el_list <- list(
.tail = lapply(x[["mel"]], function(.x) vertex_names[.x[["outl"]]]),
.head = lapply(x[["mel"]], function(.x) vertex_names[.x[["inl"]]])
)
} else {
el_list <- list(
.tail = lapply(lapply(x[["mel"]], `[[`, "outl"), as.integer),
.head = lapply(lapply(x[["mel"]], `[[`, "inl"), as.integer)
)
}
# list.edge.attributes() sorts, meaning we can't test round-trips
edge_attr_names <-
if (sort_attrs) list.edge.attributes(x)
else unique(
unlist(lapply(x[["mel"]], function(.x) names(.x[["atl"]])),
use.names = FALSE
)
)
names(edge_attr_names) <- edge_attr_names
# extract attributes as-is (lists)
edge_attrs <- lapply(
edge_attr_names,
function(.x) get.edge.attribute(x, .x, unlist = FALSE, null.na = TRUE)
)
# if not `TRUE`, "na" is assumed `FALSE` (in the event of `NULL`s or corrupted data)
edge_attrs[["na"]] <- !vapply(
edge_attrs[["na"]], isFALSE, logical(1L),
USE.NAMES = FALSE
)
if (store_eid) edge_attrs <- c(list(.eid = seq_along(x[["mel"]])), edge_attrs)
# skip `base::as.data.frame()`'s auto-unlisting behavior
out <- structure(
c(el_list, edge_attrs),
row.names = seq_along(el_list[[1L]]),
class = "data.frame"
)
out <- out[!deleted, ]
if (na.rm) {
# drop NA edge rows
out <- out[!out[["na"]], ]
}
# reset `rownames()` so they're sequential in returned object
rownames(out) <- NULL
cols_to_keep <- c(".tail", ".head", setdiff(names(edge_attrs), attrs_to_ignore))
out <- out[cols_to_keep]
# if not hyper, `unlist()` ".tail" and ".head"
if (!is.hyper(x)) {
out[1:2] <- lapply(out[1:2], unlist, use.names = FALSE)
}
# safely vectorize non-edgelist columns
cols_to_vectorize <- setdiff(names(out), c(".tail", ".head"))
if (length(cols_to_vectorize)) {
out[cols_to_vectorize] <- .vectorize_safely(out[cols_to_vectorize])
}
out
}
.as_vertex_df <- function(x, attrs_to_ignore, na.rm, name_vertices, sort_attrs, ...) {
if (network.size(x) == 0L) {
empty_vertex_df <- structure(
list(vertex.names = logical(), na = logical()),
class = "data.frame", row.names = integer()
)
if ("na" %in% attrs_to_ignore) {
empty_vertex_df <- empty_vertex_df[, "vertex.names", drop = FALSE]
}
return(empty_vertex_df)
}
# list.vertex.attributes() sorts the result, meaning we can't test round-trips
vertex_attr_names <-
if (sort_attrs)
list.vertex.attributes(x)
else
unique(unlist(lapply(x[["val"]], names), use.names = FALSE))
vertex_attrs <- lapply(
`names<-`(vertex_attr_names, vertex_attr_names),
function(.x) get.vertex.attribute(x, .x, unlist = FALSE)
)
vertex_attrs[["na"]] <- lapply(
vertex_attrs[["na"]],
function(.x) if (is.null(.x)) TRUE else .x
)
out <- structure(
vertex_attrs,
row.names = seq_len(network.size(x)),
class = "data.frame"
)
if (!"vertex.names" %in% names(out)) {
out[["vertex.names"]] <- network.vertex.names(x)
}
if (na.rm) {
out <- out[!vapply(out[["na"]], isTRUE, logical(1L), USE.NAMES = FALSE), ]
rownames(out) <- NULL
}
out_cols <- c(
"vertex.names",
setdiff(names(out), c("vertex.names", attrs_to_ignore))
)
.vectorize_safely(out[, out_cols, drop = FALSE])
}
#' Coerce a Network Object to a \code{data.frame}
#'
#' The \code{as.data.frame} method coerces its input to a \code{data.frame} containing
#' \code{x}'s edges or vertices.
#'
#' @param x an object of class \code{network}
#' @param ... additional arguments
#' @param unit whether a \code{data.frame} of edge or vertex
#' attributes should be returned.
#' @param na.rm logical; ignore missing edges/vertices when constructing the
#' data frame?
#' @param attrs_to_ignore character; a vector of attribute names to
#' exclude from the returned \code{data.frame} (Default:
#' \code{"na"})
#' @param name_vertices logical; for `unit="edges"`, should the
#' `.tail` and the `.head` columns contain vertex names as opposed
#' to vertex indices?
#' @param sort_attrs logical; should the attribute columns in the
#' returned data frame be sorted alphabetically?
#' @param store_eid logical; for `unit="edges"`, should the edge ID in
#' the network's internal representation be stored in a column
#' `.eid`?
#'
#' @export as.data.frame.network
#' @export
as.data.frame.network <- function(x, ..., unit = c("edges", "vertices"),
na.rm = TRUE,
attrs_to_ignore = "na", name_vertices = TRUE,
sort_attrs = FALSE, store_eid = FALSE) {
helper <-
switch(match.arg(unit, c("edges", "vertices")),
edges = .as_edge_df,
vertices = .as_vertex_df,
# `match.arg()` used, so this should never be reached...
stop('`unit` must be one of `"edges"` or `"vertices".') # nocov
)
helper(x,
attrs_to_ignore = attrs_to_ignore, sort_attrs = sort_attrs,
na.rm = na.rm, name_vertices = name_vertices, store_eid = store_eid,
...
)
}
|