Package {emln}

emln: Organize, Handle, and Explore Ecological Multilayer Networks

Description

Data and analysis of ecological multilayer networks, including standardization of data structures and functions to convert between them. Includes an interactive multilayer network visualizer (beta, paper forthcoming), and a collection of 78 empirical ecological multilayer network datasets. This work was supported by research grant ISF (Israel Science Foundation) 1281/20 to Shai Pilosof. Noa Frydman (2023) doi:10.1111/2041-210X.14225.

Author(s)

Maintainer: Geut Galai geutg@post.bgu.ac.il

Authors:

• Noa Frydman

• Shai Pilosof pilos@bgu.ac.il [funder]

• Shirly Freilikhman

See Also

Useful links:

• https://emln.ecomplab.com/

• Report bugs at https://github.com/Ecological-Complexity-Lab/emln/issues

Convert a data.frame to a list of named lists (one per row)

Description

Convert a data.frame to a list of named lists (one per row)

Usage

.df_to_list_of_rows(df)

Resolve path to the bundled multilayer_viz web app

Description

Looks first for an installed copy at system.file("multilayer_viz", package = "emln"), then falls back to sibling/dev locations for in-source development.

Usage

.resolve_viz_path(viz_path = NULL)

Minimal JSON serializer (no dependency on jsonlite)

Description

Converts an R list structure to a JSON string. Supports: lists, vectors, strings, numbers, logicals, NULL.

Usage

.to_json(x, indent = 0)

Creates a monolayer network object.

Description

Automatically identifies if the input is a matrix or an edge list and creates a monolayer object.

Usage

create_monolayer_network(
  x,
  directed = NULL,
  bipartite = NULL,
  group_names = c("set_cols", "set_rows"),
  node_metadata = NULL
)

Arguments

Details

Converts between edge list and matrix formats and creates a monolayer object. It a wrapper function for list_to_matrix, matrix_to_list_unipartite, matrix_to_list_bipartite. Node metadata can only be included with an edge list input.

Value

A monolayer object.

See Also

list_to_matrix, matrix_to_list_unipartite, monolayer.

Examples

library(igraph)

# A bipartite network from package bipartte
x <- create_monolayer_network(bipartite::memmott1999, bipartite = TRUE,
directed = FALSE, group_names = c('Animals','Plants'))

# A bipartite network as an igraph object

# Generate a random bipartite network in igraph
g <- igraph::sample_bipartite(10,16,p=0.3, type = 'gnp', directed = TRUE, mode = 'in')
V(g)$name <- letters # name the nodes
V(g)$gender <- sample(c('F','M'), size = 26, replace = TRUE) # Add a node attribute
E(g)$weight=runif(ecount(g)) # Add edge weights
plot(g, layout=layout.bipartite)
create_monolayer_network(g, group_names = c('Parasites','Hosts'))

Create Multilayer Network

Description

This function creates a multilayer network from multiple matrices / link lists.

Usage

create_multilayer_network(
  list_of_layers,
  bipartite,
  directed,
  interlayer_links = NULL,
  layer_attributes = NULL,
  state_node_attributes = NULL,
  physical_node_attributes = NULL
)

Arguments

Details

Input of list_of_layers is handled by the function create_monolayer_network; see it's description for details on input. If using matrices as input, they should contain row and column names. If link lists are provided as input column names should be from to weight.

When using link lists, it is possible to include link attributes. In that case the headers of all the link lists and, if included, the interlayer links, must be the same (after the weight), even if some attributes are included in only some layers (see detailed example in the code accompanying the package). Missing link attributes can be set to NA.

If interlayer links are provided, then layer_attributes must also be provided. Specify layer and nodes by UNIQUE names (not IDs). Layer names should correspond to those provided in layer_attributes.

Attributes of state nodes can be provided with state_node_attributes. If provided, then columns layer_name and node_name must be included.

For compatibility with function load_emln the output contains description and references. The value of any missing data frames in the multilayer object will be set to NULL.

See multiple example in the code accompanying the package

Value

A multilayer object (see ?multilayer).

See Also

multilayer, create_monolayer_network

Examples

library(tibble)
pond_1 <- matrix(c(0,1,1,0,0,1,0,0,0), byrow = TRUE,
nrow = 3, ncol = 3, dimnames = list(c('pelican','fish','crab'),
c('pelican','fish','crab')))
pond_2 <- matrix(c(0,1,0,0,0,1,0,0,0), byrow = TRUE,
nrow = 3, ncol = 3, dimnames = list(c('pelican','fish','crab'),
c('pelican','fish','crab')))
pond_3 <- matrix(c(0,1,1,0,0,1,0,0,0), byrow = TRUE,
nrow = 3, ncol = 3, dimnames = list(c('pelican','fish','tadpole'),
c('pelican','fish','tadpole')))

layer_attrib <- tibble(layer_id=1:3,
                       layer_name=c('pond_1','pond_2','pond_3'),
                       location=c('valley','mid-elevation','uphill'))

# Create the ELL tibble with interlayer links.
interlayer <- tibble(layer_from=c('pond_1','pond_1','pond_1'),
                     node_from=c('pelican','crab','pelican'),
                     layer_to=c('pond_2','pond_2','pond_3'),
                    node_to=c('pelican','crab','pelican'),
                     weight=1)

# This is a directed network so the links should go both ways,
# even though they are symmetric.
interlayer_2 <- interlayer[,c(3,4,1,2,5)]
names(interlayer_2) <- names(interlayer)
interlayer <- rbind(interlayer, interlayer_2)

multilayer <- create_multilayer_network(list_of_layers =
list(pond_1, pond_2, pond_3), layer_attributes = layer_attrib,
interlayer_links = interlayer, bipartite = FALSE, directed = TRUE)

View the data sets

Description

@format Data set of multilayer networks

Usage

descriptions

Format

An object of class tbl_df (inherits from tbl, data.frame) with 89 rows and 10 columns.

Details

@source create

@examples data(descriptions)

emln10_environment_temporal_parker_huryn_2006

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln11_environment_thompson_townsend_2004

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln12_environment_fryer_1959

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln13_multiplex_kefi_2016

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.b4vg0

emln14_multiplex_mello_2019

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es

emln15_environment_petipa_1970

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln16_multiplex_pocock_2012

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.3s36r118

emln17_multiplex_traveset_2020

Description

Network Description:

Source

Figshare

https://doi.org/10.6084/m9.figshare.c.5208546.v1

emln18_perturbation_stewart_sprules_2011

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln19_spatial_angelini

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln1_environment_schleuning_2010

Description

Network Description:

Source

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/schleuning-et-al-2010.html

emln20_spatial_angelini_2013

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln21_spatial_arroyo_1982

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php

http://www.ecologia.ib.usp.br/iwdb/html/arroyo_1982.html

emln22_spatial_beaver_1985

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln23_spatial_canadian_fish_parasite

Description

Network Description:

Source

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/canadian_fish.html

emln24_spatial_carlo_2003

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln25_spatial_carstensen_2014

Description

Network Description:

Source

figshare

https://figshare.com/articles/dataset/Beta_Diversity_of_Plant_Pollinator_Networks_and_the_Spatial_Turnover_of_Pairwise_Interactions/1234708

emln26_spatial_chacoff_2020

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.8cz8w9gm1

emln27_spatial_dexter_1947

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln28_spatial_dicks_2002

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php?type=6

emln29_spatial_dupont_olesen_2009

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln2_environment_benadi_jae_2013

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.8mn44

emln30_spatial_elberling_1999

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php?type=6

http://www.ecologia.ib.usp.br/iwdb/

emln31_spatial_environment_cornaby_1974

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln32_spatial_environment_mckinnerney_1978

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln33_spatial_hadfield_2013

Description

Network Description:

Source

Web_of_Life

Dryad

http://www.web-of-life.es/map.php

https://datadryad.org/stash/dataset/doi:10.5061/dryad.jf3tj

emln34_spatial_havens_1992

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln35_spatial_ingversen_2006

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln36_spatial_joern_1979

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php?type=6

http://www.ecologia.ib.usp.br/iwdb/html/joern_1979.htm

emln37_spatial_jordano_unpubl

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln38_spatial_kyoto

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php

http://www.ecologia.ib.usp.br/iwdb/resources.html

emln39_spatial_leather_1991

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php

http://www.ecologia.ib.usp.br/iwdb/html/leather_1991.htm

emln3_environment_bird_1930

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln40_spatial_medan_2002

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/medan_et_al_2002.html

http://www.web-of-life.es/map.php

emln41_spatial_melian_2015

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.06bb5

emln42_spatial_menge_sutherland_1976

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln43_spatial_montero_2005

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln44_spatial_olesen_2003

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln45_spatial_olesen_2002

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln46_spatial_p_jordano_unpubl

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln47_spatial_paine_1963

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln48_environment_perturbation_bartomeus_2008

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/bartomeus_2008.html

http://www.web-of-life.es/map.php

emln49_spatial_perturbation_vazquez_2002

Description

Network Description:

Source

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/vazquez_2002.html

emln4_environment_hawkins_goeden_1984

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln50_spatial_poulin_1999

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php

http://www.ecologia.ib.usp.br/iwdb/resources.html

emln51_spatial_primack_1983

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es

emln52_spatial_ricciardi_2010

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln53_spatial_slovakia

Description

Network Description:

Source

NA

NA

emln54_spatial_snow b_k_&snow_1988

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.ecologia.ib.usp.br/iwdb/html/snow_snow_1971.htm

http://www.web-of-life.es/map.php?type=6

emln55_spatial_temporal_alcorlo_2001

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln56_spatial_temporal_closs_1994

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln57_spatial_temporal_kolpelke_2017

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln58_spatial_temporal_martins_2020

Description

Network Description:

Source

Dryad

https://doi.org/10.5061/dryad.vmcvdncq0

emln59_spatial_thompson_2003

Description

Network Description:

Source

Web_of_Life

http://www.web-of-life.es/map.php

emln5_environment_jones_1949

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln60_spatial_trojelsgaard_2015

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.76173

emln61_spatial_yanez_1978

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln62_temporal_angelini_2006

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln63_temporal_brodeur_1992

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln64_temporal_caradona_2020

Description

Network Description:

Source

EDI_data_portal

https://portal.edirepository.org/nis/mapbrowse?packageid=edi.512.1

emln65_temporal_chacoff_2020

Description

Network Description:

Source

Dryad

https://datadryad.org/stash/dataset/doi:10.5061/dryad.8cz8w9gm1

emln66_temporal_cohen_2003

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln67_temporal_douglas_2011

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln68_temporal_environment_baeta_2011

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln69_temporal_fang_2012

Description

Network Description:

Source

web

https://figshare.com/articles/dataset/Relative_Stability_of_Core_Groups_in_Pollination_Networks_in_a_Biodiversity_Hotspot_over_Four_Years/127797

emln6_environment_kohler_2011

Description

Network Description:

Source

Web_of_Life

Interaction_Web_DataBase

http://www.web-of-life.es/map.php?type=6

http://www.ecologia.ib.usp.br/iwdb/html/schleuning-et-al-2010.html

emln70_temporal_mayse_price_1978

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln71_temporal_perturbation_kaiser_bunbury_2009

Description

Network Description:

Source

Interaction_Web_DataBase

Web_of_Life

http://www.ecologia.ib.usp.br/iwdb/html/kaiser-bunbury_2009.html

http://www.web-of-life.es/map.php

emln72_temporal_ponisio_2017

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln73_temporal_ramos_robles_2016

Description

Network Description:

Source

PeerJ

https://peerj.com/articles/2048/#supplemental-information

emln74_temporal_ruzicka_2012

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln75_temporal_schoenly_reid_1983

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln76_temporal_tavares_cromar_1996

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln77_temporal_vaiela_1974

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln78_temporal_zackenberg_2013

Description

Network Description:

Source

plos

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081694

emln7_environment_rejmanek_stary_1979

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln8_environment_savely_1939

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

emln9_environment_seifert_1976

Description

Network Description:

Source

mangal

https://mangal.io/doc/api/

Convert a multilayer class to a a list of igraph objects

Description

This function creates a list of igraph objects from the network layers. Interlayer links are not included.

Usage

get_igraph(multilayer, bipartite, directed)

Arguments

Details

If link, physical node or state node attributes are included in the multilayer network they are passed to the igraph objects.

Value

A list:

• layers_igraph A list of igraph objects, one per layer

• nodes A table of physical nodes, as in the multlayer object.

• state_nodes_map A table with state nodes to map the nodes to the row and columns of a SAM.

Examples

# See examples in:
# https://emln.ecomplab.com/multilayer.html#To_igraph_objects

Convert a multilayer class to a supra-adjacency matrix

Description

This function creates a supra-adjacency matrix from a multilayer object.

Usage

get_sam(
  multilayer,
  bipartite,
  directed,
  sparse = FALSE,
  remove_zero_rows_cols = FALSE
)

Arguments

Details

By default, a SAM contains all the nodes in all the layers. However, not all nodes always occur in all layers. This will be reflected in the state_nodes_map: When layer and node ids are NA that means that the node did not occur in the layer.

A node may not have links across all the layers. In that case, its row or column sum will be zero. This can happen in a directed matrix (see toy example for unipartite network), or in diagonally-coupled networks (see toy bipartite example). The user can choose to remove rows and columns that sum to zero by setting remove_zero_rows_cols to TRUE.

Value

A list:

• M The SAM. Can also be sparse.

• nodes A table of physical nodes, as in the multlayer object.

• state_nodes_map A table with state nodes to map the nodes to the row and columns of the SAM.

Examples

# See examples in:
# https://emln.ecomplab.com/multilayer.html#To_supra-adjacency_matrices

Edge list to matrix conversion

Description

Convert an edge list to a matrix. Can handle unipartite and bipartite networks.

Usage

list_to_matrix(
  x,
  directed = FALSE,
  bipartite = TRUE,
  group_names = c("set_cols", "set_rows"),
  node_metadata = NULL
)

Arguments

Details

It is also possible to add node attributes. For this, it uses igraph. The first column in the node_metadata data frame should have the names of the nodes in the edge list.

Value

A monolayer object.

See Also

Functions create_monolayer_network, monolayer and graph_from_data_frame from igraph.

Examples

library(dplyr)
network <- load_emln(17)
nodes <- network$nodes
links<-subset(network$extended_ids %>% filter(layer_from==1), select=c(node_from, node_to, weight))

list_to_matrix(links, directed = TRUE, bipartite = FALSE, node_metadata = nodes)


# See examples in:
# https://emln.ecomplab.com/monolayer.html#Unipartite

Internal function - loads an RData file, and returns it

Description

Internal function - loads an RData file, and returns it

Usage

loadRData(fileName)

Arguments

Load networks include din the package

Description

Load a specific network by specifying its ID.

Usage

load_emln(network_id)

Arguments

Details

Use the search_emln and view_emln functions to obtain network IDs.

Value

A multilayer object (see ?multilayer).

See Also

multilayer

Examples

load_emln(network_id = 38)

Incidence matrix to edge list conversion

Description

Convert an incidence matrix to an edge list.

Usage

matrix_to_list_bipartite(x, group_names = c("set_cols", "set_rows"))

Arguments

Details

Assigns column and row names if those do not exist. Cannot handle node attributes/metadata. Always assumes an undirected network.

Value

A monolayer object.

See Also

create_monolayer_network, monolayer

Examples

# See examples in: https://emln.ecomplab.com/monolayer.html#Bipartite

matrix_to_list_bipartite(bipartite::memmott1999, group_names = c('Animals', 'Plants'))

Adjacency matrix to edge list conversion

Description

Convert an adjacency matrix to an edge list.

Usage

matrix_to_list_unipartite(x, directed)

Arguments

Details

Assigns column and row names if those do not exist. Cannot handle node attributes/metadata.

Value

A monolayer object

See Also

create_monolayer_network, monolayer

Examples

# See examples in:
# https://emln.ecomplab.com/monolayer.html#Unipartite

# Generate a matrix with random weighted interactions
x <- matrix(rbinom(100,1,0.6),10,10)
x <- x*round(runif(100,1,5),0)
# run
matrix_to_list_unipartite(x, directed = TRUE)

An object of class monolayer

Description

A network object of class monolayer contains all the necessary information and R objects to perform future analyses on a monolayer network, and in particular analyses using Infomap.

Value

A list with:

• mode: bipartite (B) or unipartite (U)

• directed: TRUE/FALSE

• nodes: a tibble with information on the nodes (name, id, type, other attributes)

• mat: the network in a matrix format

• edge_list: the network in an edge list format

• igraph_object: the igraph object of the network

See Also

list_to_matrix, matrix_to_list_unipartite, matrix_to_list_bipartite, create_network_object

An object of class multilayer

Description

A network object of class multilayer contains all the necessary information and R objects that define a multilayer network.

Value

A list with:

• nodes Physical nodes. First column is a unique node id. Node attributes are included if provided as input.

• layers Information on layers.

• extended An extended link list of the format layer_from node_from layer_to node_to weight. All nodes and layers are identified by names.

• extended_ids An extended link list of the format layer_from node_from layer_to node_to weight. All nodes and layers are identified by unique IDs automoatically generated.

• state_nodes List of state nodes of the format layer_id node_id layer_name node_name. Also includes state node attributes if provided as input.

• description For compatibility with load_emln.

• references For compatibility with load_emln.

See Also

create_multilayer_network

Export a multilayer network to CSV files

Description

Writes an EMLN multilayer object as the three-file CSV set consumed by the Multilayer Network Visualizer's CSV importer.

Usage

multilayer_to_csv(
  multilayer,
  dir,
  prefix = "network",
  bipartite = FALSE,
  directed = NULL
)

Arguments

Details

The CSV files follow the schema accepted by the visualizer's CSV importer:

• edges: layer_from, node_from, layer_to, node_to, weight (+ any extra link attributes).

• layers: layer_id, layer_name (+ latitude, longitude, bipartite and any extra layer attributes).

• nodes: node_name (+ node_type and any extra physical node attributes, same across all layers). node_group is renamed to node_type.

• state_nodes (written only when extra per-(layer, node) attributes exist): layer_name, node_name + extra columns. Use this when the same node has different attribute values in different layers (e.g. abundance, module membership).

The directed flag is not written to the CSV files; it is a property you specify in the visualizer's CSV import dialog at load time.

Value

Invisibly returns a named character vector of file paths written (edges, layers, nodes, and optionally state_nodes).

Note

The Multilayer Network Visualizer that this function targets is currently in beta. Feedback and bug reports are welcome at https://github.com/Ecological-Complexity-Lab/emln/issues.

See Also

multilayer_to_json, plot_multilayer

Examples

net <- load_emln(14)
multilayer_to_csv(net, dir = "tests/out/", prefix = "kefi", bipartite = TRUE)

Export a multilayer network to JSON

Description

Converts an EMLN multilayer object to JSON format compatible with the Multilayer Network Visualizer web app.

Usage

multilayer_to_json(multilayer, file = NULL, bipartite = FALSE, directed = NULL)

Arguments

Details

The JSON output contains four arrays matching the visualizer's expected format:

• nodes: Physical nodes with node_id, node_name, and any extra attributes. For bipartite networks, node_group is mapped to node_type.

• layers: Layer metadata with layer_id, layer_name, and extra attributes. For bipartite networks, a bipartite: true flag is added.

• extended: The extended edge list with layer_from, node_from, layer_to, node_to, weight, and any link attributes. For directed networks, a directed: true flag is added to each link.

• state_nodes: State node map with layer_id, node_id, layer_name, node_name.

Value

If file is NULL, returns the JSON string invisibly. If file is specified, writes JSON to disk and returns the file path invisibly.

Note

The Multilayer Network Visualizer that this function targets is currently in beta. Feedback and bug reports are welcome at https://github.com/Ecological-Complexity-Lab/emln/issues.

See Also

plot_multilayer, create_multilayer_network, load_emln

Examples

# Export to file
net <- load_emln(14)
multilayer_to_json(net, file = "tests/my_network.json", bipartite = TRUE)

# Get JSON string
json_str <- multilayer_to_json(net)

Plot a multilayer network in the browser

Description

Converts an EMLN multilayer object to JSON and opens the Multilayer Network Visualizer in the default web browser.

Usage

plot_multilayer(
  multilayer,
  bipartite = FALSE,
  directed = NULL,
  port = 8080,
  viz_path = NULL,
  browser = getOption("browser")
)

Arguments

Details

The function:

1. Converts the multilayer object to JSON via multilayer_to_json

2. Starts a local HTTP server (using httpuv) that serves the visualizer app and the network JSON

3. Opens the browser with auto-load enabled

The server runs in the background. Call httpuv::stopServer(handle) or close R to stop it. The JSON data is kept in memory and never written to disk.

Value

Invisibly returns the server handle. Use httpuv::stopServer(handle) to stop the server when done.

Note

The Multilayer Network Visualizer that this function targets is currently in beta. Feedback and bug reports are welcome at https://github.com/Ecological-Complexity-Lab/emln/issues.

See Also

multilayer_to_json, create_multilayer_network, load_emln

Examples

if (interactive()){
net <- load_emln(60)
srv <- plot_multilayer(net, bipartite = TRUE)

# When done:
httpuv::stopServer(srv)
}

Search networks

Description

Search the database for networks depending on search parameters specified below.

Usage

search_emln(
  ecological_network_type = NULL,
  multilayer_network_type = NULL,
  state_nodes = NULL,
  node_number_minimum = NULL,
  layer_number_minimum = NULL,
  weighted = NULL,
  interlayer = NULL,
  directed = NULL
)

Arguments

Value

A tibble containing the network id, and all the search arguments for each of the networks that are compatible with the search.

Examples

# See examples in:
# https://emln.ecomplab.com/data.html#Browsing_the_data

# Generates a tibble of all the networks in the package that are pollination networks
search_emln(ecological_network_type = 'Plant-Ant')

# Generates a tibble of all the networks in the package that have state nodes and are temporal
search_emln(multilayer_network_type = 'Temporal', state_node = TRUE)

View networks

Description

View the database interactively.

Usage

view_emln()

Value

An interactive GUI for browinsg through networks.