A graph object of class igraph.

A character string indicating the nature of the input data from which come the attributes to add to the nodes.

• If 'input = "shp"', then attributes come from the attribute table of a shapefile layer of type point.

• If 'input = "df"', then attributes come from an object of class data.frame

In both cases, input attribute table or dataframe must have a column with the exact same values as the node IDs.

(only if 'input = "df"') The name of the object of class data.frame with the attributes to add to the nodes.

(only if 'input = "shp"') The path (character string) to the directory containing the shapefile layer of type point whose attribute table contains the attributes to add to the nodes.

(only if 'input = "shp"') The name (character string) of the shapefile layer of type point (without extension, ex.: "nodes" refers to "nodes.shp" layer) whose attribute table contains the attributes to add to the nodes.

The name (character string) of the column with the nodes names in the input data (column of the attribute table or of the dataframe).

A character string (vector) indicating which columns of the input data will be added as nodes' attributes. By default, 'include = "all"', i.e. every column of the input data is added. Alternatively, 'include' can be a vector with the names of the columns to add (ex.: "c('x', 'y', 'pop_name')").

The path to the project .xml file.

An object of class data.frame with at least 4 columns of data used to perform the test. 4 columns must be called "n1", "n2", "r1" and "r2".

• n1 and n2 are the sizes of the samples from which r1 and r2 were computed respectively.

• r1 and r2 are Pearson's correlation coefficients

An object of class igraph. Its nodes must have names.

A character string indicating the algorithm used to create the modules with igraph.

• If algo = 'fast_greedy' (default), function cluster_fast_greedy from igraph is used (Clauset et al., 2004).

• If algo = 'walktrap', function cluster_walktrap from igraph is used (Pons et Latapy, 2006) with 4 steps (default options).

• If algo = 'louvain', function cluster_louvain from igraph is used (Blondel et al., 2008). In that case, the number of modules created in each graph is imposed.

• If algo = 'optimal', function cluster_optimal from igraph is used (Brandes et al., 2008) (can be very long). In that case, the number of modules created in each graph is imposed.

(optional, default = NULL) A character string indicating whether the links of the graph are weighted by distances or by similarity indices. It is only used to compute the modularity index. It can be:

• 'distance': Link weights correspond to distances. Nodes that are close to each other will more likely be in the same module.

• 'similarity': Link weights correspond to similarity indices. Nodes that are similar to each other will more likely be in the same module. Inverse link weights are then used to compute the modularity index.

(optional , default = NULL) A numeric or integer value indicating the number of modules in the graph. When this number is not specified, the optimal value is retained.

An object of class igraph. Its nodes must have names.

Character vector specifying the graph-theoretic metrics computed at the node-level in the graphs Graph-theoretic metrics can be:

• Degree (metrics = c("deg", ...))

• Closeness centrality index (metrics = c("close",...))

• Betweenness centrality index (metrics = c("btw",...))

• Strength (sum of the weights of the links connected to a node) (metrics = c("str",...))

• Sum of the inverse weights of the links connected to a node (metrics = c("siw", ...), default)

• Mean of the inverse weights of the links connected to a node (metrics = c("miw", ...))

By default, the vector metrics includes all these metrics.

Logical which indicates whether the links are weighted during the calculation of the centrality indices betweenness and closeness. (default: weight = TRUE). Link weights are interpreted as distances when computing the shortest paths. They should then be inversely proportional to the strength of the relationship between nodes (e.g. to fluxes).

A symmetric matrix or dist object with pairwise geographical Euclidean distances between populations or sample sites. It will be the explanatory variable, and only values from the off diagonal lower triangle will be used.

A symmetric matrix or dist object with pairwise landscape distances between populations or sample sites. These distances can be cost-distances or resistance distances, among others. It will be the explained variable, and only values from the off diagonal lower triangle will be used.

A numeric value or numeric vector with Euclidean distances to convert into cost-distances.

A character string indicating the method used to fit the model.

• If 'method = "log-log"' (default), then the model takes the following form : log(ld) ~ A + B * log(euc)

• If 'method = "lm"', then the model takes the following form : ld ~ A + B * euc

Logical (default = TRUE) indicating whether a figure is plotted

(if 'fig = TRUE') Character string indicating the color used to plot the line (default: "blue"). It must be a hexadecimal color code or a color used by default in R.

(if 'fig = TRUE') Character string indicating the color used to plot the points (default: "#999999"). It must be a hexadecimal color code or a color used by default in R.

A coordinate in degrees

An object of class data.frame

A character string indicating the name of the column with the ID of the origins

A character string indicating the name of the column with the ID of the arrivals

A character string indicating the name of the column with the values corresponding to each pair

Point 1 longitude in radians

Point 1 latitude in radians

Point 2 longitude in radians

Point 2 latitude in radians

Point 1 longitude in radians

Point 1 latitude in radians

Point 2 longitude in radians

Point 2 latitude in radians

Point 1 longitude in radians

Point 1 latitude in radians

Point 2 longitude in radians

Point 2 latitude in radians

project name, project dir in which proj_name.xml is found

raster.tif INT2S path or present in wd,

habitat code in the raster file

default 0, minimum habitat size in ha

default NULL nodata code in the raster file

A symmetric matrix or dist object with pairwise genetic distances between populations or sample sites.

A symmetric matrix or dist object with pairwise landscape distances between populations or sample sites. These distances can be Euclidean distances, cost-distances or resistance distances, among others.

A numeric or integer value indicating the interval between the different distance thresholds for which the correlation coefficients are computed.

(optional) The minimum distance threshold value at which the correlation coefficient is computed.

(optional) The maximum distance threshold value at which the correlation coefficient is computed.

Logical (default = TRUE) indicating whether a figure is plotted.

(optional) A numeric or integer value used to remove genetic distance values from the data before the calculation. All genetic distances values above 'thr_gd' are removed from the data. This parameter can be used especially when there are outliers.

(optional, if fig = TRUE) A character string indicating the color used to plot the line (default: "blue"). It must be a hexadecimal color code or a color used by default in R.

(optional, if fig = TRUE) A character string indicating the color used to plot the points (default: "#999999"). It must be a hexadecimal color code or a color used by default in R.

A symmetric matrix or a dist object with pairwise distances between nodes

The number of classes to create to search for the threshold value without testing all the possibilities. By default, 'val_step = 20'.

An object of class genind that contains the multilocus genotype (format 'locus') of the individuals as well as their population and their geographical coordinates.

A character string indicating the method used to compute the multilocus genetic distance between populations

• If 'dist = 'basic” (default), then the multilocus genetic distance is computed using a Euclidean genetic distance formula (Excoffier et al., 1992)

• If 'dist = 'weight”, then the multilocus genetic distance is computed as in Fortuna et al. (2009). It is a Euclidean genetic distance giving more weight to rare alleles

• If 'dist = 'PG”, then the multilocus genetic distance is computed as in popgraph::popgraph function, following several steps of PCA and SVD (Dyer et Nason, 2004).

• If 'dist = 'PCA”, then the genetic distance is computed following a PCA of the matrix of allelic frequencies by population. It is a Euclidean genetic distance between populations in the multidimensional space defined by all the independent principal components.

A character string indicating the formula used to compute the covariance matrix from the distance matrix

• If 'cov = 'sq” (default), then the covariance matrix is calculated from the matrix of squared distances as in Everitt et Hothorn (2011)

• If 'cov = 'dist”, then the covariance matrix is calculated from the matrix of distances as in Dyer et Nason (2004) and popgraph function

A character string indicating the way the partial correlation matrix is computed from the covariance matrix.

• If 'pcor = 'magwene”, the steps followed are the same as in Magwene (2001) and in popgraph::popgraph function. It is the recommended option as it meets mathematical requirements.

• If 'pcor = 'other”, the steps followed are the same as used by Fortuna et al. (2009). They are not consistent with the approach of Magwene (2001).

A numeric value corresponding to the statistical tolerance threshold used to test the difference from 0 of the partial correlation coefficients. By default, 'alpha=0.05'.

A character string indicating the method used to test the significance of the partial correlation coefficients.

• If 'test = 'EED” (default), then the Edge Exclusion Deviance criterion is used (Whittaker, 2009). Although other methods exist, this is the most common and thus the only one implemented here.

A character string indicating the way of adjusting p-values to assess the significance of the p-values

• If 'adj = 'none” (default), there is no p-value adjustment correction

• If 'adj = 'holm”, p-values are adjusted using the sequential Bonferroni correction (Holm, 1979)

• If 'adj = 'bonferroni”, p-values are adjusted using the classic Bonferroni correction

• If 'adj = 'BH”, p-values are adjusted using Benjamini et Hochberg (1995) correction controlling false discovery rate

A character string indicating the matrices included in the output list.

• If 'output = 'all” (default), then D (distance matrix), C (covariance matrix), Rho (partial correlation matrix), M (graph incidence matrix) and S (strength matrix) are included

• If 'output = 'dist_graph”, then the distance matrix D is returned only with the values corresponding to the graph edges

• If 'output = 'str_graph”, then the strength values matrix S is returned only with the values corresponding to the graph edges

• If 'output = 'inc”, then the binary adjacency matrix M is returned

• If 'output = 'igraph”, then a graph of class igraph is returned

A symmetric (pairwise) matrix or a dist object whose elements will be the links' weights

(optional) A symmetric (pairwise) distance matrix or a dist object whose values will be used for the pruning based on the threshold value.

The threshold value (logically between min(mat_thr) and max(mat_thr))(integer or numeric)

• If 'mode = 'larger” (default), all the links whose weight is larger than 'thr' are removed.

• If 'mode = 'lower”, all the links whose weight is lower than 'thr' are removed.

A symmetric (pairwise) matrix or a dist object whose elements will be the links' weights

(optional) A symmetric (pairwise) distance matrix or a dist object whose values will be used for the pruning method.

Which topology does the created graph have?

• If 'topo = 'gabriel” (default), the resulting graph will be a Gabriel graph (Gabriel et al., 1969). It means that there is a link between nodes x and y if and only if d_{xy}^{2} \leq \min(\sqrt{d_{xz}^{2}+d_{yz}^{2}}) , with z any other node of the graph.

• If 'topo = 'mst”, the resulting graph will have the topology of a minimum spanning tree. It means that the graph will not include any cycle (tree) and it will be the subgraph with a tree topology with the minimum total links' weight (based on 'mat_topo' values).

• If 'topo = 'percol”, if the link of the resulting graph with the minimum weight is removed, then the graph breaks into two components.

• If 'topo = 'comp”, a complete graph whose links are weighted with values from 'mat_w' is created.

• If 'topo = 'knn”, a k-nearest neighbor graph whose links are weighted with values from 'mat_w' is created. If the distance between node i and node j is among the k-th smallest distances between node i and the other nodes according to distances in matrix 'mat_topo', then there is a link between i and j in the resulting graph. Therefore, a node can be connected to more than two nodes because the nearest node to node j is not necessarily among the k nearest neighbors to node i. Let d1 be the smallest distance from node i to other nodes, if there are k nodes or more at this distance from node i, they are all connected to i. If there are less than k nodes connected to i at a distance d1, then we consider nodes at a distance d2 from i. In the latter case, all the nodes at a distance d2 from i are connected to i.

(if 'topo = 'knn”) An integer which indicates the number of nearest neighbors considered to create the K-nearest neighbor graph. k must be lower than the total number of nodes minus 1.

A character string with the path leading to the GENEPOP file in format .txt, or alternatively the name of this file in the working directory.

The number of loci in the GENEPOP file (integer or numeric).

(optional) Populations' names in the same order as in the GENEPOP file. Vector object (class character) of the same length as the number of populations. Without this parameter, populations are numbered from 1 to the number of populations.

Number indicating whether alleles are coded with 3 (default) or 2 digits.

An object of class genind from package adegenet.

A character string indicating the option used to select what the function will return:

• If output = "data.frame"(default), then the function will return an object 'x' of class data.frame ready to be saved as a text file with the following command: write.table(x, file = "file_name.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)

• If output = "path_to_file/file_name.txt", then the function will write a text file named 'file_name.txt' in the directory corresponding to 'path_to_file'. Without 'path_to_file', the text file is written in the current working directory. The text file has the format required by GENEPOP software.

An object of class genind from package adegenet.

A character string of the form output = "path_to_file/file_name.txt". Then, the function will write a text file named 'file_name.txt' in the directory corresponding to 'path_to_file'. Without 'path_to_file', the text file is written in the current working directory. The text file has the format required by STRUCTURE software.

Logical indicating whether a message says if Graphab has been downloaded or not.

Logical indicating whether the function returns a 1 or a 0 to indicate if Graphab has been downloaded or not.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

A character string indicating the name of the link set whose properties are imported. The link set has been created with Graphab or using graphab_link function.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml will be created.

(optional, default=NULL) A character string indicating the name of the link set used to create the graph. Link sets can be created with graphab_link.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml will be created.

A character string equal to either 'all' (default) or 'habitat' indicating whether the returned codes are all the codes of the source raster used for creating the project or only the code corresponding to the habitat patches.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

A numeric vector with positive values

A logical value indicating whether the computed coefficient is biased or not. Unbiased value are equal to n/(n-1) times the biased ones.

The first graph object

• If mode = 'graph' (default), x is a graph object of class igraph. Then, its nodes must have the same names as in graph y.

• If mode = 'data.frame', x refers to a column of the data.frame 'data'. Then x must be a character string indicating the name of the column of 'data' with the modules' labels of the nodes in the first graph. In that case, the column can be of class numeric, character or factor but will be converted into a numeric vector in any case.

• If mode = 'vector', x is a vector of class character, factor or numeric. In that case, it must have the same length as vector y and will be converted into a numeric vector.

The second graph object Same classes possible as for x. Must be of the same format as x

A character string indicating whether x and y are igraph objects, vectors or columns from a data.frame. mode can be 'graph', 'data.frame' or 'vector'.

(if x and y are igraph objects) A numeric or integer value or a numeric vector with 2 elements indicating the number of modules to create in both graphs.

• If nb_modul is a numeric value, then the same number of modules are created in both graphs.

• If nb_modul is a numeric vector of length 2, then the numbers of modules created in graphs x and y are the first and second elements of nb_modul, respectively.

(if x and y are igraph objects) A character string indicating the algorithm used to create the modules with igraph.

• If algo = 'fast_greedy' (default), function cluster_fast_greedy from igraph is used (Clauset et al., 2004).

• If algo = 'walktrap' (default), function cluster_walktrap from igraph is used (Pons et Latapy, 2006) with 4 steps (default options).

• If algo = 'louvain', function cluster_louvain from igraph is used (Blondel et al., 2008). In that case, the number of modules created in each graph is imposed.

• If algo = 'optimal', function cluster_optimal from igraph is used (Brandes et al., 2008) (can be very long). In that case, the number of modules created in each graph is imposed.

(optional, if x and y are igraph objects, default is 'none') A character string indicating whether the links of the graph are weighted by distances or by similarity indices. It is only used to compute the modularity index. It can be:

• 'distance': Link weights correspond to distances. Nodes that are close to each other will more likely be in the same module.

• 'similarity': Link weights correspond to similarity indices. Nodes that are similar to each other will more likely be in the same module. Inverse link weights are then used to compute the modularity index.

• 'none': Links are not weighted for the computation, which is only based on graph topology.

Two different weightings can be used to create the modules of the two graphs.

• If node_inter is a character string, then the same link weighting is used for both graphs.

• If node_inter is a character vector of length 2, then the link weighting used by the algorithm to create the modules of graphs x and y is determined by the first and second elements of node_inter, respectively.

(if x and y are columns from a data.frame) An object of class data.frame with at least two columns and as many rows as there are nodes in the graphs compared. The columns indicate the modules of each node in 2 different classifications.

An object of class igraph. Its nodes must have the same names as in graph y.

An object of class igraph. Its nodes must have the same names as in graph x.

Two-element character vector specifying the graph-theoretic metrics computed at the node-level in the graphs or the node attribute values to be correlated to these metrics. Graph-theoretic metrics can be:

• Degree (metrics = c("deg", ...))

• Closeness centrality index (metrics = c("close",...))

• Betweenness centrality index (metrics = c("btw",...))

• Strength (sum of the weights of the links connected to a node) (metrics = c("str",...))

• Sum of the inverse weights of the links connected to a node (metrics = c("siw", ...), default)

• Mean of the inverse weights of the links connected to a node (metrics = c("miw", ...))

Node attributes must have the same names as in the igraph object, and must refer to an attribute with numerical values. The vector metrics is composed of two character values. When a node attribute has the same name as a metric computable from the graph, node attributes are given priority.

A character string indicating which correlation coefficient is to be computed ("pearson", "kendall" or "spearman" (default)).

Logical which indicates whether the links are weighted during the calculation of the centrality indices betweenness and closeness. (default: weight = TRUE). Link weights are interpreted as distances when computing the shortest paths. They should then be inversely proportional to the strength of the relationship between nodes (e.g. to fluxes).

Logical. Should significance testing be performed? (default = TRUE)

A data.frame with the spatial coordinates of the point set (the graph nodes). It must have three columns:

• ID: A character string indicating the name of the points(graph nodes).

• x: A numeric or integer indicating the longitude of the graph nodes.

• y: A numeric or integer indicating the latitude of the graph nodes.

A character string indicating the name of the column of crds with the point IDs

A character string indicating the name of the column of crds with the point longitude

A character string indicating the name of the column of crds with the point latitude

A character string indicating whether the links of the graph are weighted by Euclidean distances (TRUE)(default) or not (FALSE). When the graph links do not have weights in Euclidean distances, each link is given a weight of 1.

A graph object of class igraph. Its nodes must have the same names as in graph y.

A graph object of class igraph. Its nodes must have the same names as in graph x.

A data.frame with the spatial coordinates of the graph nodes (both x and y). It must have three columns:

• ID: Name of the graph nodes (character string). The names must be the same as the node names of the graphs of class igraph (igraph::V(graph)$name)

• x: Longitude of the graph nodes (numeric or integer).

• y: Latitude of the graph nodes (numeric or integer).

A graph object of class igraph

Logical. If TRUE (default), then the column 'link' of the output data.frame contains the weights of the links. If FALSE, it contains only 0 and 1.

A graph object of class igraph

(if 'mode = 'spatial”) A data.frame with the spatial coordinates of the graph nodes. It must have three columns:

• ID: Name of the graph nodes (will be converted into character string). The names must the same as the node names of the graph object of class igraph (igraph::V(graph)$name)

• x: Longitude (numeric or integer) of the graph nodes in the coordinates reference system indicated with the argument crds_crs.

• y: Latitude (numeric or integer) of the graph nodes in the coordinates reference system indicated with the argument crds_crs.

Indicates which shapefile layers will be created

• If 'mode = 'both” (default), then two shapefile layers are created, one for the nodes and another for the links.

• If 'mode = 'node”, a shapefile layer is created for the nodes only.

• If 'mode = 'link”, a shapefile layer is created for the links only.

An integer indicating the EPSG code of the coordinates reference system to use. The projection and datum are given in the PROJ.4 format.

A character string indicating the suffix of the name of the layers to be created.

A character string corresponding to the path to the directory in which the shapefile layers will be exported. If dir_path = "wd", then the layers are created in the current working directory.

(not considered if 'mode = 'link”) Logical. Should graph node attributes integrated in the attribute table of the node shapefile layer? (default: FALSE)

A graph object of class igraph with n nodes. It is the observed graph that pred_graph is supposed to approach.

A graph object of class igraph with n nodes. It is the predicted graph that is supposed to be akin to obs_graph.

A character string specifying which index to compute in order to compare the topologies of the graphs.

• If 'mode = 'mcc” (default), the Matthews Correlation Coefficient (MCC) is computed.

• If 'mode = 'kappa”, the Kappa index is computed.

• If 'mode = 'fdr”, the False Discovery Rate (FDR) is computed.

• If 'mode = 'acc”, the Accuracy is computed.

• If 'mode = 'sens”, the Sensitivity is computed.

• If 'mode = 'spec”, the Specificity is computed.

• If 'mode = 'prec”, the Precision is computed.

Logical (TRUE or FALSE) specifying whether both graphs are directed or not.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

A character string indicating the way capacities are computed. It must be either:

• mode='area'(default): The capacity of the patches is computed as the area of each habitat patch. The argument exp makes it possible to raise area to a power given by an exposant.

• mode='ext_file': The capacity of the patches is given by an external .csv file. See argument ext_file below.

• mode='neigh': The capacity is computed depending on the neighbouring raster cells from each habitat patch. The number of cells with a value given by codes argument is summed up to the distance thr. This number can be weighted according to the weight argument.

(optional, default=NULL) An integer value or vector specifying the codes corresponding to the habitat pixel whose corresponding patches are included to compute the capacity as the area of the habitat when mode='area'. Patches corresponding to other initial habitat codes are weighted by 0.

An integer value specifying the power to which patch area are raised when mode='area'. When not specified, exp=1 by default.

A character string specifying the name of the .csv file in which patch capacities are stored. It must be located either in the working directory or in the directory defined by proj_path. It must have as many rows as there are patches in the project and its column names must include 'Id' and 'Capacity'. The 'Id' column must correspond to the patch ID in the 'patches' layer (see get_graphab_metric). The 'Capacity' column must contain the corresponding patch capacities to assign each patch.

(optional, default=NULL) An integer or numeric value indicating the maximum distance in cost distance units (except when cost_conv = TRUE) at which cells are considered for computing the capacity when mode='neigh'.

(optional, default=NULL) A character string indicating the name of the link set used to take distance into account when computing the capacity. Only used when mode='neigh'. Link sets can be created with graphab_link.

An integer value or a vector of integer values specifying the codes of the raster cells taken into account when computing the capacity in the neighbourhood of the patches, when mode='neigh'.

FALSE (default) or TRUE. Logical indicating whether numeric thr values are converted from cost-distance into Euclidean distance using a log-log linear regression. See also convert_cd function. Only used when mode='neigh'.

A logical indicating whether the cells are weighted by a weight decreasing with the distance from the patches (TRUE) or not (FALSE). The weights follow a negative exponential decline such that wi = exp(-alpha*di), where wi is the weight of cell i, di its distance from the patch and alpha a parameter determined such that wi = 0.05 when di = thr.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

A character string indicating the name of the graph with the links from which the corridors are computed. This graph has been created with Graphab or using graphab_graph function and is associated with a link set. Only the links present in the graph will be used in the computation.

An integer or numeric value indicating the maximum cost distance from the least-cost paths considered for creating the corridors, in cost distance units (except when cost_conv = TRUE).

(optional, default = "raster") A character string indicating whether the output is a raster file or a shapefile layer.

FALSE (default) or TRUE. Logical indicating whether numeric thr values are converted from cost-distance into Euclidean distance using a log-log linear regression. See also convert_cd function. Only used when mode='neigh'.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

(optional, default=NULL) A character string indicating the name of the link set used to create the graph. If linkset=NULL, every link set present in the project will be used to create a graph. Link sets can be created with graphab_link.

(optional, default=NULL) A character string indicating the name of the graph created. If name=NULL, a name will be created. If both linkset=NULL and name=NULL, then a graph will be created for every link set present in the project and a name will be created every time. In the latter case, a unique name cannot be specified. Link sets can be created with graphab_link.

(optional, default=NULL) An integer or numeric value indicating the maximum distance associated with the links of the created graph. It allows users to create a pruned graph based on a distance threshold. Note that when the link set used has a planar topology, the graph is necessarily a pruned graph (not complete) and adding this threshold parameter can remove other links. When the link set has been created with cost-distances, the parameter is expressed in cost-distance units whereas when the link set is based upon Euclidean distances, the parameter is expressed in meters.

FALSE (default) or TRUE. Logical indicating whether numeric thr values are converted from cost-distance into Euclidean distance using a log-log linear regression. See also convert_cd function.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

A character string indicating the name of the raster to be created after the interpolation.

An integer indicating the spatial resolution in meters of the raster resulting from the metric interpolation.

A character string indicating the name of the link set used for the interpolation. It should be the one used to create the used graph and the metric.

A character string indicating the name of the graph from which the metric was computed and whose links are considered for a potential multi-linkage with patches. This graph has been created with Graphab or using graphab_graph function and is associated with a link set.

A character string indicating the name of the already computed metric to be interpolated.

A numeric or integer value specifying the distance at which we assume a probability equal to prob during the interpolation. It is used to set \alpha for computing probabilities associated with distances between each pixel and the neighboring patch(es) such that probability between patch i and pixel j is p_{ij}= e^{-\alpha d_{ij}}.

A numeric or integer value specifying the probability at distance dist. By default, code=0.05. It is used to set \alpha (see param dist above).

(default NULL) If NULL, the value of each pixel is computed from the value of the metric at the nearest habitat patch, weighted by a probability depending on distance. If an integer, the value of each pixel depends on the values of the metric taken at several of the nearest habitat patches, up to a distance (cost or Euclidean distance, depending on the type of linkset) equal to thr.

Logical (default = FALSE) only used if thr is not NULL, and specifying whether multiple values are summed up (TRUE) or averaged after being weighted by probabilities.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

A character string indicating whether links between patches are computed based on:

• Shortest cost distances: distance='cost' (default)

• Straight Euclidean distances: distance='euclid'

In the resulting link set, each link will be associated with its corresponding cost-distance and the length of the least-cost path in meters (if distance='cost') or with its length in Euclidean distance (if distance='euclid')

A character string indicating the name of the created linkset.

This argument could be:

• A data.frame indicating the cost values associated to each raster cell value. These values refer to the raster used to create the project with graphab_project. The data.frame must have two columns:

  • 'code': raster cell values

  • 'cost': corresponding cost values

• The path to an external raster file in .tif format with cost values.

A character string indicating the topology of the created link set. It can be:

• Planar (topo='planar' (default)): a planar set of links is created. It speeds up the computation but will prevent from creating complete graphs with graphab_graph.

• Complete (topo='complete'): a complete set of links is created. A link is computed between every pair of patches.

(optional, default = FALSE) A logical indicating whether links crossing patches are removed (TRUE).

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

A character string indicating the name of the graph on which the metric is computed. This graph has been created with Graphab or using graphab_graph function and is associated with a link set. Only the links present in the graph and their corresponding weights will be used in the computation, together with patch areas.

A character string indicating the metric which will be computed on the graph. This metric can be:

• A global metric:

  • Probability of Connectivity (metric = 'PC'): Sum of products of area of all pairs of patches weighted by their interaction probability, divided by the square of the area of the study zone. This ratio is the equivalent to the probability that two points randomly placed in the study area are connected.

  • Equivalent Connectivity (metric = 'EC'): Square root of the sum of products of capacity of all pairs of patches weighted by their interaction probability. This is the size of a single patch (maximally connected) that would provide the same probability of connectivity as the actual habitat pattern in the landscape (Saura et al., 2011).

  • Integral Index of Connectivity (metric = 'IIC'): For the entire graph: product of patch areas divided by the number of links between them, the sum is divided by the square of the area of the study zone. IIC is built like the PC index but using the inverse of a topological distance rather than a negative exponential function of the distance based on the link weight.

• A local metric:

  • Flux (metric = 'F'): For the focal patch i : sum of area of patches other than i and weighted according to their minimum distance to the focal patch through the graph. This sum is an indicator of the potential dispersion from the patch i or, conversely to the patch i

  • Betweenness Centrality index (metric = 'BC'): Sum of the shortest paths through the focal patch i, each path is weighted by the product of the areas of the patches connected and of their interaction probability. All possible paths between every pair of patches is considered in this computation.

  • Interaction Flux (metric = 'IF'): Sum of products of the focal patch area with all the other patches, weighted by their interaction probability.

  • Degree (metric = 'Dg'): Number of edges connected to the node i i.e. number of patches connected directly to the patch i.

  • Closeness Centrality index (metric = 'CCe'): Mean distance from the patch i to all other patches of its component k.

  • Current Flux (metric = 'CF'): Sum of currents passing through the patch i. c_{i}^{j} represents the current through the patch i when currents are sent from all patches (except j) to the patch j. The patch j is connected to the ground.

• A delta metric:

  • delta Probability of Connectivity (metric = 'dPC'): Rate of variation between the value of PC index and the value of PC' corresponding to the removal of the patch i. The value of dPC is decomposed into three parts:

    • dPC_{area} is the variation induced by the area lost after removal;

    • dPC_{flux} is the variation induced by the loss of interaction between the patch i and other patches;

    • dPC_{connector} is the variation induced by the modification of paths connecting other patches and initially routed through i.

For most metrics, the interaction probability is computed for each pair of patches from the path that minimizes the distance d (or the cost) between them. It then maximizes {e}^{-\alpha d_{ij}} for patches i and j. To use patch capacity values different from the patch area, please use directly Graphab software.

A logical (default = FALSE) indicating whether the 'multihabitat' mode is used when computing the metric. It only applies to the following metrics: 'EC', 'F', 'IF' and 'BC'. If TRUE, then the project must have been created with the option nomerge=TRUE. It then returns several columns with metric values including the decomposition of the computation according to the type of habitat of every patch. Be careful, this option is in development and we cannot guarantee the results are correct.

A numeric or integer value specifying the distance at which dispersal probability is equal to prob. This argument is mandatory for weighted metrics (PC, F, IF, BC, dPC, CCe, CF) but not used for others. It is used to set \alpha for computing dispersal probabilities associated with all inter-patch distances such that dispersal probability between patches i and j is p_{ij}= e^{-\alpha d_{ij}}.

A numeric or integer value specifying the dispersal probability at distance dist. By default, code=0.05. It is used to set \alpha (see param dist above).

A numeric or integer value between 0 and 1 specifying the exponent associated with patch areas in the computation of metrics weighted by patch area. By default, beta=1. When beta=0, patch areas do not have any influence in the computation.

FALSE (default) or TRUE. Logical indicating whether numeric dist values are converted from cost-distance into Euclidean distance using a log-log linear regression. See also convert_cd function.

Logical (default = TRUE) indicating whether metric values are returned in R (TRUE) or only stored in the patch attribute layer (FALSE)

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

A character string indicating the name of the graph on which the modularity index is computed. This graph has been created with Graphab or using graphab_graph function and is associated with a link set. Only the links present in the graph and their corresponding weights will be used in the computation, together with patch areas.

A numeric or integer value specifying the distance at which dispersal probability is equal to prob. This argument is mandatory for weighted metrics (PC, F, IF, BC, dPC, CCe, CF) but not used for others. It is used to set \alpha for computing dispersal probabilities associated with all inter-patch distances such that dispersal probability between patches i and j is p_{ij}= e^{-\alpha d_{ij}}.

A numeric or integer value specifying the dispersal probability at distance dist. By default, code=0.05. It is used to set \alpha (see param dist above).

A numeric or integer value between 0 and 1 specifying the exponent associated with patch areas in the computation of metrics weighted by patch area. By default, beta=1. When beta=0, patch areas do not have any influence in the computation.

(optional, default=NULL) An integer or numeric value indicating the number of modules to be created. By default, it is the number that maximises the modularity index.

Logical (default=TRUE) indicating whether results are returned to user.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

A character string indicating the name of the link set used. The link set is here used to get the defined cost values and compute the distance from the point to the patches. Link sets can be created with graphab_link.

Can be either;

• A character string indicating the path (absolute or relative) to a shapefile point layer

• A character string indicating the path to a .csv file with three columns: ID, x and y, respectively indicating the point ID, longitude and latitude.

• A data.frame with three columns: ID, x and y, respectively indicating the point ID, longitude and latitude.

• A SpatialPointsDataFrame

The point ID column must be 'ID' by default but can also be specified by the id argument in all three cases.

A character string indicating the name of the column in either the .csv table, data.frame or attribute table, corresponding to the ID of the points. By default, it should be 'ID'. This column is used for naming the points when returning the output.

Logical (default=TRUE) indicating whether the metrics associated with closest habitat patches from the points are returned to users.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml will be created.

A character string indicating the name of the .tif raster file or of its path. If the path is not specified, the raster must be present in the current working directory. Raster cell values must be in INT2S encoding.

An integer or numeric value or vector indicating the code.s (cell value.s) of the habitat cells in the raster file.

(optional, default=FALSE) A logical indicating whether contiguous patches corresponding to different pixel codes are merged (FALSE, default) or not merged (TRUE). Be careful, the nomerge = TRUE option is in development and we cannot guarantee the results are correct.

(optional, default=0) An integer or numeric value specifiying the minimum area in hectares for a habitat patch size to become a graph node.

(optional, default=NULL) An integer or numeric value specifying the code in the raster file associated with nodata value (often corresponding to peripheric cells)

(optional, default=NULL) An integer or numeric value specifying the maximum side length of the rectangular full extent of each habitat patch in metric units. If this side length exceeds maxsize m, then several patches are created. (often corresponding to peripheric cells)

(optional, default=FALSE) A logical indicating whether a neighborhood of 8 pixels (TRUE) is used for patch definition. By default, con8=4, corresponding to 4 pixel neighborhood.

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is.

A character string indicating the objects of the project that are described. It must be either:

• mode='patches'(default): The habitat patches are described with synthetic descriptors (code, number, mean capacity, median capacity, capacity harmonic mean, capacity Gini coefficient) and a histogram of capacity distribution.

• mode='linkset': The links of a link set are described with synthetic descriptors (codes, costs, number, mean cost distance, median cost distance, cost distance harmonic mean, cost distance Gini coefficient) and a histogram of cost distance distribution.

• mode='both': Both the patches and links of a linkset are described

A character string indicating the name of the link set whose properties are imported. The link set has been created with Graphab or using graphab_link function.

(optional) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

Logical (default = FALSE) indicating whether to plot a figure of the resulting spatial graph. The figure is plotted using function plot_graph_lg. The plotting can be long if the graph has many nodes and links.

Logical (default = TRUE) indicating whether the project features are returned as a list (TRUE) or only displayed in the R console (FALSE).

A character string indicating the project name. It is also the name of the directory in which proj_name.xml file is found. By default, 'proj_name' is searched into the current working directory

A character string indicating the name of the linkset used to create the graph links. The linkset must have been created previously (see the function graphab_link). It can be complete or planar. The graph is given the topology of the selected link set.

A character string indicating whether the nodes of the created graph are given all the attributes or metrics computed in Graphab or only those specific to a given graph previously created with graphab_graph It can be:

• nodes = "patches"(default): all the attributes and metrics of the habitat patches are included as node attributes in igraph object.

• nodes = "graph_name"(default): only the metrics of the habitat patches computed from the graph 'graph_name' created with graphab_graph are included as node attributes in igraph object, along with some basic patch attributes.

A character string ("euclid" or "cost") indicating whether to weight the links with Euclidean distance or cost-distance (default) values.

(optional) A character string indicating the path to the directory that contains the project directory ('proj_name'). By default, 'proj_name' is searched into the current working directory

Logical (default = FALSE) indicating whether to plot a figure of the resulting spatial graph. The figure is plotted using function plot_graph_lg. The plotting can be long if the graph has many nodes and links.

Logical (default = FALSE) indicating whether to create an object of class data.frame with the node centroid spatial coordinates. Such a data.frame has 3 columns: 'ID', 'x', 'y'.

An object of class data.frame with loci columns in format locus (defined in package gstudio) with as many rows as individuals and as many columns in format locus as there are loci and additional columns

A character string indicating the name of the column with populations' names in x

(optional) A character string indicating the name of the column with individuals' ID in x

A numeric vector

A numeric value indicating the dispersal probability at a distance equal to 'd_disp' under a negative exponential distribution.

A numeric value indicating the distance to which dispersal probability is equal to 'p' under a negative exponential distribution.

A character string indicating the value to return:

• If 'mode = 'A” (default), the returned value 'alpha' is such that exp(-alpha * d_disp) = p

• If 'mode = 'B”, the returned value 'alpha' is such that 10(-alpha * d_disp) = p

A character string indicating the Graphab project name. The project name is also the name of the project directory in which the file proj_name.xml is. It can be created with graphab_project

A character string indicating the name of the first link set involved in the comparison. The link set has to be present in the project and can be created with graphab_link.

A character string indicating the name of the second link set involved in the comparison. The link set has to be present in the project and can be created with graphab_link.

(default=200) An integer or numeric value indicating the width of the buffer created in each side of the links prior to spatial intersection. It is expressed in meters.

(optional, default=NULL) An integer or numeric value indicating the minimum length in meters of the links to be compared. Links whose length is larger than min_length will be ignored in the comparison.

(optional, default=NULL) A character string indicating the path to the directory that contains the project directory. It should be used when the project directory is not in the current working directory. Default is NULL. When 'proj_path = NULL', the project directory is equal to getwd().

An object of class loci to convert

An integer indicating the ploidy level (by default, 'ploidy = 2')

A character vector indicating the coding of the alleles to be treated as missing data (by default, 'na.alleles = c("NA")')

A parameter indicating the raster file on which cost distances are computed. It can be:

• A character string indicating the path to a raster file in format .tif or .asc.

• A RasterLayer object already loaded in R environment

All the raster cell values must be present in the column 'code' from cost argument.

A parameter indicating the points between which cost distances are computed. It can be either:

• A character string indicating the path to a .csv file. It must have three columns:

  • ID: The ID of the points.

  • x: A numeric or integer indicating the longitude of the points.

  • y: A numeric or integer indicating the latitude of the points.

• A data.frame with the spatial coordinates of the points. It must have three columns:

  • ID: The ID of the points.

  • x: A numeric or integer indicating the longitude of the points.

  • y: A numeric or integer indicating the latitude of the points.

• A SpatialPointsDataFrame with at least an attribute column named "ID" with the point IDs.

The point coordinates must be in the same spatial coordinate reference system as the raster file.

A data.frame indicating the cost values associated to each raster value. It must have two columns:

• 'code': raster cell values

• 'cost': corresponding cost values

A character string indicating the method used to compute the cost distances. It must be:

• 'gdistance': uses the functions from the package gdistance assuming that movement is possible in 8 directions from each cell, that a geo-correction is applied to correct for diagonal movement lengths and that raster cell values correspond to resistance (and not conductance).

• 'java': uses a .jar file which is downloaded on the user's machine if necessary and if java is installed. This option substantially reduces computation times and makes possible the parallelisation.

A character string indicating whether the returned object is a data.frame (return="df") or a pairwise matrix (return="mat").

An integer (4, 8, 16) indicating the directions in which movement can take place from a cell. Only used when method="gdistance". By default, direction=8.

An integer indicating how many computer cores are used to run the .jar file. By default, parallel.java=1.

(optional, default = NULL) Integer or numeric value indicating RAM gigabytes allocated to the java process when used. Increasing this value can speed up the computations. Too large values may not be compatible with your machine settings.

An object of class genind that contains the multilocus genotypes (format 'locus') of the individuals as well as their populations.

A character string indicating the method used to compute the multilocus genetic distance between populations

• If 'dist = 'basic” (default), then the multilocus genetic distance is computed using a formula of Euclidean genetic distance (Excoffier et al., 1992)

• If 'dist = 'weight”, then the multilocus genetic distance is computed as in Fortuna et al. (2009). It is a Euclidean genetic distance giving more weight to rare alleles

• If 'dist = 'PG”, then the multilocus genetic distance is computed as in popgraph::popgraph function, following several steps of PCA and SVD (Dyer et Nason, 2004).

• If 'dist = 'DPS”, then the genetic distance used is equal to 1 - the proportion of shared alleles (Bowcock, 1994)

• If 'dist = 'FST”, then the genetic distance used is the pairwise FST (Weir et Cockerham, 1984)

• If 'dist = 'FST_lin”, then the genetic distance used is the linearised pairwise FST (Weir et Cockerham, 1984)(FST_lin = FST/(1-FST))

• If 'dist = 'PCA”, then the genetic distance is computed following a PCA of the matrix of allelic frequencies by population. It is a Euclidean genetic distance between populations in the multidimensional space defined by all the independent principal components.

• If 'dist = 'GST”, then the genetic distance used is the G'ST (Hedrick, 2005). See graph4lg <= 1.6.0 only, because it used diveRsity

• If 'dist = 'D”, then the genetic distance used is Jost's D (Jost, 2008). See graph4lg <= 1.6.0 only, because it used diveRsity

(optional) Logical. Should negative and null FST, FST_lin, GST or D values be replaced by half the minimum positive value? This option allows to compute Gabriel graphs from these "distances". Default is null_val = FALSE. This option only works if 'dist = 'FST” or 'FST_lin' or 'GST' or 'D'

An object of class :

• data.frame with 3 columns: 2 columns with the point spatial coordinates and another column with point IDs

• SpatialPointsDataFrame

(if data is of class data.frame) A character string indicating the name of the column of data with the point IDs

(if data is of class data.frame) A character string indicating the name of the column of data with the point longitude

(if data is of class data.frame) A character string indicating the name of the column of data with the point latitude

A character string indicating the type of coordinate reference system:

• 'proj' (default): a projected coordinate reference system

• 'polar': a polar coordinate reference system, such as WGS84

A character string indicating the formula used to compute the Great Circle distance:

• 'vicenty'(default): Vincenty inverse formula for ellipsoids

• 'slc': Spherical Law of Cosines

• 'hvs': Harversine formula

An object of class genind

An object of class genind

A RasterLayer object corresponding to a categorical raster layer

An integer value or vector with the value(s) corresponding to the code values of the raster layer within which points will be sampled. are computed.

An integer value indicating the width of the edge (in meters) of the raster layer which is ignored during the sampling (default = 0). It prevents from sampling in the margins of the study area.

An integer value indicating which cells are considered adjacent when contiguous patches are delineated (it should be 8 (default, Queen's case) or 4 (Rook's case)). This parameter is ignored when by_patch = FALSE.

An integer value indicating the minimum surface of a patch considered for the sampling in number of raster cells. This parameter is used whatever the by_patch argument is. Default is 0.

A graph object of class igraph

(optional, default = NULL) If 'mode = 'spatial”, it is a data.frame with the spatial coordinates of the graph nodes. It must have three columns :

• ID: A character string indicating the name of the graph nodes. The names must be the same as the node names of the graph of class igraph (igraph::V(graph)$name)

• x: A numeric or integer indicating the longitude of the graph nodes.

• y: A numeric or integer indicating the latitude of the graph nodes.

This argument is not used when 'mode = 'aspatial” and mandatory when 'mode = 'spatial”.

A character string indicating whether the graph is spatial ('mode = 'spatial”) or not ('mode = 'aspatial” (default))

(optional, default = NULL) A character string indicating whether the links of the graph are weighted by distances or by similarity indices. It is only used when 'mode = 'aspatial” to compute the node positions with Fruchterman and Reingold algorithm. It can be equal to:

• 'distance': Link weights correspond to distances. Nodes that are close to each other will be close on the figure.

• 'similarity': Link weights correspond to similarity indices. Nodes that are similar to each other will be close on the figure.

(optional, default = NULL) A character string indicating how the width of the link is set on the figure. Their width can be:

• inversely proportional to link weights ("inv_w", convenient with distances, default)

• proportional to link weights ("w")

(optional, default = NULL) A character string indicating the graph node attribute used to set the node size on the figure. It must be the name of a numeric or integer node attribute from the graph.

(optional, default = NULL) A character string indicating the graph node modules used to set the node color on the figure. It must be the name of a node attribute from the graph with discrete values.

(optional, default = NULL) A character string indicating the color used to plot the nodes (default: "#F2B950"). It must be a hexadecimal color code or a color used by default in R. It cannot be used if 'module' is specified.

A graph object of class igraph whose links are weighted

A character string indicating the color used to fill the bars (default: "#396D35"). It must be a hexadecimal color code or a color used by default in R.

(default values: NULL) A numeric or an integer specifying the width of the classes displayed on the histogram. When it is not specified, the width is equal to the difference between the minimum and maximum values divided by 80.

An object of class genind from package adegenet.

(optional) A character vector indicating population names. It is of the same length as the number of populations. Without this argument, populations are given the names they have initially in the 'genind' object (which is sometimes only a number). The order of the population names must match with their order in the 'genind' object. The function does not reorder them. Users must be careful.

(optional) A character vector indicating the population-level indices to compute. These indices can be:

• Mean allelic richness by locus by population (indices = c("A", ...))

• Mean expected heterozygosity by locus by population (indices = c("He",...))

• Mean observed heterozygosity by locus by population (indices = c("Ho",...))

• Number of individuals by population (indices = c("Nb_ind", ...))

• Total allelic richness by population (indices = c("A_tot",...))

By default, indices = c("Nb_ind", "A", "He", "Ho").

An object of class genind from package adegenet.

(optional default = NULL) The maximum standardized sample size used by ADZE software (MAX_G) in ADZE manual. It is equal to twice the minimum number of individuals considered for the rarefaction analysis. By default, it is equal to twice the number of individuals in the smallest population. Ohterwise, it must be either a numeric or integer value.

(optional) A character vector indicating population names. It is of the same length as the number of populations. Without this argument, populations are given the names they have initially in the 'genind' object (which is sometimes only a number). The order of the population names must match with their order in the 'genind' object. The function does not reorder them. Users must be careful.

A character string indicating whether you use a Linux ('linux') or Windows ('win') operating system.

A pairwise matrix which can be:

• An object of class matrix. It must have the same row names and column names. If values represent distances, diagonal elements should be equal to 0.

• An object of class dist. In that, its column numbers are used to create IDs in the resulting data.frame.

An object of class matrix

A character vector with the rows and columns names of the matrix in the order in which they will be ordered by the function. All its elements must be rows and columns names of the matrix mat.

A RasterLayer object corresponding to a categorical raster layer

An integer value or vector with the value(s) corresponding to the code values of the raster layer within which points will be sampled.

An integer value indicating the number of points to be sampled

An integer value indicating the minimum distance separating the sampled points (default = 0).

An integer value indicating the width of the edge of the raster layer which is ignored during the sampling (default = 0). It prevents from sampling in the margins of the study area.

A logical value indicating whether contiguous patches with cells having the same code value are delineated prior to sampling (default = TRUE). It prevents from sampling several points in the same contiguous patch.

An integer value indicating which cells are considered adjacent when contiguous patches are delineated (it should be 8 (default, Queen's case) or 4 (Rook's case)). This parameter is ignored when by_patch = FALSE.

An integer value indicating the minimum surface of a patch considered for the sampling in number of raster cells. This parameter is used whatever the by_patch argument is. Default is 0.

A logical value indicating whether sampling in large patches is more likely (default = TRUE). If by_patch = FALSE, this parameter is ignored. When prop_area = TRUE, the probability to sample a given patch is proportional to its area.

An integer value indicating how many sampling steps are performed to identify a point set satisfying all the conditions before returning an error.

A character string indicating the type of returned output:

• 'data.frame': A data.frame with three/four columns:

  • ID: The point or patch centroid ID

  • x: The point or patch centroid longitude

  • y: The point or patch centroid latitude

  • area: The area of the sampled patch (only if by_patch = TRUE)

• 'pts_layer': A SpatialPointsDataFrame layer corresponding to the sampled point (points or patch centroids)

• 'poly_layer': A SpatialPolygonsDataFrame layer corresponding to the sampled patch polygons

A logical value indicating whether the result should be described or not (default = FALSE). If desc = TRUE, then the Gini coefficient of the distances between points and of the patch areas (if by_patch = TRUE) is computed with the gini_coeff. An histogram of the link weights is also described.

Numeric or integer vector

A symmetric matrix or dist object with pairwise genetic distances between populations or sample sites.

A symmetric matrix or dist object with pairwise landscape distances between populations or sample sites. These distances can be Euclidean distances, cost-distances or resistance distances, among others.

A character string indicating the smoothing method used to fit a line on the scatterplot. Possible values are the same as with function 'geom_smooth()' from ggplot2 : 'lm', 'glm', 'gam', 'loess' (default).

(optional) A numeric or integer value used to remove values from the data before to plot. All genetic distances values above thr_gd are removed from the data.

(optional) A numeric or integer value used to remove values from the data before to plot. All landscape distances values above thr_ld are removed from the data.

Logical (optional, default = TRUE) indicating whether the confidence interval around the smooth line is displayed.

(optional) A character string indicating the color used to plot the smoothing line (default: "blue"). It must be a hexadecimal color code or a color used by default in R.

(optional) Character string indicating the color used to plot the points (default: "#999999"). It must be a hexadecimal color code or a color used by default in R.

A symmetric (complete) matrix or dist object with pairwise (genetic or landscape) distances between populations or sample sites. These values will be the point coordinates on the y axis. mat_y is the matrix used to weight the links of the graph x, whose nodes correspond to row and column names of mat_y.

A symmetric (complete) matrix or dist object with pairwise (genetic or landscape) distances between populations or sample sites. These values will be the point coordinates on the x axis. mat_x and mat_y must have the same row and column names, ordered in the same way.

A graph object of class igraph. Its nodes must have the same names as the row and column of mat_y and mat_x matrices. x must have weighted links. Link weights have to be values from mat_y matrix. graph must be an undirected graph.

(optional) A numeric or integer value used to remove values from the data before to plot. All values from mat_y above thr_y are removed from the data.

(optional) A numeric or integer value used to remove values from the data before to plot. All values from mat_x above thr_x are removed from the data.

(optional) A character string indicating the color used to plot the points associated to all populations or sample sites pairs (default: "#999999"). It must be a hexadecimal color code or a color used by default in R.

(optional) A character string indicating the color used to plot the points associated to populations or sample sites pairs connected on the graph (default: "black"). It must be a hexadecimal color code or a color used by default in R.

A character string indicating the path to the STRUCTURE file in format .txt, or alternatively the name of the file in the working directory. The STRUCTURE file must only have :

• A first column with the IDs of the individuals (can be a simple number)

• A second column with the IDs of the populations (can be a simple number)

• Some loci columns : as many columns as loci in the data

The row for loci names is optional but recommended. Each individual is displayed on 2 rows.

(optional) A character vector indicating the population names in the same order as in the STRUCTURE file. It is of the same length as the number of populations. Without this argument, populations are numbered from 1 to the total number of individuals.

A character vector with the names of the loci if not specified in the file first row. This argument is mandatory if the STRUCTURE file does not include the names of the loci in the first row. In other cases, the names of the loci is extracted from the file first row

(optional) A character vector indicating the individual names in the same order as in the STRUCTURE file. It is of the same length as the number of individuals. Without this argument, individuals are numbered from 1 to the total number of individuals.