NEWS.md

In graph4lg: Build Graphs for Landscape Genetics Analysis

graph4lg 1.8.0

-- Major changes - Removal of diveRsity dependency - Removal of mat_pw_gst and mat_pw_d_jost - Update of mat_gen_dist to depend on hierfstat package - Creation of graphab_interpol function -- Minor changes - Bug fixed in link_compar

graph4lg 1.6.0

-- Minor changes - Update of Graphab software download URL - Copy of graphab-1.8.jar in the sub-directory plugins within graph4lg_jar for using the development versions of Graphab functions. - Add comments regarding development versions of Graphab functions and potential error when returning metric values already computed previously.

graph4lg 1.5.0

-- Minor changes - Update of pop_rare_gen_index() for allowing the shell/system command to run on both Linux or Windows OS

graph4lg 1.4.0

-- Major changes: - Creation of a new genetic data conversion function (genind_to_structure) (internal function for the moment) - Creation of a function for rarefied genetic diversity indices called pop_rare_gen_index() (internal function for the moment) - Creation of a new function for computing corridors in a Graphab project - Addition of a new contributor to the package - Modification of graphab_project for allowing users to create multi-habitat graph projects - Modification of graphab_metric for allowing users to compute multi-habitat graph metrics - Modification of graphab_link for allowing users to include an external cost surface

-- Minor changes: - Update of Graphab software to 2.8 - Creation of a function checking for multihabitat graph projects - Modification of functions using ggplot2 to avoid aes_string() - Update of spatstat versions and package names - Creation of a git repository on Gitlab

-- Bug fixes:

• Modifications of the way the current directory are managed in graphab-based functions

graph4lg 1.2.0

-- Major changes: - Creation of 9 new functions linked to Graphab software and internal - Change of the author email address - Addition of a CITATION file following the publication of a software paper

-- Minor changes: - Update of Graphab software to 2.6 - Update of costdist software to 0.4 because of a bug with no data values - Use of .xml project files for checking arguments - Update of spatstat versions and package names

-- Bug fixes: - Reset working directory before stopping when it is changed - Bug due to unique population in file input of genind_to_genepop - nb argument in graphab_modul was not active

graph4lg 1.0.1

-- Minor changes: - RdMacros packages in Imports instead of Suggests - RAM allocated to computation when using mat_cost_dist is adjustable. And java interface launching is blocked when running this function.

-- Bug fixes: - Order of commands changed in graphab_metric - Bug due to st_write() fixed

graph4lg 1.0.0

-- Major changes: - Creation of functions to use Graphab java software tool (downloaded by users) from R (get_graphab, graphab_project, graphab_link, graphab_graph, graphab_metric, graphab_modul, graphab_pointset, get_graphab_metric, get_graphab_linkset) - Creation of mat_cost_dist function integrating costDistance from gdistance and another java code (downloaded by users) - Inclusion of geographical distance calculations from polar coordinates in mat_geo_dist function - Compatibility with SNPs markers and 2 allele-digits coded microsatellites - Creation of compute_node_metric and compute_graph_modul integrating options previously included in graph_node_compar and graph_modul_compar, and modification of these two latter functions to integrate the two former - plot_graph_lg now allows users to change node sizes according to node attribute variables - Change from proj4string CRS to EPSG when given by users - Change from rgdal functions to sf functions when the former returned too many warning messages - Creation of four vignettes instead of one

• Bug fixes: bug fixes in graph_plan, genepop_to_genind and gstud_to_genind

graph4lg 0.5.0

• Minor change: change in package dependencies to stick with CRAN requirements

graph4lg 0.4.0

• Addition of new parameters to gen_graph_topo to allow the construction of k-nearest neighbor graphs
• Removal of a dataset and addition of a new simulated small dataset
• Minor change: modification of function examples to reduce their duration, vignette update, minor changes in functions 'plot_w_hist' and 'scatter_dist_g'
• Bug fixes: modification of pw_mat_to_df function

graph4lg 0.3.0

• Minor change: weight option in graph_plan
• Bug fixes: vignette modification to solve a Debian error

graph4lg 0.2.0

• Addition of several functions (pw_mat_to_df, df_to_pw_mat, graph_to_df, graph_plan, set_AB_prob)
• Changes to replace 'class()' instances by 'inherits()' instances in order to make the package compatible with R 4.0.0.
• Minor changes: spelling errors, code lines length

graph4lg 0.1.1

• Minor changes in the DESCRIPTION file and modifications of the commands writing files in the examples, the vignette and in two functions to conform with CRAN policies.

graph4lg 0.1.0

• Initial release

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.