Skip to contents

Changelog

Source: NEWS.md

comdynamite 0.5.2

Corrections that change results:

  • node_test(): draws are now ranked on F statistics. The statistic of each predictor, taken from the original code, depended on the scale of the response, and neither statistic took into account that draws of species occupy different numbers of sites. p_partial, p_partial_joint, p_taxa, p_max and p_joint differ from those of 0.5.1, and so do the same p-values of events. statistic, p_site and p_partial_site of predictors do not.
  • node_test(): a node with a clade without individuals is no longer tested, as it was a repeat of another node.
  • node_test(): with cores above 1, each call now uses its own random streams.
  • pcc_test() and phylo_beta_test(): species without individuals leave the analysis. In pcc_test() they could turn numerical noise into an axis.
  • trait_partition(): species without individuals leave the analysis, which could stop it.

Checks of data:

  • All analysis functions match sites by name when the data have row names, and stop if the names differ. Before, misordered predictors gave a wrong result without warning.
  • Missing values, predictors without variance and columns that are not numeric now stop with a message that names them. phylo_vector() gave p = 1 in these cases.
  • node_test() checks biogeography before the permutations and explains a tree in nodes.
  • Results keep the numbers of permutations and the null model, and print() shows them with the smallest possible p-value. Nodes that were not tested are reported, and phylo_vector() says when no vector was retained.

comdynamite 0.5.1

  • node_contrasts(): branch_lengths = TRUE gives the coding with branch lengths of the supplement of Leibold et al. (2010).
  • plot_node_test(): with type = "fan", the names of the variables follow the radii and no longer overlap the names of the species.
  • plot_node_heatmap(): semipartial correlations of node_test() as a table of nodes by variables.
  • simulate_logistic() now uses the values of the code of Ives & Helmus (2011): the default of intercept_sd is 0.5, and slopes have a standard deviation of slope_sd among species.
  • logistic_gradients(): in scenario 3, the error is added to y with unit variance and only in y_test, and in scenarios 5 and 6 x is in random order along the transect.
  • New article on analysing clades and traits. The article on validation now compares Table 5 of Peres-Neto et al. (2012).

comdynamite 0.5.0

  • simulate_static(): static metacommunities from the Gaussian response of Dray & Legendre (2008), also used by Peres-Neto et al. (2012), as a baseline without population dynamics. Data can be Poisson counts, binomial presences or the expected values. With several gradients, for example environment and space, the expected abundance is the product of the responses.
  • simulate_logistic() and logistic_gradients(): presences and absences from logistic responses to two gradients, with the seven scenarios of Appendix C of Peres-Neto et al. (2012).
  • phylo_vector() and trait_partition(): phylogenetic gradient analysis of Peres-Neto et al. (2012), tested against the original code in Octave. The test between a trait and the environment stays in ade4::fourthcorner().
  • Functions that take a community and a phylogeny, traits or contrasts now match species by name and, as picante::match.phylo.comm(), drop with a warning the species found in only one of them. Repeated names are an error.
  • trait_partition(): semipartial correlations of each predictor, with their tests, following Appendix A of Peres-Neto et al. (2012).
  • plot_node_test(): results of node_test() on the tree, as in Figure 3 of Leibold et al. (2010), as a phylogram or a fan. plot_trait_partition(): fractions of trait_partition().
  • daphniids: data of Leibold et al. (2010), rebuilt from the public survey.
  • node_contrasts() now keeps nodes that join two tips, as the article does. cherries = FALSE gives the original code.
  • node_test(): semipartial replaces partial_r2, following the article, and there are p_adjusted (false discovery rate), biogeographic events, the joint permutation of the article (p_joint), 9999 permutations by default and cores.
  • pcc_test() and phylo_eigenvectors(): phylogenetic community composition of Peres-Neto & Kembel (2015), with site and species permutations.
  • phylo_beta_test() and phylo_beta(): phylogenetic beta-diversity framework of the same article, a distance-based redundancy analysis of the mean phylogenetic distance between communities.
  • node_test() and node_contrasts(): regression of clades on the environment, node by node, from Leibold et al. (2010), with site and species permutations.
  • simulate_metacommunity() and mc_dynamics(): stochastic extirpation of populations (extirpation), used by Thompson et al. (2020) in their competition-colonisation scenario.
  • New article on the validation of the model, with the differences between the article of Thompson et al. (2020) and the code archived with it.
  • New article with animations of metacommunity dynamics.

comdynamite 0.1.0

  • First version: the model of Thompson et al. (2020) with phylogenetic traits and competition, spatially implicit and grid landscapes, torus permutations and time-varying environments. Code from the pcps-sim project.

  • Rule-based assembly (assemble_community()): limiting similarity (GAUSE algorithm of Colwell & Winkler 1984), habitat filtering and neutral assembly, as in Kraft et al. (2007).

  • traits_ou(): traits under an Ornstein-Uhlenbeck process with one or several optima (multi-peak OU; Brownian motion when alpha = 0), with paint_regimes() to assign regimes to clades.

  • New vignettes: vignette("phylogenetic-structure"), on how dispersal, niche conservatism and competition shape phylogenetic community structure, and vignette("evaluating-methods"), on type I error and power with simulations.

  • vignette("evaluating-methods") shows tree shape as a factor of the design, with trees from treeshapesim (in Suggests).