**Exact Spike Train Inference via L0 Optimization** (**LZeroSpikeInference**)

An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.

**Inference of Fuzzy Cognitive Maps (FCMs)** (**fcm**)

Provides a selection of 6 different inference rules and 4 threshold functions in order to obtain the inference of the FCM (Fuzzy Cognitive Map). Moreover, the ‘fcm’ package returns a data frame of the concepts’ values of each state after the inference procedure. Fuzzy cognitive maps were introduced by Kosko (1986) <doi:10.1002/int.4550010405> providing ideal causal cognition tools for modeling and simulating dynamic systems.

**Efficient Bayesian Linear Regression with Time-Varying Coefficients** (**walker**)

Fully Bayesian linear regression where the regression coefficients are allowed to vary over ‘time’, either as independent random walks. All computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling.

**Convert Files Between Markdown or Rmarkdown Files and Mindmaps** (**mindr**)

Convert Markdown (‘.md’) or Rmarkdown (‘.Rmd’) files into FreeMind mindmap (‘.mm’) files, and vice versa. FreeMind mindmap (‘.mm’) files can be opened by or imported to common mindmap software such as ‘FreeMind’ (<http://…/Main_Page> ) and ‘XMind’ (<http://www.xmind.net> ).

**Dendrograms for Evolutionary Analysis** (**phylogram**)

Contains functions for importing and exporting ‘dendrogram’ objects in parenthetic text format, and several functions for command-line tree manipulation. With an emphasis on speed and computational efficiency, the package also includes a suite of tools for rapidly computing distance matrices and building large trees using fast alignment-free ‘k-mer’ counting and divisive clustering techniques.

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