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Claddis  

Measuring Morphological Diversity and Evolutionary Tempo
View on CRAN: Click here


Download and install Claddis package within the R console
Install from CRAN:
install.packages("Claddis")

Install from Github:
library("remotes")
install_github("cran/Claddis")

Install by package version:
library("remotes")
install_version("Claddis", "0.7.0")



Attach the package and use:
library("Claddis")
Maintained by
Graeme T. Lloyd
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-04-28
Latest Update: 2020-09-26
Description:
Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) ) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) ). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) , Brusatte et al. (2014) , Close et al. (2015) , and Lloyd (2016) , and MatrixDistances(), which implements multiple discrete character distance metrics from Gower (1971) , Wills (1998) , Lloyd (2016) , and Hopkins and St John (2018) . This also includes the GED correction from Lehmann et al. (2019) . Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) , plot_morphospace() implements Wills et al. (1994) , plot_changes_on_tree() implements Wang and Lloyd (2016) , and plot_morphospace_stack() implements Foote (1993) . Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) , map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) , and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) .
How to cite:
Graeme T. Lloyd (2015). Claddis: Measuring Morphological Diversity and Evolutionary Tempo. R package version 0.7.0, https://cran.r-project.org/web/packages/Claddis. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1 (2015-04-28 06:57), 0.3.0 (2019-02-12 14:19), 0.3.4 (2019-12-05 07:50), 0.6.1 (2020-08-27 01:00), 0.6.3 (2020-09-26 06:30)
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Other R packages that Claddis depends, imports, suggests or enhances
Complete documentation for Claddis
Functions, R codes and Examples using the Claddis R package
Some associated functions: Claddis-package . align_matrix_block . assign_taxa_to_bins . bin_changes . bin_character_completeness . bin_edge_lengths . build_cladistic_matrix . calculate_morphological_distances . compactify_matrix . date_nodes . day_2016 . estimate_ancestral_states . find_descendant_edges . find_linked_edges . find_minimum_spanning_edges . find_mrca . fix_root_time . gauthier_1986 . map_dollo_changes . map_stochastic_changes . match_tree_edges . michaux_1989 . ordinate_cladistic_matrix . partition_time_bins . plot_changes_on_tree . plot_chronophylomorphospace . plot_morphospace . plot_morphospace_stack . plot_multi_morphospace . plot_rates_character . plot_rates_time . plot_rates_tree . print.cladisticMatrix . prune_cladistic_matrix . read_nexus_matrix . safe_taxonomic_reduction . safe_taxonomic_reinsertion . test_rates . trim_marginal_whitespace . trim_matrix . write_nexus_matrix . write_tnt_matrix . 
Some associated R codes: Claddis-package.R . align_matrix_block.R . assign_taxa_to_bins.R . bin_changes.R . bin_character_completeness.R . bin_edge_lengths.R . build_cladistic_matrix.R . calculate_morphological_distances.R . compactify_matrix.R . date_nodes.R . estimate_ancestral_states.R . find_descendant_edges.R . find_linked_edges.R . find_minimum_spanning_edges.R . find_mrca.R . fix_root_time.R . map_dollo_changes.R . map_stochastic_changes.R . match_tree_edges.R . ordinate_cladistic_matrix.R . partition_time_bins.R . plot_changes_on_tree.R . plot_chronophylomorphospace.R . plot_morphospace.R . plot_morphospace_stack.R . plot_multi_morphospace.R . plot_rates_character.R . plot_rates_time.R . plot_rates_tree.R . prune_cladistic_matrix.R . read_nexus_matrix.R . safe_taxonomic_reduction.R . safe_taxonomic_reinsertion.R . test_rates.R . trim_matrix.R . write_nexus_matrix.R . write_tnt_matrix.R .  Full Claddis package functions and examples
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