R-universe search: extinction

richfitz

diversitree:Comparative 'Phylogenetic' Analyses of Diversification

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

Maintained by Richard G. FitzJohn. Last updated 5 months ago.

fftw3 gsl openblas cpp

25.1 match 33 stars 8.51 score 524 scripts 4 dependents

thej022214

hisse:Hidden State Speciation and Extinction

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.

Maintained by Jeremy Beaulieu. Last updated 1 months ago.

20.9 match 6 stars 8.45 score 152 scripts

biometry

bipartite:Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.

Maintained by Carsten F. Dormann. Last updated 5 days ago.

cpp

12.9 match 37 stars 10.93 score 592 scripts 15 dependents

derek-corcoran-barrios

NetworkExtinction:Extinction Simulation in Ecological Networks

Simulates the extinction of species in ecological networks and it analyzes its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.

Maintained by Derek Corcoran. Last updated 4 months ago.

21.2 match 5 stars 5.15 score 19 scripts

hoehna

TESS:Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.

Maintained by Sebastian Hoehna. Last updated 3 years ago.

cpp

16.2 match 2 stars 5.93 score 95 scripts 1 dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 26 days ago.

6.8 match 218 stars 13.85 score 4.8k scripts 76 dependents

divdyn

divDyn:Diversity Dynamics using Fossil Sampling Data

Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.

Maintained by Adam T. Kocsis. Last updated 4 months ago.

diversity extinction fossil-data occurrences origination paleobiology cpp

13.6 match 11 stars 6.48 score 137 scripts

r-forge

Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"

Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.

Maintained by Berwin A Turlach. Last updated 1 years ago.

11.5 match 6.38 score 522 scripts

r-forge

Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"

Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.

Maintained by Berwin A Turlach. Last updated 1 years ago.

11.5 match 5.70 score 191 scripts

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 1 months ago.

openblas cpp

3.4 match 64 stars 17.18 score 13k scripts 601 dependents

rsetienne

DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.

Maintained by Rampal S. Etienne. Last updated 1 months ago.

fortran cpp

6.8 match 9 stars 8.59 score 55 scripts 1 dependents

lukejharmon

geiger:Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.

Maintained by Luke Harmon. Last updated 2 years ago.

openblas cpp

7.3 match 1 stars 7.84 score 2.3k scripts 28 dependents

rsetienne

secsse:Several Examined and Concealed States-Dependent Speciation and Extinction

Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) <doi:10.1093/sysbio/syy057>.

Maintained by Rampal S. Etienne. Last updated 11 months ago.

cpp

9.1 match 1 stars 5.83 score 34 scripts

vjontiveros

island:Stochastic Island Biogeography Theory Made Easy

Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.

Maintained by Vicente Jimenez. Last updated 1 years ago.

gsl

16.4 match 3.10 score 42 scripts

squidlobster

castor:Efficient Phylogenetics on Large Trees

Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.

Maintained by Stilianos Louca. Last updated 4 months ago.

cpp

8.6 match 2 stars 5.75 score 450 scripts 9 dependents

dwbapst

paleotree:Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Maintained by David W. Bapst. Last updated 8 months ago.

6.0 match 21 stars 7.53 score 216 scripts 2 dependents

ropensci

rredlist:'IUCN' Red List Client

'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

Maintained by William Gearty. Last updated 1 months ago.

iucn biodiversity api web-services traits habitat species conservation api-wrapper iucn-red-list taxize

3.7 match 53 stars 11.49 score 195 scripts 24 dependents

robinhankin

untb:Ecological Drift under the UNTB

Hubbell's Unified Neutral Theory of Biodiversity.

Maintained by Robin K. S. Hankin. Last updated 3 months ago.

6.3 match 4 stars 6.53 score 80 scripts

rsetienne

DDD:Diversity-Dependent Diversification

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <DOI:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.

Maintained by Rampal S. Etienne. Last updated 4 months ago.

cpp

5.6 match 4 stars 7.10 score 80 scripts 7 dependents

vascobranco

red:IUCN Redlisting Tools

Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <https://www.iucn.org/> for more information) red list criteria.

Maintained by Vasco V. Branco. Last updated 3 months ago.

biodiversity extinction-risk

8.0 match 1 stars 4.54 score 29 scripts 1 dependents

tguillerme

dispRity:Measuring Disparity

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

Maintained by Thomas Guillerme. Last updated 16 hours ago.

disparity ecology multidimensionality palaeobiology

4.0 match 26 stars 8.69 score 220 scripts 1 dependents

cran

popbio:Construction and Analysis of Matrix Population Models

Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

Maintained by Chris Stubben. Last updated 12 months ago.

5.4 match 6.24 score 1.0k scripts 5 dependents

joe-wayman

avotrex:A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder

Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.

Maintained by Joseph Wayman. Last updated 7 months ago.

6.8 match 4.74 score 8 scripts

tguillerme

treats:Trees and Traits Simulations

A modular package for simulating phylogenetic trees and species traits jointly. Trees can be simulated using modular birth-death parameters (e.g. changing starting parameters or algorithm rules). Traits can be simulated in any way designed by the user. The growth of the tree and the traits can influence each other through modifiers objects providing rules for affecting each other. Finally, events can be created to modify both the tree and the traits under specific conditions ( Guillerme, 2024 <DOI:10.1111/2041-210X.14306>).

Maintained by Thomas Guillerme. Last updated 2 months ago.

6.4 match 3 stars 4.63 score 19 scripts

hmorlon

RPANDA:Phylogenetic ANalyses of DiversificAtion

Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>, Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>, Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592>, Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>, Perez-Lamarque & Morlon (2022) <DOI:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <DOI:10.1101/2021.08.30.458192>, Mazet et al. (2023) <DOI:10.1111/2041-210X.14195>, Drury et al. (2024) <DOI:10.1016/j.cub.2023.12.055>.

Maintained by Hélène Morlon. Last updated 2 months ago.

3.3 match 24 stars 8.50 score 255 scripts

thijsjanzen

treestats:Phylogenetic Tree Statistics

Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all statistics, all balance associated statistics, or all branching time related statistics. Furthermore, the 'treestats' package supports summary statistic calculations on Ltables, provides speed-improved coding of branching times, Ltable conversion and includes algorithms to create intermediately balanced trees. Full description can be found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.

Maintained by Thijs Janzen. Last updated 6 months ago.

cpp

5.2 match 16 stars 5.43 score 16 scripts 1 dependents

ax3man

phylopath:Perform Phylogenetic Path Analysis

A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) <doi:10.1111/j.1558-5646.2012.01790.x>.

Maintained by Wouter van der Bijl. Last updated 6 months ago.

analysis comparative-methods path phylogenetics

3.4 match 13 stars 8.10 score 81 scripts 1 dependents

mjanuario

evolved:Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.

Maintained by Matheus Januario. Last updated 1 months ago.

4.1 match 3 stars 6.73 score 23 scripts

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Maintained by Martin R. Smith. Last updated 1 months ago.

evolutionary-biology phylogenetic-trees phylogenetics cpp

2.8 match 21 stars 9.92 score 124 scripts 10 dependents

bjoelle

FossilSim:Simulation and Plots for Fossil and Taxonomy Data

Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.

Maintained by Joelle Barido-Sottani. Last updated 5 months ago.

4.9 match 1 stars 5.24 score 65 scripts 1 dependents

thijsjanzen

nLTT:Calculate the NLTT Statistic

Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.

Maintained by Thijs Janzen. Last updated 2 years ago.

nltt nltt-statistic phylogenetic-trees phylogenetics

3.3 match 6 stars 6.93 score 59 scripts

epiverse-trace

superspreading:Understand Individual-Level Variation in Infectious Disease Transmission

Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions ('Kremer et al.' (2021) <doi:10.1038/s41598-021-93578-x>), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct ('Kucharski et al.' (2020) <doi:10.1016/S1473-3099(20)30144-4>), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission ('Lloyd-Smith et al.' (2005) <doi:10.1038/nature04153>).

Maintained by Joshua W. Lambert. Last updated 2 months ago.

disease-transmission epidemiology epiverse

3.3 match 4 stars 6.98 score 16 scripts

middleton-lab

abd:The Analysis of Biological Data

The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).

Maintained by Kevin M. Middleton. Last updated 11 months ago.

4.0 match 6 stars 5.53 score 182 scripts 1 dependents

atsa-es

MARSS:Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

Maintained by Elizabeth Eli Holmes. Last updated 1 years ago.

multivariate-timeseries state-space-models statistics time-series

1.9 match 52 stars 10.34 score 596 scripts 3 dependents

sbgraves237

Ecfun:Functions for 'Ecdat'

Functions and vignettes to update data sets in 'Ecdat' and to create, manipulate, plot, and analyze those and similar data sets.

Maintained by Spencer Graves. Last updated 3 months ago.

2.3 match 7.94 score 85 scripts 4 dependents

statmanrobin

Stat2Data:Datasets for Stat2

Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.

Maintained by Robin Lock. Last updated 6 years ago.

3.4 match 5 stars 4.94 score 544 scripts

cran

cdfquantreg:Quantile Regression for Random Variables on the Unit Interval

Employs a two-parameter family of distributions for modelling random variables on the (0, 1) interval by applying the cumulative distribution function (cdf) of one parent distribution to the quantile function of another.

Maintained by Yiyun Shou. Last updated 2 years ago.

4.9 match 2 stars 3.43 score 34 scripts

jsocolar

flocker:Flexible Occupancy Estimation with Stan

Fit occupancy models in 'Stan' via 'brms'. The full variety of 'brms' formula-based effects structures are available to use in multiple classes of occupancy model, including single-season models, models with data augmentation for never-observed species, dynamic (multiseason) models with explicit colonization and extinction processes, and dynamic models with autologistic occupancy dynamics. Formulas can be specified for all relevant distributional terms, including detection and one or more of occupancy, colonization, extinction, and autologistic depending on the model type. Several important forms of model post-processing are provided. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Socolar & Mills (2023) <doi:10.1101/2023.10.26.564080>.

Maintained by Jacob B. Socolar. Last updated 2 months ago.

2.3 match 30 stars 6.78 score 20 scripts

thijsjanzen

nodeSub:Simulate DNA Alignments Using Node Substitutions

Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

Maintained by Thijs Janzen. Last updated 1 years ago.

cpp openjdk

4.9 match 1 stars 2.70 score 3 scripts

rsetienne

DAMOCLES:Dynamic Assembly Model of Colonization, Local Extinction and Speciation

Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.

Maintained by Rampal S. Etienne. Last updated 3 months ago.

cpp

2.9 match 1 stars 4.34 score 11 scripts

brpetrucci

paleobuddy:Simulating Diversification Dynamics

Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.

Maintained by Bruno do Rosario Petrucci. Last updated 1 months ago.

evolution macroevolution paleobiology paleontology phylogenetics

2.4 match 6 stars 4.95 score 4 scripts

mikeblazanin

gcplyr:Wrangle and Analyze Growth Curve Data

Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.

Maintained by Mike Blazanin. Last updated 2 months ago.

dplyr ggplot2 tidyverse

1.5 match 30 stars 7.90 score 75 scripts

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

5.1 match 2.28 score 38 scripts

revbayes

RevGadgets:Visualization and Post-Processing of 'RevBayes' Analyses

Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.

Maintained by Carrie Tribble. Last updated 1 years ago.

1.9 match 13 stars 6.09 score 208 scripts

ropensci

phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Maintained by Shixiang Wang. Last updated 8 months ago.

blastn genbank peer-reviewed phylogenetics sequence-alignment

1.9 match 23 stars 5.86 score 156 scripts

ropensci

paleobioDB:Download and Process Data from the Paleobiology Database

Includes functions to wrap most endpoints of the 'PaleobioDB' API and functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>.

Maintained by Adrián Castro Insua. Last updated 1 years ago.

1.8 match 42 stars 6.19 score 74 scripts

ohagen

TreeSimGM:Simulating Phylogenetic Trees under General Bellman Harris and Lineage Shift Model

Provides a flexible simulation tool for phylogenetic trees under a general model for speciation and extinction. Trees with a user-specified number of extant tips, or a user-specified stem age are simulated. It is possible to assume any probability distribution for the waiting time until speciation and extinction. Furthermore, the waiting times to speciation / extinction may be scaled in different parts of the tree, meaning we can simulate trees with clade-dependent diversification processes. At a speciation event, one species splits into two. We allow for two different modes at these splits: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. The symmetric mode can be seen as an vicariant or allopatric process where divided populations suffer equal evolutionary forces while the asymmetric mode could be seen as a peripatric speciation where a mother lineage continues to exist. Reference: O. Hagen and T. Stadler (2017). TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R. Methods in Ecology and Evolution. <doi:10.1111/2041-210X.12917>.

Maintained by Oskar Hagen. Last updated 5 years ago.

4.0 match 2.73 score 18 scripts

macroecology

letsR:Data Handling and Analysis in Macroecology

Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.

Maintained by Bruno Vilela. Last updated 2 months ago.

1.2 match 29 stars 8.87 score 104 scripts

tanja819

TreeSim:Simulating Phylogenetic Trees

Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.

Maintained by Tanja Stadler. Last updated 6 years ago.

2.4 match 4.19 score 172 scripts 3 dependents

jjustison

SiPhyNetwork:A Phylogenetic Simulator for Reticulate Evolution

A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.

Maintained by Joshua Justison. Last updated 6 months ago.

cpp

1.8 match 11 stars 5.25 score 16 scripts

afmagee

CRABS:Congruent Rate Analyses in Birth-Death Scenarios

Features tools for exploring congruent phylogenetic birth-death models. It can construct the pulled speciation- and net-diversification rates from a reference model. Given alternative speciation- or extinction rates, it can construct new models that are congruent with the reference model. Functionality is included to sample new rate functions, and to visualize the distribution of one congruence class. See also Louca & Pennell (2020) <doi:10.1038/s41586-020-2176-1>.

Maintained by Bjørn Tore Kopperud. Last updated 1 years ago.

2.2 match 7 stars 4.02 score 5 scripts

seananderson

metafolio:Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization

A tool to simulate salmon metapopulations and apply financial portfolio optimization concepts. The package accompanies the paper Anderson et al. (2015) <doi:10.1101/2022.03.24.485545>.

Maintained by Sean C. Anderson. Last updated 1 years ago.

openblas cpp

1.7 match 2 stars 4.89 score 77 scripts

cran

DDM:Death Registration Coverage Estimation

A set of three two-census methods to the estimate the degree of death registration coverage for a population. Implemented methods include the Generalized Growth Balance method (GGB), the Synthetic Extinct Generation method (SEG), and a hybrid of the two, GGB-SEG. Each method offers automatic estimation, but users may also specify exact parameters or use a graphical interface to guess parameters in the traditional way if desired.

Maintained by Tim Riffe. Last updated 8 years ago.

3.8 match 2.00 score

nmatzke

cladoRcpp:C++ Implementations of Phylogenetic Cladogenesis Calculations

Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.

Maintained by Nicholas J. Matzke. Last updated 9 months ago.

cpp

1.7 match 4.38 score 240 scripts

cran

ATNr:Run Allometric Trophic Networks Models

Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.

Maintained by Benoit Gauzens. Last updated 2 years ago.

openblas cpp openmp

2.0 match 3.36 score 23 scripts

marcodvisser

ccrtm:Coupled Chain Radiative Transfer Models

A set of radiative transfer models to quantitatively describe the absorption, reflectance and transmission of solar energy in vegetation, and model remotely sensed spectral signatures of vegetation at distinct spatial scales (leaf,canopy and stand). The main principle behind ccrtm is that many radiative transfer models can form a coupled chain, basically models that feed into each other in a linked chain (from leaf, to canopy, to stand, to atmosphere). It allows the simulation of spectral datasets in the solar spectrum (400-2500nm) using leaf models as PROSPECT5, 5b, and D which can be coupled with canopy models as 'FLIM', 'SAIL','SAIL2' and 'INFORM' for top of canopy reflectance, and with atmospheric models such as 'SKYL'and 'SMAC' for calculation of top of the atmosphere reflectance. All models can run in forward mode, and a selection are invertable (backward simulations) if provided with spectral data. Jacquemoud et al 2008 provides a comprehensive overview of these and other models <doi:10.1016/j.rse.2008.01.026>.

Maintained by Marco D. Visser. Last updated 3 days ago.

cpp

1.5 match 15 stars 4.18 score 1 scripts

chabert-liddell

robber:Using Block Model to Estimate the Robustness of Ecological Network

Implementation of a variety of methods to compute the robustness of ecological interaction networks with binary interactions as described in <doi:10.1002/env.2709>. In particular, using the Stochastic Block Model and its bipartite counterpart, the Latent Block Model to put a parametric model on the network, allows the comparison of the robustness of networks differing in species richness and number of interactions. It also deals with networks that are partially sampled and/or with missing values.

Maintained by Saint-Clair Chabert-Liddell. Last updated 1 years ago.

ecological-network robber robustness

1.7 match 1 stars 3.70 score 4 scripts

prabhanjan-tattar

gpk:100 Data Sets for Statistics Education

Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.

Maintained by Prabhanjan Tattar. Last updated 12 years ago.

3.8 match 1.69 score 49 scripts

wangwm2017

RLeafAngle:Estimates, Plots and Evaluates Leaf Angle Distribution Functions, Calculates Extinction Coefficients

Leaf angle distribution is described by a number of functions (e.g. ellipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle distributions functions are estimated through different empirical relationship. This package includes estimations of parameters of different leaf angle distribution function, plots and evaluates leaf angle distribution functions, calculates extinction coefficients given leaf angle distribution. Reference: Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>.

Maintained by Wei-Min Wang. Last updated 8 years ago.

3.3 match 1.51 score 32 scripts

rorynolan

filesstrings:Handy File and String Manipulation

This started out as a package for file and string manipulation. Since then, the 'fs' and 'strex' packages emerged, offering functionality previously given by this package (but it's done better in these new ones). Those packages have hence almost pushed 'filesstrings' into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.

Maintained by Rory Nolan. Last updated 1 years ago.

0.5 match 22 stars 8.59 score 632 scripts 4 dependents

cran

EcoVirtual:Simulation of Ecological Models

Computer simulations of classical ecological models as a learning resource.

Maintained by Alexandre Adalardo de Oliveira. Last updated 6 years ago.

1.7 match 1.48 score 1 dependents

gplates

rgplates:R Interface for the GPlates Web Service and Desktop Application

Query functions to the GPlates <https://www.gplates.org/> Desktop Application and the GPlates Web Service <https://gws.gplates.org/> allow users to reconstruct past positions of geographic entities based on user-selected rotation models without leaving the R running environment. The online method (GPlates Web Service) makes the rotation of static plates, coastlines, and a low number of geographic coordinates available using nothing but an internet connection. The offline method requires an external installation of the GPlates Desktop Application, but allows the efficient batch rotation of thousands of coordinates, Simple Features (sf) and Spatial (sp) objects with custom reconstruction trees and partitioning polygons. Examples of such plate tectonic models are accessible via the chronosphere <https://cran.r-project.org/package=chronosphere>. This R extension is developed under the umbrella of the DFG (Deutsche Forschungsgemeinschaft) Research Unit TERSANE2 (For 2332, TEmperature Related Stressors in ANcient Extinctions).

Maintained by Adam T. Kocsis. Last updated 6 months ago.

0.5 match 4 stars 4.82 score 55 scripts

sophiekersting

poweRbal:Phylogenetic Tree Models and the Power of Tree Shape Statistics

The first goal of this package is to provide a multitude of tree models, i.e., functions that generate rooted binary trees with a given number of leaves. Second, the package allows for an easy evaluation and comparison of tree shape statistics by estimating their power to differentiate between different tree models. Please note that this R package was developed alongside the manuscript "Tree balance in phylogenetic models" by S. J. Kersting, K. Wicke, and M. Fischer (2024) <doi:10.48550/arXiv.2406.05185>, which provides further background and the respective mathematical definitions. This project was supported by the project ArtIGROW, which is a part of the WIR!-Alliance ArtIFARM – Artificial Intelligence in Farming funded by the German Federal Ministry of Education and Research (No. 03WIR4805).

Maintained by Sophie Kersting. Last updated 7 months ago.

1.7 match 1.30 score

cran

radar:Fundamental Formulas for Radar

Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet

Maintained by Jose Gama. Last updated 10 years ago.

1.9 match 1 stars 1.00 score

cbracis

pdmod:Proximal/Distal Modeling Framework for Pavlovian Conditioning Phenomena

Fits a model of Pavlovian conditioning phenomena, such as response extinction and spontaneous recovery, and partial reinforcement extinction effects. Competing proximal and distal reward predictions, computed using fast and slow learning rates, combine according to their uncertainties and the recency of information. The resulting mean prediction drives the response rate.

Maintained by Chloe Bracis. Last updated 7 years ago.

0.8 match 2.00 score 8 scripts

theropod1

gdi:Volumetric Analysis using Graphic Double Integration

Tools implementing an automated version of the graphic double integration technique (GDI) for volume implementation, and some other related utilities for paleontological image-analysis. GDI was first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145> and is primarily used for volume or mass estimation of (extinct) animals. The package 'gdi' aims to make this technique as convenient and versatile as possible. The core functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files and calculating volume via graphic double integration with simple elliptical, superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional models. Additionally, the package provides functions for estimating the center of mass position (COM), the moment of inertia (I) for 3D shapes and the second moment of area (Ix, Iy, Iz) of 2D cross-sections, as well as for visualization of results.

Maintained by Darius Nau. Last updated 11 months ago.

0.5 match 2.68 score 16 scripts

harithmorgadinho

WEGE:A Metric to Rank Locations for Biodiversity Conservation

Calculates the WEGE (Weighted Endemism including Global Endangerment index) index for a particular area. Additionally it also calculates rasters of KBA's (Key Biodiversity Area) criteria (A1a, A1b, A1e, and B1), Weighted endemism (WE), the EDGE (Evolutionarily Distinct and Globally Endangered) score, Evolutionary Distinctiveness (ED) and Extinction risk (ER). Farooq, H., Azevedo, J., Belluardo F., Nanvonamuquitxo, C., Bennett, D., Moat, J., Soares, A., Faurby, S. & Antonelli, A. (2020) <doi:10.1101/2020.01.17.910299>.

Maintained by Harith Farooq. Last updated 5 years ago.

0.5 match 1.70 score 7 scripts

paulesantos

iucnr:IUCN Red List Data

Facilitates access to the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, a comprehensive global inventory of species at risk of extinction. This package streamlines the process of determining conservation status by matching species names with Red List data, providing tools to easily query and retrieve conservation statuses. Designed to support biodiversity research and conservation planning, this package relies on data from the 'iucnrdata' package, available on GitHub <https://github.com/PaulESantos/iucnrdata>. To install the data package, use pak::pak('PaulESantos/iucnrdata').

Maintained by Paul Efren Santos Andrade. Last updated 4 months ago.

0.5 match 1.70 score

cran

GrimR:Calculate Optical Parameters from Spindle Stage Measurements

Calculates optical parameters of crystals like the optical axes, the axis angle 2V, and the direction of the principal axes of the indicatrix from extinction angles measured on a spindle stage mounted on a polarisation microscope stage. Details of the method can be found in Dufey (2017) <arXiv:1703.00070>.

Maintained by Florian Dufey. Last updated 7 years ago.

0.5 match 1.00 score

cran

ShapePattern:Tools for Analyzing Shapes and Patterns

This is an evolving and growing collection of tools for the quantification, assessment, and comparison of shape and pattern. This collection provides tools for: (1) the spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking; the spectra of results are returned in graphic and tabular formats (Remmel 2015) <doi:10.1111/cag.12222>, (2) simulating landscape patterns, (3) provision of tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps (Remmel and Fortin 2013) <doi:10.1007/s10980-013-9905-x>, (4) counting the number of each first-order pattern element and converting that information into both frequency and empirical probability vectors (Remmel 2020) <doi:10.3390/e22040420>, and (5) computing the porosity of raster patches <doi:10.3390/su10103413>. NOTE: This is a consolidation of existing packages ('PatternClass', 'ShapePattern') to begin warehousing all shape and pattern code in a common package. Additional utility tools for handling data are provided and this package will be added to as more tools are created, cleaned-up, and documented. Note that all future developments will appear in this package and that 'PatternClass' will eventually be archived.

Maintained by Tarmo K. Remmel. Last updated 3 months ago.

0.5 match 1.00 score