Showing 52 of total 52 results (show query)
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 6 months ago.
135.9 match 1 stars 5.24 score 65 scripts 1 dependents
cran
fossil:Palaeoecological and Palaeogeographical Analysis Tools
A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.
Maintained by Matthew J. Vavrek. Last updated 5 years ago.
56.8 match 1 stars 5.18 score 532 scripts 7 dependents
palaeoverse
palaeoverse:Prepare and Explore Data for Palaeobiological Analyses
Provides functionality to support data preparation and exploration for palaeobiological analyses, improving code reproducibility and accessibility. The wider aim of 'palaeoverse' is to bring the palaeobiological community together to establish agreed standards. The package currently includes functionality for data cleaning, binning (time and space), exploration, summarisation and visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>) and auxiliary functions are also provided. Details can be found in: Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.
Maintained by Lewis A. Jones. Last updated 5 months ago.
biodiversityfossilpalaeobiologypaleobiology
22.0 match 21 stars 8.57 score 44 scripts 1 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.
diversityextinctionfossil-dataoccurrencesoriginationpaleobiologycpp
17.0 match 11 stars 6.48 score 137 scripts
ropensci
CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections
Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Maintained by Alexander Zizka. Last updated 1 years ago.
10.1 match 82 stars 10.93 score 306 scripts 3 dependentsropensci
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.
15.2 match 42 stars 6.19 score 74 scripts
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.
10.0 match 6 stars 8.45 score 152 scripts
gavinsimpson
analogue:Analogue and Weighted Averaging Methods for Palaeoecology
Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.
Maintained by Gavin L. Simpson. Last updated 6 months ago.
8.6 match 14 stars 8.96 score 185 scripts 4 dependents
dwbapst
paleoAM:Simulating Assemblage Models of Abundance for the Fossil Record
Provides functions for fitting abundance distributions over environmental gradients to the species in ecological communities, and tools for simulating the fossil assemblages from those abundance models for such communities, as well as simulating assemblages across various patterns of sedimentary history and sampling. These tools are for particular use with fossil records with detailed age models and abundance distributions used for calculating environmental gradients from ordinations or other indices based on fossil assemblages.
Maintained by David W Bapst. Last updated 5 months ago.
15.9 match 4 stars 4.38 score 1 scripts
neotomadb
neotoma2:Working with the Neotoma Paleoecology Database
Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>.
Maintained by Dominguez Vidana Socorro. Last updated 8 months ago.
earthcubeneotomansfpaleoecology
8.9 match 8 stars 5.35 score 56 scripts
gawainantell
divvy:Spatial Subsampling of Biodiversity Occurrence Data
Divide taxonomic occurrence data into geographic regions of fair comparison, with three customisable methods to standardise area and extent. Calculate common biodiversity and range-size metrics on subsampled data. Background theory and practical considerations for the methods are described in Antell and others (2023) <doi:10.31223/X5997Z>.
Maintained by Gawain Antell. Last updated 1 years ago.
10.5 match 4.00 score 10 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 12 hours ago.
2.3 match 64 stars 17.22 score 13k scripts 599 dependents
mindthegap-erc
StratPal:Stratigraphic Paleobiology Modeling Pipelines
The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.
Maintained by Niklas Hohmann. Last updated 24 days ago.
palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy
5.9 match 1 stars 5.88 score 18 scripts
pik-piam
mrremind:MadRat REMIND Input Data Package
The mrremind packages contains data preprocessing for the REMIND model.
Maintained by Lavinia Baumstark. Last updated 3 days ago.
5.4 match 4 stars 6.25 score 15 scripts 1 dependents
wjbraun
DAAG:Data Analysis and Graphics Data and Functions
Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.
Maintained by W. John Braun. Last updated 11 months ago.
4.0 match 8.25 score 1.2k scripts 1 dependents
boost-r
FDboost:Boosting Functional Regression Models
Regression models for functional data, i.e., scalar-on-function, function-on-scalar and function-on-function regression models, are fitted by a component-wise gradient boosting algorithm. For a manual on how to use 'FDboost', see Brockhaus, Ruegamer, Greven (2017) <doi:10.18637/jss.v094.i10>.
Maintained by David Ruegamer. Last updated 3 months ago.
boostingboosting-algorithmsfunction-on-function-regressionfunction-on-scalar-regressionmachine-learningscalar-on-function-regressionvariable-selection
3.8 match 17 stars 8.00 score 98 scripts
richardjtelford
palaeoSig:Significance Tests for Palaeoenvironmental Reconstructions
Several tests of quantitative palaeoenvironmental reconstructions from microfossil assemblages, including the null model tests of the statistically significant of reconstructions developed by Telford and Birks (2011) <doi:10.1016/j.quascirev.2011.03.002>, and tests of the effect of spatial autocorrelation on transfer function model performance using methods from Telford and Birks (2009) <doi:10.1016/j.quascirev.2008.12.020> and Trachsel and Telford (2016) <doi:10.5194/cp-12-1215-2016>. Age-depth models with generalized mixed-effect regression from Heegaard et al (2005) <doi:10.1191/0959683605hl836rr> are also included.
Maintained by Richard Telford. Last updated 2 years ago.
5.2 match 3 stars 5.45 score 31 scripts
mcomas
coda.base:A Basic Set of Functions for Compositional Data Analysis
A minimum set of functions to perform compositional data analysis using the log-ratio approach introduced by John Aitchison (1982). Main functions have been implemented in c++ for better performance.
Maintained by Marc Comas-Cufí. Last updated 1 years ago.
4.0 match 7 stars 6.93 score 81 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.
evolutionmacroevolutionpaleobiologypaleontologyphylogenetics
5.4 match 6 stars 4.95 score 4 scripts
pasraia
RRphylo:Phylogenetic Ridge Regression Methods for Comparative Studies
Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Maintained by Silvia Castiglione. Last updated 7 months ago.
3.6 match 10 stars 7.48 score 83 scripts
rmi-pacta
pacta.executive.summary:Creates Plots for the PACTA COP Executive Summary
This package contains plotting functions and a template for generating the executive summary that displays aggregated results of a PACTA COP exercise.
Maintained by Monika Furdyna. Last updated 4 months ago.
climate-changesustainable-finance
5.1 match 2 stars 4.70 score 3 scripts 1 dependents
dreamrs
vchartr:Interactive Charts with the 'JavaScript' 'VChart' Library
Provides an 'htmlwidgets' interface to 'VChart.js'. 'VChart', more than just a cross-platform charting library, but also an expressive data storyteller. 'VChart' examples and documentation are available here: <https://www.visactor.io/vchart>.
Maintained by Victor Perrier. Last updated 2 months ago.
3.4 match 9 stars 6.89 score 96 scripts
goepp
aspline:Spline Regression with Adaptive Knot Selection
Perform one-dimensional spline regression with automatic knot selection. This package uses a penalized approach to select the most relevant knots. B-splines of any degree can be fitted. More details in 'Goepp et al. (2018)', "Spline Regression with Automatic Knot Selection", <arXiv:1808.01770>.
Maintained by Vivien Goepp. Last updated 3 years ago.
adaptive-splinesfitting-splinesknotsregression-splinecpp
4.5 match 6 stars 4.52 score 11 scripts
maarten14c
coffee:Chronological Ordering for Fossils and Environmental Events
While individual calibrated radiocarbon dates can span several centuries, combining multiple dates together with any chronological constraints can make a chronology much more robust and precise. This package uses Bayesian methods to enforce the chronological ordering of radiocarbon and other dates, for example for trees with multiple radiocarbon dates spaced at exactly known intervals (e.g., 10 annual rings). For methods see Christen 2003 <doi:10.11141/ia.13.2>. Another example is sites where the relative chronological position of the dates is taken into account - the ages of dates further down a site must be older than those of dates further up (Buck, Kenworthy, Litton and Smith 1991 <doi:10.1017/S0003598X00080534>; Nicholls and Jones 2001 <doi:10.1111/1467-9876.00250>). The paper accompanying this R package is Blaauw et al. 2024 <doi:10.1017/RDC.2024.56>.
Maintained by Maarten Blaauw. Last updated 3 months ago.
3.0 match 7 stars 6.02 score 6 scripts
jverzani
UsingR:Data Sets, Etc. for the Text "Using R for Introductory Statistics", Second Edition
A collection of data sets to accompany the textbook "Using R for Introductory Statistics," second edition.
Maintained by John Verzani. Last updated 3 years ago.
3.4 match 1 stars 4.97 score 1.4k scripts
pnovack-gottshall
ecospace:Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks
Implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.
Maintained by Phil Novack-Gottshall. Last updated 5 years ago.
3.4 match 5 stars 4.51 score 13 scriptscran
paleoTS:Analyze Paleontological Time-Series
Facilitates analysis of paleontological sequences of trait values. Functions are provided to fit, using maximum likelihood, simple evolutionary models (including unbiased random walks, directional evolution,stasis, Ornstein-Uhlenbeck, covariate-tracking) and complex models (punctuation, mode shifts).
Maintained by Gene Hunt. Last updated 6 months ago.
3.4 match 1 stars 4.48 score 2 dependentspik-piam
remind2:The REMIND R package (2nd generation)
Contains the REMIND-specific routines for data and model output manipulation.
Maintained by Renato Rodrigues. Last updated 6 days ago.
1.6 match 8.88 score 161 scripts 5 dependents
jclavel
mvMORPH:Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.
Maintained by Julien Clavel. Last updated 1 months ago.
1.5 match 17 stars 9.46 score 189 scripts 3 dependents
willgearty
deeptime:Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
Maintained by William Gearty. Last updated 3 months ago.
geologyggplot2paleontologyvisualization
1.3 match 92 stars 10.61 score 207 scripts 3 dependentscran
SemiPar:Semiparametic Regression
Functions for semiparametric regression analysis, to complement the book: Ruppert, D., Wand, M.P. and Carroll, R.J. (2003). Semiparametric Regression. Cambridge University Press.
Maintained by Billy Aung Myint. Last updated 7 years ago.
4.5 match 3.03 score 8 dependents
lewisajones
sepkoski:Sepkoski's Fossil Marine Animal Genera Compendium
Stratigraphic ranges of fossil marine animal genera from Sepkoski's (2002) published compendium. No changes have been made to any taxonomic names. However, first and last appearance intervals have been updated to be consistent with stages of the International Geological Timescale. Functionality for generating a plot of Sepkoski's evolutionary fauna is also included. For specific details on the compendium see: Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletins of American Paleontology, 363, pp. 1–560 (ISBN 0-87710-450-6). Access: <https://www.biodiversitylibrary.org/item/40634#page/5/mode/1up>.
Maintained by Lewis A. Jones. Last updated 6 months ago.
3.7 match 2 stars 3.30 score 3 scripts
arne-henningsen
micEcon:Microeconomic Analysis and Modelling
Various tools for microeconomic analysis and microeconomic modelling, e.g. estimating quadratic, Cobb-Douglas and Translog functions, calculating partial derivatives and elasticities of these functions, and calculating Hessian matrices, checking curvature and preparing restrictions for imposing monotonicity of Translog functions.
Maintained by Arne Henningsen. Last updated 3 years ago.
3.4 match 3 stars 3.18 score 39 scripts 3 dependents
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.
2.3 match 3 stars 4.63 score 19 scripts
puttickmacroevolution
motmot:Models of Trait Macroevolution on Trees
Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.
Maintained by Mark Puttick. Last updated 5 years ago.
1.7 match 4 stars 6.05 score 35 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.
1.6 match 2 stars 5.93 score 95 scripts 1 dependents
jf15558
fossilbrush:Automated Cleaning of Fossil Occurrence Data
Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Maintained by Joe Flannery-Sutherland. Last updated 1 years ago.
3.5 match 2.70 score 5 scripts
ijun2018
MLEce:Asymptotic Efficient Closed-Form Estimators for Multivariate Distributions
Asymptotic efficient closed-form estimators (MLEces) are provided in this package for three multivariate distributions(gamma, Weibull and Dirichlet) whose maximum likelihood estimators (MLEs) are not in closed forms. Closed-form estimators are strong consistent, and have the similar asymptotic normal distribution like MLEs. But the calculation of MLEces are much faster than the corresponding MLEs. Further details and explanations of MLEces can be found in. Jang, et al. (2023) <doi:10.1111/stan.12299>. Kim, et al. (2023) <doi:10.1080/03610926.2023.2179880>.
Maintained by Jun Zhao. Last updated 1 years ago.
3.3 match 2.70 score
aazaff
velociraptr:Fossil Analysis
Functions for downloading, reshaping, culling, cleaning, and analyzing fossil data from the Paleobiology Database <https://paleobiodb.org>.
Maintained by Andrew A Zaffos. Last updated 6 years ago.
4.3 match 1 stars 2.04 score 22 scriptspik-piam
reporttransport:Reporting package for edgeTransport
This package contains edgeTransport-specific routines to report model results. The main functionality is to generate transport reporting variables in MIF format from a given edgeTransport model run folder or REMIND input data.
Maintained by Johanna Hoppe. Last updated 2 months ago.
1.7 match 4.60 score 9 scripts 3 dependentsbjoelle
FossilSimShiny:Shiny Application for 'FossilSim'
A shiny application based on 'FossilSim'. Used for simulating tree, taxonomic and fossil data under mechanistic models of speciation, preservation and sampling.
Maintained by Joelle Barido-Sottani. Last updated 11 months ago.
2.0 match 3.00 score
niklashohmann
DAIME:Effects of Changing Deposition Rates
Reverse and model the effects of changing deposition rates on geological data and rates. Based on Hohmann (2018) <doi:10.13140/RG.2.2.23372.51841> .
Maintained by Niklas Hohmann. Last updated 5 years ago.
1.3 match 3.00 score
jonchang
fishtree:Interface to the Fish Tree of Life API
An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.
Maintained by Jonathan Chang. Last updated 3 months ago.
0.5 match 11 stars 6.57 score 56 scripts 1 dependents
kylebittinger
abdiv:Alpha and Beta Diversity Measures
A collection of measures for measuring ecological diversity. Ecological diversity comes in two flavors: alpha diversity measures the diversity within a single site or sample, and beta diversity measures the diversity across two sites or samples. This package overlaps considerably with other R packages such as 'vegan', 'gUniFrac', 'betapart', and 'fossil'. We also include a wide range of functions that are implemented in software outside the R ecosystem, such as 'scipy', 'Mothur', and 'scikit-bio'. The implementations here are designed to be basic and clear to the reader.
Maintained by Kyle Bittinger. Last updated 1 years ago.
0.5 match 9 stars 4.14 score 31 scriptscran
SDAR:Stratigraphic Data Analysis
A fast, consistent tool for plotting and facilitating the analysis of stratigraphic and sedimentological data. Taking advantage of the flexible plotting tools available in R, 'SDAR' uses stratigraphic and sedimentological data to produce detailed graphic logs for outcrop sections and borehole logs. These logs can include multiple features (e.g., bed thickness, lithology, samples, sedimentary structures, colors, fossil content, bioturbation index, gamma ray logs) (Johnson, 1992, <ISSN 0037-0738>).
Maintained by John R. Ortiz. Last updated 4 years ago.
0.5 match 3.30 score 5 scripts
