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ORCIDJournal of Open Source Software, Volume 3
Volume 3, Number 21, 2018
- Brandon LeBeau
:
highlightHTML: CSS Formatting of R Markdown Documents. 185 - Gilbert Marzolin, Olivier Gimenez:
Fitting a Gamma-Gompertz survival model to capture-recapture data collected on free-ranging animal populations. 216 - Alexander D. Lindsay, Kathryn D. Huff:
Moltres: finite element based simulation of molten salt reactors. 298 - Jason Keith Moore, Antonie J. van den Bogert:
opty: Software for trajectory optimization and parameter identification using direct collocation. 300 - Paul B. Govan:
BayesianNetwork: Interactive Bayesian Network Modeling and Analysis. 425 - Lester James V. Miranda:
PySwarms: a research toolkit for Particle Swarm Optimization in Python. 433 - Jiao Y. Y. Lin, Fahima Islam, Max Kresh:
Multiphonon: Phonon Density of States tools for Inelastic Neutron Scattering Powder Data. 440 - Nathan C. Sheffield, V. P. Nagraj, Vincent P. Reuter:
simpleCache: R caching for reproducible, distributed, large-scale projects. 463 - Markus J. Ankenbrand, Simon Pfaff, Niklas Terhoeven, Musga Qureischi, Maik Gündel, Clemens L. Weiß, Thomas Hackl, Frank Förster:
chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data. 464 - Anton Rodenhauser, Wilson Good, Brian Zenger, Jess D. Tate, Kedar Aras, Brett M. Burton, Rob S. MacLeod:
PFEIFER: Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings. 472 - Pablo G. Garay, Jorge A. Vila, Osvaldo A. Martin:
CheSweet: An application to predict glycan's chemicals shifts. 488 - Björn Dahlgren:
pyodesys: Straightforward numerical integration of ODE systems from Python. 490 - Pamphile T. Roy, Sophie Ricci, Romain Dupuis, Robin Campet, Jean-Christophe Jouhaud, Cyril Fournier:
BATMAN: Statistical analysis for expensive computer codes made easy. 493 - René L. Warren:
Visualizing genome synteny with xmatchview. 497 - William McGinnis, Chapman Siu, Andre S., Hanyu Huang:
Category Encoders: a scikit-learn-contrib package of transformers for encoding categorical data. 501 - Jeremy R. Coyle, Nima S. Hejazi:
origami: A Generalized Framework for Cross-Validation in R. 512 - Stephanie J. Spielman:
phyphy: Python package for facilitating the execution and parsing of HyPhy standard analyses. 514 - R. Daniel Kortschak:
arrgh: a Go interface to the OpenCPU R server system. 517 - Björn Dahlgren:
pyneqsys: Solve symbolically defined systems of non-linear equations numerically. 531 - Sébastien Boisgérault:
Bitstream - Binary Data for Humans. 541 - Joshua T. Karpel:
IDESolver: a general purpose integro-differential equation solver. 542 - William Michael Landau:
The drake R package: a pipeline toolkit for reproducibility and high-performance computing. 550
Volume 3, Number 22, 2018
- Benny Malengier, Pavol Kison, James Tocknell, Claas Abert, Florian Bruckner, Marc-Antonio Bisotti:
ODES: a high level interface to ODE and DAE solvers. 165 - James Hiebert, Alex J. Cannon, Trevor Murdock, Stephen Sobie, Arelia Werner:
ClimDown: Climate Downscaling in R. 360 - Danilo Freire, Robert Myles McDonnell:
prisonbrief: An R package that returns tidy data from the World Prison Brief website. 361 - Shadia Mikhael, Calum D. Gray:
Masks2Metrics (M2M): A Matlab Toolbox for Gold Standard Morphometrics. 436 - Dominique Makowski:
The psycho Package: an Efficient and Publishing-Oriented Workflow for Psychological Science. 470 - James P. Howard II:
Phonetic Algorithms in R. 480 - Parker Owan, Cameron Devine, W. Tony Piaskowy:
CoreRobotics: An object-oriented C++ library with cross-language wrappers for cross-platform robot control. 489 - Jeongseok Lee, Michael X. Grey, Sehoon Ha, Tobias Kunz, Sumit Jain, Yuting Ye, Siddhartha S. Srinivasa, Mike Stilman, C. Karen Liu:
DART: Dynamic Animation and Robotics Toolkit. 500 - Roderick Bovee, Nick Greenfield:
Finch: a tool adding dynamic abundance filtering to genomic MinHashing. 505 - Kevin M. Moerman:
GIBBON: The Geometry and Image-Based Bioengineering add-On. 506 - Robert Gieseke, Sven N. Willner, Matthias Mengel:
Pymagicc: A Python wrapper for the simple climate model MAGICC. 516 - Vanessa V. Sochat:
The Experiment Factory: Reproducible Experiment Containers. 521 - Taha Zaghdoudi:
ivprobit: An R package to estimate the instrumental variables probit model. 523 - Niklas Terhoeven, Jörg Schultz, Thomas Hackl:
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. 527 - Jakob Bossek:
grapherator: A Modular Multi-Step Graph Generator. 528 - Nicola Demo, Marco Tezzele, Gianluigi Rozza:
PyDMD: Python Dynamic Mode Decomposition. 530 - Matthew Pitkin:
psrqpy: a python interface for querying the ATNF pulsar catalogue. 538 - Aleksey Bilogur:
Missingno: a missing data visualization suite. 547 - Robert Reinecke:
G³M-f a global gradient-based groundwater modelling framwork. 548 - Matilda Åslin, Monika Brandt, Johan Dahlberg:
CheckQC: Quick quality control of Illumina sequencing runs. 556 - Julia Wrobel:
register: Registration for Exponential Family Functional Data. 557 - Chi-Lin Yu, Ching-Fan Sheu:
EFAshiny: An User-Friendly Shiny Application for Exploratory Factor Analysis. 567 - Ian H. Bell, Bradley Alpert, Lucas Bouck:
ChebTools: C++11 (and Python) tools for working with Chebyshev expansions. 569 - Stefanie E. LaZerte, Sam J. Albers:
weathercan: Download and format weather data from Environment and Climate Change Canada. 571 - James Tocknell:
h5preserve: Thin wrapper around h5py, inspired by camel. 581
Volume 3, Number 23, 2018
- Lincoln Mullen, Jordan Bratt:
USAboundaries: Historical and Contemporary Boundaries of the United States of America. 314 - Nuno Fachada, Agostinho C. Rosa:
micompm: A MATLAB/Octave toolbox for multivariate independent comparison of observations. 430 - David J. Mulryne, John W. Ronayne:
PyTransport: A Python package for the calculation of inflationary correlation functions. 494 - Pierre Morel:
Gramm: grammar of graphics plotting in Matlab. 568 - Peter Laurinec:
TSrepr R package: Time Series Representations. 577 - Michael Hirsch:
PyMap3D: 3-D coordinate conversions for terrestrial and geospace environments. 580 - John Mount, Nina B. Zumel:
The vtreat R package: a statistically sound data processor for predictive modeling. 584 - Donald E. Willcox, Michael Zingale:
pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations. 588 - Sander Wahls, Shrinivas Chimmalgi, Peter J. Prins:
FNFT: A Software Library for Computing Nonlinear Fourier Transforms. 597 - George Datseris:
DynamicalSystems.jl: A Julia software library for chaos and nonlinear dynamics. 598 - Andreas Bender, Alexander Bauer:
coalitions: Coalition probabilities in multi-party democracies. 606 - Grega Vrbancic, Lucija Brezocnik, Uros Mlakar, Dusan Fister, Iztok Fister Jr.:
NiaPy: Python microframework for building nature-inspired algorithms. 613 - Joe Thorley:
checkr: An R package for Assertive Programming. 624 - Konstantinos Vantas:
hydroscoper: R interface to the Greek National Data Bank for Hydrological and Meteorological Information. 625 - Rory Nolan, Sergi Padilla-Parra:
ijtiff: An R package providing TIFF I/O for ImageJ users. 633 - Alessandro Gasparini:
comorbidity: An R package for computing comorbidity scores. 648 - Lincoln Mullen, Kenneth Benoit, Os Keyes, Dmitriy Selivanov, Jeffrey Arnold:
Fast, Consistent Tokenization of Natural Language Text. 655
Volume 3, Number 24, 2018
- Björn Dahlgren:
ChemPy: A package useful for chemistry written in Python. 565 - Sergio Ibarra-Espinosa, Daniel Schuch, Edmilson Dias de Freitas:
eixport: An R package to export emissions to atmospheric models. 607 - Giuseppe Cardellini, Christopher Lucien Mutel:
Temporalis: an open source software for dynamic LCA. 612 - Patrick Kofod Mogensen, Asbjørn Nilsen Riseth:
Optim: A mathematical optimization package for Julia. 615 - Daniel Amsel, André Billion, Andreas Vilcinskas, Frank Förster:
microPIECE - microRNA pipeline enhanced by CLIP experiments. 616 - Louise A. Dennis:
The MCAPL Framework including the Agent Infrastructure Layer an Agent Java Pathfinder. 617 - Sebastian Raschka:
MLxtend: Providing machine learning and data science utilities and extensions to Python's scientific computing stack. 638 - Moti Ben-Ari:
LearnSAT: A SAT Solver for Education. 639 - Casey Youngflesh:
MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output. 640 - Caley Finn:
OpenEPSim: An Open Exclusion Process Simulation Tool. 650 - Michael Hucka:
Spiral: splitters for identifiers in source code files. 653 - Yuan (Terry) Tang:
autoplotly: An R package for automatic generation of interactive visualizations for statistical results. 657 - Brian E. J. Rose:
CLIMLAB: a Python toolkit for interactive, process-oriented climate modeling. 659 - Nicola Demo, Marco Tezzele, Gianluigi Rozza:
EZyRB: Easy Reduced Basis method. 661 - Jasper Ginn:
qualtRics: retrieve survey data using the Qualtrics API. 690 - Júlio Hoffimann:
GeoStats.jl - High-performance geostatistics in Julia. 692 - Sebastian S. Zeki:
EndoMineR for the extraction of endoscopic and associated pathology data from medical reports. 701
Volume 3, Number 25, 2018
- Benjamin Allévius:
scanstatistics: space-time anomaly detection using scan statistics. 515 - Pi-Yueh Chuang, Olivier Mesnard, Anush Krishnan, Lorena A. Barba:
PetIBM: toolbox and applications of the immersed-boundary method on distributed-memory architectures. 558 - Ignacio Ferrés, Gregorio Iraola:
Phylen: automatic phylogenetic reconstruction using the EggNOG database. 593 - Michael Hucka:
Nostril: A nonsense string evaluator written in Python. 596 - Mike Innes:
Flux: Elegant machine learning with Julia. 602 - David E. Hudak, Douglas Johnson, Alan Chalker, Jeremy W. Nicklas, Eric Franz, Trey Dockendorf, Brian McMichael:
Open OnDemand: A web-based client portal for HPC centers. 622 - Andrew P. Smith:
humanleague: a C++ microsynthesis package with R and python interfaces. 629 - Ryan C. Brown, Joshua Moser:
HSImage: A Python and C++ library to allow interaction with ENVI-BIL hyperspectral images. 630 - Amelia Ortiz-Gil, Jordi Burguet-Castell:
Mapelia and friends: create 3D models from maps. 660 - Arjun Chennu:
MicroBenthos: a modeling framework for microbial benthic ecology. 674 - Mikkel Meyer Andersen:
malan: MAle Lineage ANalysis. 684 - Boaz Blankrot, Clemens Heitzinger:
ParticleScattering: Solving and optimizing multiple-scattering problems in Julia. 691 - Jacob Anhøj:
qicharts2: Quality Improvement Charts for R. 699 - Will Pearse, Scott Chamberlain:
Suppdata: Downloading Supplementary Data from Published Manuscripts. 721 - Sepand Haghighi, Masoomeh Jasemi, Shaahin Hessabi, Alireza Zolanvari:
PyCM: Multiclass confusion matrix library in Python. 729 - Stephen D. Turner:
qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. 731 - Ryan G. James, Christopher J. Ellison, James P. Crutchfield:
dit: a Python package for discrete information theory. 738 - Rickichard Izzo, David A. Steinman, Simone Manini, Elena Faggiano, Luca Antiga:
The Vascular Modeling Toolkit: A Python Library for the Analysis of Tubular Structures in Medical Images. 745
Volume 3, Number 26, 2018
- João P. Faria, Nuno C. Santos, Pedro Figueira, Brendon J. Brewer:
kima: Exoplanet detection in radial velocities. 487 - Antoine Cully, Konstantinos I. Chatzilygeroudis, Federico Allocati, Jean-Baptiste Mouret:
Limbo: A Flexible High-performance Library for Gaussian Processes modeling and Data-Efficient Optimization. 545 - Edward W. Doddridge, Alexey Radul:
Aronnax: An idealised isopycnal ocean model. 592 - Laurent Fasnacht:
mmappickle: Python 3 module to store memory-mapped numpy array in pickle format. 651 - Tobias C. Wood:
QUIT: QUantitative Imaging Tools. 656 - Manuel Krebber, Henrik Barthels:
MatchPy: Pattern Matching in Python. 670 - Russell Y. Neches, Camille Scott:
SuchTree: Fast, thread-safe computations with phylogenetic trees. 678 - Gregory M. Green:
dustmaps: A Python interface for maps of interstellar dust. 695 - Karl Wette, Reinhard Prix, David Keitel, Matthew Pitkin, Christoph Dreissigacker, John T. Whelan, Paola Leaci:
OctApps: a library of Octave functions for continuous gravitational-wave data analysis. 707 - Shahriar Iravanian:
fib-tf: A TensorFlow-based Cardiac Electrophysiology Simulator. 719 - Ryan R. Curtin, Marcus Edel, Mikhail Lozhnikov, Yannis Mentekidis, Sumedh Ghaisas, Shangtong Zhang:
mlpack 3: a fast, flexible machine learning library. 726 - Inom Mirzaev, Drew F. K. Williamson, Jacob G. Scott:
egtplot: A Python Package for Three-Strategy Evolutionary Games. 735 - Alessandro Gasparini, Michel Lang:
rsimsum: Summarise results from Monte Carlo simulation studies. 739 - James Bourbeau, Zigfried Hampel-Arias:
PyUnfold: A Python package for iterative unfolding. 741 - Mikkel Meyer Andersen:
Discrete Laplace mixture model with applications in forensic genetics. 748 - Daniel G. A. Smith, Johnnie Gray:
opt\_einsum - A Python package for optimizing contraction order for einsum-like expressions. 753 - Daniel Lüdecke:
sjmisc: Data and Variable Transformation Functions. 754 - Hajk-Georg Drost:
Philentropy: Information Theory and Distance Quantification with R. 765 - Jeroen F. J. Laros:
General binary file parser. 766 - Daniel Lüdecke:
ggeffects: Tidy Data Frames of Marginal Effects from Regression Models. 772 - Adam J. Jackson, Alex M. Ganose, Anna Regoutz, Russel G. Egdell, David O. Scanlon:
Galore: Broadening and weighting for simulation of photoelectron spectroscopy. 773 - Vanessa V. Sochat:
HelpMe Command Line Helper Utility. 775 - David Hagan, Andrew Tolmie, Jakub Trochim:
py-opc: operate the Alphasense OPC-N2 from a raspberry pi or other popular microcontrollers/microcomputers. 782 - Christoph Molnar, Giuseppe Casalicchio, Bernd Bischl:
iml: An R package for Interpretable Machine Learning. 786 - Shaun P. Wilkinson, Simon K. Davy:
phylogram: an R package for phylogenetic analysis with nested lists. 790
Volume 3, Number 27, 2018
- Brandon LeBeau:
pdfsearch: Search Tools for PDF Files. 668 - Sepand Haghighi, Kasra Askari, Sarmin Hamidi, Mohammad Mahdi Rahimi:
OPEM : Open Source PEM Cell Simulation Tool. 676 - Bryan Brancotte, Christophe Blanchet, Hervé Ménager:
A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. 698 - Ashlee N. Ford Versypt, James D. Crall, Biswadip Dey:
BeeNestABM: An open-source agent-based model of spatiotemporal distribution of bumblebees in nests. 718 - Hilary James Oliver, Matthew Shin, Oliver Sanders:
Cylc: A Workflow Engine for Cycling Systems. 737 - Amirsina Torfi:
SpeechPy - A Library for Speech Processing and Recognition. 749 - Ruud van der Ham:
salabim: discrete event simulation and animation in Python. 767 - Vyas Ramasubramani, Sharon C. Glotzer:
rowan: A Python package for working with quaternions. 787 - Robert William Schlegel, Albertus Jacobus Smit:
heatwaveR: A central algorithm for the detection of heatwaves and cold-spells. 821 - Evan Odell:
nomisr: Access 'Nomis' UK Labour Market Data. 859
Volume 3, Number 28, 2018
- Jarvist Moore Frost:
PolaronMobility.jl: Implementation of the Feynman variational polaron model. 566 - Kirill Tsyganov, Andrew James Perry, Stuart Kenneth Archer, David R. Powell:
RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease. 583 - Momar Hughes:
MCycle: A Python package for 1D sizing and analysis of thermodynamic power cycles. 710 - Federico Reghenzani, Giuseppe Massari, William Fornaciari:
chronovise: Measurement-Based Probabilistic Timing Analysis framework. 711 - Alex M. Ganose, Adam J. Jackson, David O. Scanlon:
sumo: Command-line tools for plotting and analysis of periodic *ab initio* calculations. 717 - David Topping, Paul Connolly, Jonathan Reid:
PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations. 755 - Lucy D. Whalley:
effmass: An effective mass package. 797 - Andrew P. Smith, Tom Russell:
ukpopulation: unified national and subnational population estimates and projections, including variants. 803 - Nathan J. Goldbaum, John ZuHone, Matthew J. Turk, Kacper Kowalik, Anna L. Rosen:
unyt: Handle, manipulate, and convert data with units in Python. 809 - John-Philippe Coene:
sigmajs: An R htmlwidget interface to the sigma.js visualization library. 814 - Jason Keith Moore, Mont Hubbard:
skijumpdesign: A Ski Jump Design Tool for Specified Equivalent Fall Height. 818 - Marcus D. Shermann, Ryan Mills:
BAMnostic: an OS-agnostic toolkit for genomic sequence analysis. 826 - Shawn D. Taylor:
pyPhenology: A python framework for plant phenology modelling. 827 - Philip D. Waggoner:
The hhi Package: Streamlined Calculation and Visualization of Herfindahl-Hirschman Index Scores. 828 - Christopher Ostrouchov, Yanwen Zhang, William J. Weber:
pysrim: Automation, Analysis, and Plotting of SRIM Calculations. 829 - David A. Wiley:
RISE: An R package for RISE analysis. 846 - Vincent Arel-Bundock, Nils Enevoldsen, C. J. Yetman:
countrycode: An R package to convert country names and country codes. 848 - Will Handley:
fgivenx: A Python package for functional posterior plotting. 849 - Steven G. Murray:
powerbox: A Python package for creating structured fields with isotropic power spectra. 850 - Brett M. Morris, Trevor Dorn-Wallenstein:
aesop: ARC Echelle Spectroscopic Observation Pipeline. 854 - Raoul R. Wadhwa, Drew F. K. Williamson, Andrew Dhawan, James G. Scott:
TDAstats: R pipeline for computing persistent homology in topological data analysis. 860 - Michael T. Porter:
js-emass: A flexible JavaScript implementation of the emass algorithm. 869 - Andrew T. Jones, Hien Duy Nguyen, Geoffrey J. McLachlan:
logKDE: log-transformed kernel density estimation. 870 - Pierre de Buyl:
tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. 877 - Vanessa V. Sochat:
Containershare: Open Source Registry to build, test, deploy with CircleCI. 878 - Thomas Klebel:
jstor: Import and Analyse Data from Scientific Texts. 883 - Jared M. Andrews, Mohamed El-Alawi, Jacqueline E. Payton:
Genotify: Fast, lightweight gene lookup and summarization. 885 - Benjamin Williams:
Combining a Probability and a Non-Probability Sample in a Capture-Recapture Setting. 886 - Anwar Nunez-Elizalde, James S. Gao, Tianjiao Zhang, Jack L. Gallant:
cottoncandy: scientific python package for easy cloud storage. 890 - David Naves Sousa, João R. Daniel:
bor: An R Package for Transforming Behavioral Observation Records into Data Matrices. 909 - Simon Dirmeier:
datastructures: An R package for organisation and storage of data. 910
Volume 3, Number 29, 2018
- Lionel Roubeyrie, Sebastien Celles:
Windrose: A Python Matplotlib, Numpy library to manage wind and pollution data, draw windrose. 268 - David P. Fleming, Jake VanderPlas:
approxposterior: Approximate Posterior Distributions in Python. 781 - Georg Raiser:
SeqPeelSort: a spike sorting algorithm for single sensillum recordings. 792 - Jean Bilheux:
NeuNorm: Neutron Imaging Normalization Library. 815 - Johnnie Gray:
quimb: A python package for quantum information and many-body calculations. 819 - Stefan Pfenninger, Bryn Pickering:
Calliope: a multi-scale energy systems modelling framework. 825 - Boyan Angelov:
sdmbench: R package for benchmarking species distribution models. 847 - Leland McInnes, John Healy, Nathaniel Saul, Lukas Großberger:
UMAP: Uniform Manifold Approximation and Projection. 861 - Palash Goyal, Emilio Ferrara:
GEM: A Python package for graph embedding methods. 876 - William F. Holmgren, Clifford W. Hansen, Mark Mikofski:
pvlib python: a python package for modeling solar energy systems. 884 - R. Hadian, Blazej Grabowski, Jörg Neugebauer:
GB code: A grain boundary generation code. 900 - Edward Higson:
nestcheck: error analysis, diagnostic tests and plots for nested sampling calculations. 916 - Christopher J. Tralie, Nathaniel Saul, Rann Bar-On:
Ripser.py: A Lean Persistent Homology Library for Python. 925 - Marius D. Pascariu, Maciej J. Danko, Jonas Schöley, Silvia Rizzi:
ungroup: An R package for efficient estimation of smooth distributions from coarsely binned data. 937 - Edward Higson:
dyPolyChord: dynamic nested sampling with PolyChord. 965 - Carl Boettiger:
Managing Larger Data on a GitHub Repository. 971
Volume 3, Number 30, 2018
- Weixin Cai, Alan E. Hubbard, Nima S. Hejazi:
adaptest: Data-Adaptive Statistics for High-Dimensional Testing in R. 161 - Daniel Schuch, Sergio Ibarra-Espinosa, Edmilson Dias de Freitas:
EmissV: an R package to create vehicular and other emissions for air quality models. 662 - Hooman Sedghamiz:
BioSigKit: A Matlab Toolbox and Interface for Analysis of BioSignals. 671 - Kenneth Benoit, Kohei Watanabe, Haiyan Wang, Paul Nulty, Adam Obeng, Stefan Müller, Akitaka Matsuo:
quanteda: An R package for the quantitative analysis of textual data. 774 - Cole Brokamp:
DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies. 812 - Devarshi Ghoshal, Lavanya Ramakrishnan:
MaDaTS: Managing Data on Tiered Storage for Scientific Workflows. 830 - Valentino Constantinou:
PyNomaly: Anomaly detection using Local Outlier Probabilities (LoOP). 845 - Marco A. Lopez-Sanchez:
GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size. 863 - Ali Kamandi, Hamed Karimi:
YAD: A Learning-based Inductive Logic Programming Tool. 892 - Stuart E. Lacy:
Estimating statistics from multi-state models using simulation with multistateutils. 893 - Pradeep Reddy Raamana, Stephen C. Strother:
mrivis: Medical image visualization library for neuroscience in python. 897 - Vincent A. Knight, James Campbell:
Nashpy: A Python library for the computation of Nash equilibria. 904 - Benjamin D. Lee:
Python Implementation of Codon Adaptation Index. 905 - Pradeep Reddy Raamana, Stephen C. Strother:
graynet: single-subject morphometric networks for neuroscience connectivity applications. 924 - Nicholas A. Bokulich, Matthew R. Dillon, Evan Bolyen, Benjamin D. Kaehler, Gavin A. Huttley, J. Gregory Caporaso:
q2-sample-classifier: machine-learning tools for microbiome classification and regression. 934 - Umberto Villa, Noemi Petra, Omar Ghattas:
hIPPYlib: An Extensible Software Framework for Large-Scale Inverse Problems. 940 - Christian B. Mendl:
PyTeNet: A concise Python implementation of quantum tensor network algorithms. 948 - Leonardo Uieda:
Verde: Processing and gridding spatial data using Green's functions. 957 - Péter Volf:
Local clustering. 960 - Tristan Salles:
eSCAPE: parallel global-scale landscape evolution model. 964 - David Naves Sousa, Hugo Alexandre Ferreira:
MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues. 966 - Daniel Schalk, Janek Thomas, Bernd Bischl:
compboost: Modular Framework for Component-Wise Boosting. 967 - Jiao Y. Y. Lin, Gian Song:
bem: modeling for neutron Bragg-edge imaging. 973 - Joshua M. Rosenberg, Patrick N. Beymer, Daniel J. Anderson, Jennifer A. Schmidt:
tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software. 978 - Katherine R. Barnhart, Eric W. H. Hutton, Nicole M. Gasparini, Gregory E. Tucker:
Lithology: A Landlab submodule for spatially variable rock properties. 979 - Edward Higson:
perfectns: perfect dynamic and standard nested sampling for spherically symmetric likelihoods and priors. 985 - Hao Yu:
PyGeoPressure: Geopressure Prediction in Python. 992 - Nicolas Granger, Mounîm A. El-Yacoubi:
SeqTools: A python package for easy transformation, combination and evaluation of large datasets. 1006 - Georgios Gerasimou, Matus Tejiscak:
Prest: Open-Source Software for Computational Revealed Preference Analysis. 1015 - Anthony R. Ives, Daijiang Li:
rr2: An R package to calculate R2s for regression models. 1028 - Adam H. Sparks:
nasapower: A NASA POWER Global Meteorology, Surface Solar Energy and Climatology Data Client for R. 1035 - Yuan (Terry) Tang, Tao Gao, Nan Xiao:
dml: Distance Metric Learning in R. 1036
Volume 3, Number 31, 2018
- Christopher T. DeGroot:
WEdiff: A Python and C++ package for automatic differentiation. 820 - Eshin Jolly:
Pymer4: Connecting R and Python for Linear Mixed Modeling. 862 - Lyndon White, Sebastin Santy:
DataDepsGenerators.jl: making reusing data easy by automatically generating DataDeps.jl registration code. 921 - Vincent A. Cicirello:
JavaPermutationTools: A Java Library of Permutation Distance Metrics. 950 - Lars Arvestad:
alv: a console-based viewer for molecular sequence alignments. 955 - Aleksandra Grudziaz, Alicja Gosiewska, Przemyslaw Biecek:
survxai: an R package for structure-agnostic explanations of survival models. 961 - Jeff MacInnes, Shariq Iqbal, John M. Pearson, Elizabeth N. Johnson:
Mobile Gaze Mapping: A Python package for mapping mobile gaze data to a fixed target stimulus. 984 - Ian E. Fellows:
ipc: An R Package for Inter-process Communication. 988 - Jonathan Malmaud, Lyndon White:
TensorFlow.jl: An Idiomatic Julia Front End for TensorFlow. 1002 - Matthew D. Golub, David Sussillo:
FixedPointFinder: A Tensorflow toolbox for identifying and characterizing fixed points in recurrent neural networks. 1003 - Raoul R. Wadhwa, Vigneshwar Subramanian, Regina Stevens-Truss:
Visualizing alpha-helical peptides in R with helixvis. 1008 - Raphael Vallat:
Pingouin: statistics in Python. 1026 - Anna-Lena Wölwer, Jan Pablo Burgard, Joshua Kunst, Mauricio Vargas:
Gravity: Estimation Methods for Gravity Models in R. 1038 - Simon J. Greenhill:
treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. 1040 - Daijiang Li:
hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers. 1041 - Robert Sare, George E. Hilley:
Scarplet: A Python package for topographic template matching and diffusion dating. 1066 - Hiromu Ochiai, Kenichi Chiba, Ai Okada, Yuichi Shiraishi:
hotsub: A batch job engine for cloud services with ETL framework. 1069 - Christopher R. Madan:
ElGateau: A Library for Using the Elgato Stream Deck for Experimental Psychology Research. 1070 - Mikael Mortensen:
Shenfun: High performance spectral Galerkin computing platform. 1071 - Michael C. Heiber:
Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis. 1072 - Joe Thorley, Carl Schwarz:
ssdtools: An R package to fit Species Sensitivity Distributions. 1082 - Jonas Geschke, Kevin Cazelles, Ignasi Bartomeus:
rcites: An R package to access the CITES Speciesplus database. 1091 - Dominic J. Bennett, Hannes Hettling, Daniele Silvestro, Rutger A. Vos, Alexandre Antonelli:
restez: Create and Query a Local Copy of GenBank in R. 1102 - João Da Silva, Pedro Figueira, Nuno C. Santos, João P. Faria:
ACTIN: A tool to calculate stellar activity indices. 667
Volume 3, Number 32, 2018
- Maxime Rousseau, Jean-Marc Retrouvey:
pfla: A Python Package for Dental Facial Analysis using Computer Vision and Statistical Shape Analysis. 855 - Wim Vanderbauwhede:
The Glasgow Fortran Source-to-Source Compiler. 865 - Ashkbiz Danehkar:
proEQUIB: IDL Library for Plasma Diagnostics and Abundance Analysis. 899 - David Naves Sousa, João R. Daniel:
qsort R package: A New Tool for Scoring Q-sort Data. 911 - Alexandre Popoff:
Opycleid: A Python package for transformational music theory. 981 - Jose M. Borreguero, Fahima Islam, Utsab R. Shrestha, Loukas Petridis:
idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments. 1007 - William M. Norris, Carson J. Q. Farmer:
SWEpy: A Python Library for Quick and Easy Access and Manipulation of MEaSUREs CETB Files for SWE Analysis. 1018 - Massimiliano Pastore:
Overlapping: a R package for Estimating Overlapping in Empirical Distributions. 1023 - James R. Schloss, James Riordan:
GPUE: Graphics Processing Unit Gross-Pitaevskii Equation solver. 1037 - Jacob VanderPlas, Brian E. Granger, Jeffrey Heer, Dominik Moritz, Kanit Wongsuphasawat, Arvind Satyanarayan, Eitan Lees, Ilia Timofeev, Ben Welsh, Scott Sievert:
Altair: Interactive Statistical Visualizations for Python. 1057 - Roman Lustrik, Zan Kuralt:
wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets. 1064 - Albert D. Rich, Patrick Scheibe, Nasser M Abbasi:
Rule-based integration: An extensive system of symbolic integration rules. 1073 - Sumanta Basu, Karl Kumbier, James B. Brown, Bin Yu:
iRF: extracting interactions from random forests. 1077 - Robert C. Garrett, Austin Nar, Thomas J. Fisher, Karsten Maurer:
ggvoronoi: Voronoi Diagrams and Heatmaps with ggplot2. 1096 - Danny C. Price, Sebastien Celles, Pieter T. Eendebak, Michael M. McKerns, Eben M. Olson, Colin Raffel, Bairen Yi:
Hickle: A HDF5-based python pickle replacement. 1115 - Syver Agdestein, Kristian Valen-Sendstad, Alexandra K. Diem:
Artery.FE: An implementation of the 1D blood flow equations in FEniCS. 1107 - Kasper Peeters:
Cadabra2: computer algebra for field theory revisited. 1118
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