Table of contents for issues of Journal of Open Source Software

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Volume 1, Number 1, May, 2016
Volume 1, Number 2, June, 2016
Volume 1, Number 3, July, 2016
Volume 1, Number 4, August, 2016
Volume 1, Number 5, September, 2016
Volume 1, Number 6, October, 2016
Volume 1, Number 7, November, 2016
Volume 1, Number 8, December, 2016
Volume 2, Number 9, January, 2017
Volume 2, Number 10, February, 2017
Volume 2, Number 11, March, 2017
Volume 2, Number 12, April, 2017
Volume 2, Number 13, May, 2017
Volume 2, Number 14, June, 2017
Volume 2, Number 15, July, 2017
Volume 2, Number 16, August, 2017
Volume 2, Number 17, September, 2017
Volume 2, Number 18, October, 2017
Volume 2, Number 19, November, 2017
Volume 2, Number 20, December, 2017
Volume 3, Number 21, January, 2018
Volume 3, Number 22, February, 2018
Volume 3, Number 23, March, 2018
Volume 3, Number 24, April, 2018
Volume 3, Number 25, May, 2018
Volume 3, Number 26, June, 2018
Volume 3, Number 27, July, 2018
Volume 3, Number 28, August, 2018
Volume 3, Number 29, September, 2018


Journal of Open Source Software
Volume 1, Number 1, May, 2016

              Gilles Louppe and   
               Kyle Cranmer and   
                     Juan Pavez   \pkgcarl: a likelihood-free inference
                                  toolbox  . . . . . . . . . . . . . . . . 11:1--11:1
                Jake VanderPlas   \pkgmst\_clustering: Clustering via
                                  Euclidean Minimum Spanning Trees . . . . 12:1--12:1
              Alice Harpole and   
                      Ian Hawke   \pkgR3D2: Relativistic Reactive Riemann
                                  problem solver for Deflagrations and
                                  Detonations  . . . . . . . . . . . . . . 16:1--16:1
                 Zhao Zhang and   
             Daniel S. Katz and   
               Andre Merzky and   
             Matteo Turilli and   
               Shantenu Jha and   
                      Yadu Nand   Application Skeleton: Generating
                                  Synthetic Applications for
                                  Infrastructure Research  . . . . . . . . 17:1--17:2
           Matthew J. Wakefield   \pkgXenomapper: Mapping reads in a mixed
                                  species context  . . . . . . . . . . . . 18:1--18:1
                Peter F. Hickey   Representation and Manipulation of
                                  Genomic Tuples in R  . . . . . . . . . . 20:1--20:1
                   J. K. Tauber   \pkgpyuca: a Python implementation of
                                  the Unicode Collation Algorithm  . . . . 21:1--21:1
               James P. Balhoff   \pkgScowl: a Scala DSL for programming
                                  with the OWL API . . . . . . . . . . . . 23:1--23:1

Journal of Open Source Software
Volume 1, Number 2, June, 2016

          Daniel Foreman-Mackey   \pkgcorner.py: Scatterplot matrices in
                                  Python . . . . . . . . . . . . . . . . . 24:1--24:2
              Zachary Sloan and   
               Danny Arends and   
             Karl W. Broman and   
             Arthur Centeno and   
          Nicholas Furlotte and   
               Harm Nijveen and   
                    Lei Yan and   
                 Xiang Zhou and   
         Robert W. Williams and   
                    Pjotr Prins   \pkgGeneNetwork: framework for web-based
                                  genetics . . . . . . . . . . . . . . . . 25:1--25:3
           Conrad Sanderson and   
                    Ryan Curtin   \pkgArmadillo: a template-based C++
                                  library for linear algebra . . . . . . . 26:1--26:2
             Simon J. Greenhill   \pkgPhylogemetric: A Python library for
                                  calculating phylogenetic network metrics 28:1--28:1
        Christian T. Jacobs and   
               Alexandros Avdis   \pkgGit-RDM: A research data management
                                  plugin for the Git version control
                                  system . . . . . . . . . . . . . . . . . 29:1--29:2

Journal of Open Source Software
Volume 1, Number 3, July, 2016

           Christopher R. Madan   \pkgPrism: Multiple spline regression
                                  with regularization, dimensionality
                                  reduction, and feature selection . . . . 31:1--31:3
              Nitin Madnani and   
             Anastassia Loukina   \pkgRSMTool: collection of tools
                                  building and evaluating automated
                                  scoring models . . . . . . . . . . . . . 33:1--33:1
                Michael A. Levy   \pkggwdegree: Improving interpretation
                                  of geometrically-weighted degree
                                  estimates in exponential random graph
                                  models . . . . . . . . . . . . . . . . . 36:1--36:1
                Julia Silge and   
                 David Robinson   \pkgtidytext: Text Mining and Analysis
                                  Using Tidy Data Principles in R  . . . . 37:1--37:3
              Simon D. W. Frost   \pkgGillespie.jl: Stochastic Simulation
                                  Algorithm in Julia . . . . . . . . . . . 42:1--42:1

Journal of Open Source Software
Volume 1, Number 4, August, 2016

                 Zoran Cuckovic   Advanced viewshed analysis: a Quantum
                                  GIS plug-in for the analysis of visual
                                  landscapes . . . . . . . . . . . . . . . 32:1--32:3
             Simon Bogutzky and   
     Jan Christoph Schrader and   
          Nassrin Hajinejad and   
            Barbara Grüter   \pkgPsychoPhysioCollector: A
                                  Smartphone-Based Data Collection App for
                                  Psychophysiological Research . . . . . . 40:1--40:3
      Christopher D. Cooper and   
        Natalia C. Clementi and   
            Gilbert Forsyth and   
                Lorena A. Barba   \pkgPyGBe: Python, GPUs and Boundary
                                  elements for biomolecular electrostatics 43:1--43:1
                  Samuel Hinton   \pkgChainConsumer  . . . . . . . . . . . 45:1--45:2
             Claudia Vitolo and   
             Andrew Russell and   
                   Allan Tucker   \pkgrdefra: Interact with the UK AIR
                                  Pollution Database from DEFRA  . . . . . 51:1--51:2
     Timothée Giraud and   
                Nicolas Lambert   \pkgcartography: Create and Integrate
                                  Maps in your R Workflow  . . . . . . . . 54:1--54:2

Journal of Open Source Software
Volume 1, Number 5, September, 2016

             C. Titus Brown and   
                     Luiz Irber   \pkgsourmash: a library for MinHash
                                  sketching of DNA . . . . . . . . . . . . 27:1--27:1
         Robert T. McGibbon and   
 Carlos X. Hernández and   
        Matthew P. Harrigan and   
             Steven Kearnes and   
         Mohammad M. Sultan and   
     Stanis\law Jastrzebski and   
            Brooke E. Husic and   
                 Vijay S. Pande   \pkgOsprey: Hyperparameter Optimization
                                  for Machine Learning . . . . . . . . . . 34:1--34:2
             Simon Bogutzky and   
             Phillip Marsch and   
       Licínio Roque and   
          Nassrin Hajinejad and   
            Barbara Grüter   \pkgPsychoPhysioPipeline: A Processing
                                  and Analysis Pipeline for
                                  Psychophysiological Research . . . . . . 41:1--41:3
          Dirk Eddelbuettel and   
                        Wush Wu   \pkgRcppCNPy: Read-Write Support for
                                  NumPy Files in R . . . . . . . . . . . . 55:1--55:1
       Jonathan A. Michaels and   
      Hansjörg Scherberger   \pkghebbRNN: A Reward-Modulated Hebbian
                                  Learning Rule for Recurrent Neural
                                  Networks . . . . . . . . . . . . . . . . 60:1--60:2
                    Dean Attali   \pkgezknitr: Avoid the Typical Working
                                  Directory Pain When Using `\pkgknitr'    75:1--75:1
           Paul Constantine and   
                Ryan Howard and   
               Andrew Glaws and   
               Zachary Grey and   
                  Paul Diaz and   
                Leslie Fletcher   \pkgPython Active-subspaces Utility
                                  Library  . . . . . . . . . . . . . . . . 79:1--79:1

Journal of Open Source Software
Volume 1, Number 6, October, 2016

          Eetu Mäkelä   \pkgLAS: an integrated language analysis
                                  tool for multiple languages  . . . . . . 35:1--35:2
          Sebastian Bocquet and   
              Faustin W. Carter   \pkgpygtc: beautiful parameter
                                  covariance plots (aka. Giant Triangle
                                  Confusograms)  . . . . . . . . . . . . . 46:1--46:3
                   Kyle Barbary   \pkgSEP: Source Extractor as a library   58:1--58:2
                      Carl Ganz   \pkgrintrojs: A Wrapper for the
                                  \pkgIntro.js Library . . . . . . . . . . 63:1--63:1
             Andrew J. Page and   
           Sascha Steinbiss and   
                 Ben Taylor and   
            Torsten Seemann and   
            Jacqueline A. Keane   \pkgGFF3toEMBL: Preparing annotated
                                  assemblies for submission to EMBL  . . . 80:1--80:1
    Christos Theodoropoulos and   
       Nikolaos Skoulikidis and   
              Anastasios Stamou   \pkgHabfuzz: A tool to calculate the
                                  instream hydraulic habitat suitability
                                  using fuzzy logic and fuzzy Bayesian
                                  inference  . . . . . . . . . . . . . . . 82:1--82:2
           Manuel Holtgrewe and   
                   Dieter Beule   \pkgVCFPy: a Python 3 library with good
                                  support for both reading and writing VCF 85:1--85:1
               Danny Arends and   
                    Yang Li and   
        Gudrun A. Brockmann and   
          Ritsert C. Jansen and   
         Robert W. Williams and   
                    Pjotr Prins   Correlation Trait Loci (CTL) mapping:
                                  phenotype network inference subject to
                                  genotype . . . . . . . . . . . . . . . . 87:1--87:4
           Zachary M. Jones and   
             Fridolin J. Linder   \pkgedarf: Exploratory Data Analysis
                                  using Random Forests . . . . . . . . . . 92:1--92:4

Journal of Open Source Software
Volume 1, Number 7, November, 2016

            Matt Germonprez and   
              Thomas Gurney and   
Sai Uday Shankar Korlimarla and   
                   Robin Gandhi   \pkgDoSOCS: A System for \pkgSPDX 2.0
                                  Document Creation and Storage  . . . . . 38:1--38:1
 Guillermo Hernández and   
     Francisco Fernández   \pkgxpecgen: A program to calculate
                                  X-ray spectra generated in tungsten
                                  anodes . . . . . . . . . . . . . . . . . 62:1--62:2
       Philipp H. Boersch-Supan   \pkgrucrdtw: Fast time series
                                  subsequence search in R  . . . . . . . . 100:1--100:2
                 Sean M. Hughes   \pkgplater: Read, Tidy, and Display Data
                                  from Microtiter Plates . . . . . . . . . 106:1--106:1
                 Rene L. Warren   \pkgRAILS and \pkgCobbler: Scaffolding
                                  and automated finishing of draft genomes
                                  using long DNA sequences . . . . . . . . 116:1--116:2

Journal of Open Source Software
Volume 1, Number 8, December, 2016

                    Markus Raab   \pkgElektra: universal framework to
                                  access configuration parameters  . . . . 44:1--44:2
       Nicholas M. Van Horn and   
                Aaron Beveridge   \pkgMassMine: Your Access To Data  . . . 50:1--50:1
             Claudia Vitolo and   
                Peter Wells and   
              Martin Dobias and   
                Wouter Buytaert   \pkgfuse: An R package for ensemble
                                  Hydrological Modelling . . . . . . . . . 52:1--52:2
            Rodrigo V. Honorato   \pkgCAZy-parser a way to extract
                                  information from the Carbohydrate-Active
                                  enZYmes Database . . . . . . . . . . . . 53:1--53:1
               Julien Ponge and   
            Yannick Loiseau and   
Frédéric Le Mouël and   
             Nicolas Stouls and   
       Philippe Charri\`ere and   
             Daniel Petisme and   
           Sylvain Desgrais and   
                  Franck Verrot   Eclipse Golo . . . . . . . . . . . . . . 93:1--93:1
             Kevin DeSimone and   
                Ariel Rokem and   
                Keith Schneider   \pkgpopeye: a population receptive field
                                  estimation tool  . . . . . . . . . . . . 103:1--103:1
         Rémi Rampin and   
         Fernando Chirigati and   
              Dennis Shasha and   
             Juliana Freire and   
                  Vicky Steeves   \pkgReproZip: The Reproducibility Packer 107:1--107:3
           Matthew J. Wakefield   \pkgSurvivalVolume: interactive volume
                                  threshold survival graphs  . . . . . . . 111:1--111:2
             Andrew J. Page and   
                 Ben Taylor and   
            Jacqueline A. Keane   Multilocus sequence typing by blast from
                                  de novo assemblies against PubMLST . . . 118:1--118:2
                     Seward Lee   \pkgfinreportr: Financial Data from U.S.
                                  Securities and Exchange Commission . . . 119:1--119:1
                    Brian McFee   \pkgresampy: efficient sample rate
                                  conversion in Python . . . . . . . . . . 125:1--125:1
                 Jeff Goldsmith   \pkgvbvs.concurrent: Fitting Methods for
                                  the Functional Linear Concurrent Model   141:1--141:1


Journal of Open Source Software
Volume 2, Number 9, January, 2017

                 Claudia Vitolo   \pkghddtools: Hydrological Data
                                  Discovery Tools  . . . . . . . . . . . . 56:1--56:2
               Kelly A. Kearney   \pkgecopath\_matlab: A Matlab-based
                                  implementation of the Ecopath food web
                                  algorithm  . . . . . . . . . . . . . . . 64:1--64:2
               Andrew Halterman   \pkgMordecai: Full Text Geoparsing and
                                  Event Geocoding  . . . . . . . . . . . . 91:1--91:1
                 Jon Herman and   
                     Will Usher   \pkgSALib: An open-source Python library
                                  for Sensitivity Analysis . . . . . . . . 97:1--97:2
             Clayton Norris and   
             Philip Schrodt and   
                   John Beieler   \pkgPETRARCH2: Another Event Coding
                                  Program  . . . . . . . . . . . . . . . . 133:1--133:1
           Benjamin Naecker and   
       Niru Maheswaranathan and   
              Surya Ganguli and   
                 Stephen Baccus   \pkgPyret: A Python package for analysis
                                  of neurophysiology data  . . . . . . . . 137:1--137:1
            Kristian Jensen and   
         Joao G. R. Cardoso and   
          Nikolaus Sonnenschein   \pkgOptlang: An algebraic modeling
                                  language for mathematical optimization   139:1--139:1
                  Camille Scott   \pkgshmlast: An improved implementation
                                  of Conditional Reciprocal Best Hits with
                                  LAST and Python  . . . . . . . . . . . . 142:1--142:4
        Eduardo S. M. Alexandre   \pkgLimarka: making possible Brazilian
                                  students writing dissertation and thesis
                                  with Markdown  . . . . . . . . . . . . . 169:1--169:1

Journal of Open Source Software
Volume 2, Number 10, February, 2017

                Michel Lang and   
               Bernd Bischl and   
                   Dirk Surmann   \pkgbatchtools: Tools for R to work on
                                  batch systems  . . . . . . . . . . . . . 135:1--135:2
          Bryna J. Hazelton and   
           Daniel C. Jacobs and   
          Jonathan C. Pober and   
              Adam P. Beardsley   \pkgpyuvdata: an interface for
                                  astronomical interferometeric datasets
                                  in python  . . . . . . . . . . . . . . . 140:1--140:1
       Matthew M. McCormick and   
            Mark L. Palmeri and   
Jean-Christophe Fillion-Robin and   
                Stephen Aylward   \pkgSlicerITKUltrasound: A $3$D Slicer
                                  extension for scan conversion of B-mode
                                  and next-generation ultrasound imaging
                                  modalities . . . . . . . . . . . . . . . 153:1--153:1
           Devarshi Ghoshal and   
            Valerie Hendrix and   
                William Fox and   
    Sowmya Balasubhramanian and   
           Lavanya Ramakrishnan   \pkgFRIEDA: Flexible Robust Intelligent
                                  Elastic Data Management Framework  . . . 164:1--164:3
        R. Daniel Kortschak and   
       Josh Bleecher Snyder and   
         Manolis Maragkakis and   
               David L. Adelson   \pkgbíogo: a simple high-performance
                                  bioinformatics toolkit for the Go
                                  language . . . . . . . . . . . . . . . . 167:1--167:1
        R. Daniel Kortschak and   
          Brent S. Pedersen and   
               David L. Adelson   \pkgbíogo/hts: high throughput sequence
                                  handling for the Go language . . . . . . 168:1--168:1
         Bradley C. Boehmke and   
       Robert T. Montgomery and   
           Jeffrey A. Ogden and   
                Jason K. Freels   \pkgKraljicMatrix: An R package for
                                  implementing the Kraljic Matrix to
                                  strategically analyze a firm's
                                  purchasing portfolio . . . . . . . . . . 170:1--170:2
                David Ardia and   
                 Kris Boudt and   
    Jean-Philippe Gagnon-Fleury   \pkgRiskPortfolios: Computation of
                                  Risk-Based Portfolios in R . . . . . . . 171:1--171:1
                David Ardia and   
                  Keven Bluteau   \pkgnse: Computation of Numerical
                                  Standard Errors in R . . . . . . . . . . 172:1--172:2
              Anthony Caravaggi   \pkgremBoot: An R package for Random
                                  Encounter Modelling  . . . . . . . . . . 176:1--176:3
             Adam H. Sparks and   
             Tomislav Hengl and   
                  Andrew Nelson   \pkgGSODR: Global Summary Daily Weather
                                  Data in R  . . . . . . . . . . . . . . . 177:1--177:2

Journal of Open Source Software
Volume 2, Number 11, March, 2017

            Andy Yu Zhu Yao and   
                     David Kane   \pkgwalkr: MCMC Sampling from
                                  Non-Negative Convex Polytopes  . . . . . 61:1--61:1
            Pranay Seshadri and   
                 Geoffrey Parks   \pkgEffective-Quadratures (EQ):
                                  Polynomials for Computational
                                  Engineering Studies  . . . . . . . . . . 166:1--166:2
             Julia Niskanen and   
              Elina Salmela and   
                    Hannes Lohi   \pkgAncesTrim --- a tool for trimming
                                  complex pedigrees  . . . . . . . . . . . 179:1--179:1
        Miguel de Val-Borro and   
         Martin A. Cordiner and   
          Stefanie N. Milam and   
             Steven B. Charnley   \pkgCine: Line excitation by infrared
                                  fluorescence in cometary atmospheres . . 182:1--182:2
            Stuart W. D. Grieve   \pkgspatial-efd: A spatial-aware
                                  implementation of elliptical Fourier
                                  analysis . . . . . . . . . . . . . . . . 189:1--189:2
           Charles Crabtree and   
              Michael J. Nelson   \pkgPlotrr: Functions for making visual
                                  exploratory data analysis with nested
                                  data easier  . . . . . . . . . . . . . . 190:1--190:2
          Scott Chamberlain and   
           Jeffrey W. Hollister   \pkglawn: An R client for the Turf
                                  Javascript Library for Geospatial
                                  Analysis . . . . . . . . . . . . . . . . 194:1--194:1
                  Matti Pastell   \pkgWeave.jl: Scientific Reports Using
                                  Julia  . . . . . . . . . . . . . . . . . 204:1--204:1
             Leland McInnes and   
                 John Healy and   
                   Steve Astels   \pkghdbscan: Hierarchical density based
                                  clustering . . . . . . . . . . . . . . . 205:1--205:2
             Joshua Higgins and   
             Violeta Holmes and   
                  Colin Venters   \pkgVCC: A framework for building
                                  containerized reproducible cluster
                                  software environments  . . . . . . . . . 208:1--208:1
                    Chapman Siu   \pkgRamble: Parser Combinator for R  . . 209:1--209:1

Journal of Open Source Software
Volume 2, Number 12, April, 2017

              Nicolas Carpi and   
           Alexander Minges and   
                  Matthieu Piel   \pkgeLabFTW: An open source laboratory
                                  notebook for research labs . . . . . . . 146:1--146:1
 Carlos X. Hernández and   
        Matthew P. Harrigan and   
         Mohammad M. Sultan and   
                 Vijay S. Pande   \pkgMSMExplorer: Data Visualizations for
                                  Biomolecular Dynamics  . . . . . . . . . 188:1--188:2
           Nicholas Cortale and   
                 Dylan McNamara   \pkgskedm: Empirical Dynamic Modeling    207:1--207:2
                   Geoff Boeing   \pkgOSMnx: A Python package to work with
                                  graph-theoretic OpenStreetMap street
                                  networks . . . . . . . . . . . . . . . . 215:1--215:4
                 Adam H. Sparks   \pkggetCRUCLdata: Use and Explore
                                  \pkgCRU CL v. 2.0 Climatology Elements
                                  in R . . . . . . . . . . . . . . . . . . 230:1--230:1
                    Chris Mutel   \pkgBrightway: An open source framework
                                  for Life Cycle Assessment  . . . . . . . 236:1--236:2
            Sven N. Willner and   
             Corinne Hartin and   
                 Robert Gieseke   \pkgpyhector: A Python interface for the
                                  simple climate model Hector  . . . . . . 248:1--248:2

Journal of Open Source Software
Volume 2, Number 13, May, 2017

      Kolby L. Weisenburger and   
         Joseph Huehnerhoff and   
          Emily M. Levesque and   
                  Philip Massey   \pkgacronym: An Automatic Reduction
                                  Pipeline for Astronomical Images . . . . 102:1--102:2
               Antti Kamppi and   
            Esko Pekkarinen and   
             Janne Virtanen and   
Joni-Matti Määttä and   
         Juho Järvinen and   
           Lauri Matilainen and   
                Mikko Teuho and   
Timo D. Hämäläinen   \pkgKactus2: A graphical EDA tool built
                                  on the IP-XACT standard  . . . . . . . . 151:1--151:1
         Bradley C. Boehmke and   
                Jason K. Freels   \pkglearningCurve: An implementation of
                                  Crawford's and Wright's learning curve
                                  production functions . . . . . . . . . . 202:1--202:1
                    Luca Romano   \pkgYoungTab . . . . . . . . . . . . . . 221:1--221:1
              Davide Gerosa and   
             Michele Vallisneri   \pkgfilltex: Automatic queries to ADS
                                  and INSPIRE databases to fill LaTex
                                  bibliography . . . . . . . . . . . . . . 222:1--222:1
            Marie E. Rognes and   
         Patrick E. Farrell and   
             Simon W. Funke and   
              Johan E. Hake and   
           Molly M. C. Maleckar   \pkgcbcbeat: an adjoint-enabled
                                  framework for computational cardiac
                                  electrophysiology  . . . . . . . . . . . 224:1--224:1
             Abhinav Tushar and   
              Nicholas G. Reich   \pkgflusight: interactive visualizations
                                  for infectious disease forecasts . . . . 231:1--231:2
            Kevin D. Murray and   
             Justin O. Borevitz   \pkglibqcpp: A C++14 sequence quality
                                  control library  . . . . . . . . . . . . 232:1--232:1
             Andrew J. Page and   
                Martin Hunt and   
            Torsten Seemann and   
            Jacqueline A. Keane   \pkgSaffronTree: Fast, reference-free
                                  pseudo-phylogenomic trees from reads or
                                  contigs  . . . . . . . . . . . . . . . . 243:1--243:2
                    Chris Mutel   \pkgPandarus: GIS toolkit for
                                  regionalized life cycle assessment . . . 244:1--244:1
             Benjamin J. Morgan   \pkglattice\_mc: A Python Lattice-Gas
                                  Monte Carlo Module . . . . . . . . . . . 247:1--247:2
                     Gaute Hope   \pkgIBCAO\_py: A matplotlib library for
                                  using the International Bathymetric
                                  Chart of the Arctic Ocean with cartopy
                                  and matplotlib . . . . . . . . . . . . . 250:1--250:2
             James P. Howard II   Virtual Bumblebees Artificial Life
                                  Simulation . . . . . . . . . . . . . . . 256:1--256:1
                  Andreas Mayer   \pkgNoisyopt: A Python library for
                                  optimizing noisy functions . . . . . . . 258:1--258:1
                 Roger A. Light   \pkgMosquitto: server and client
                                  implementation of the MQTT protocol  . . 265:1--265:2

Journal of Open Source Software
Volume 2, Number 14, June, 2017

           Sean M. Anderson and   
            Bernardo S. Mendoza   \pkgSHGYield . . . . . . . . . . . . . . 242:1--242:2
                 John P. Didion   \pkgxphyle: Extraordinarily simple file
                                  handling . . . . . . . . . . . . . . . . 255:1--255:1
                 Rory Nolan and   
            Sergi Padilla-Parra   \pkgfilesstrings: An R package for file
                                  and string manipulation  . . . . . . . . 260:1--260:2
              Sebastian Raschka   \pkgBioPandas: Working with molecular
                                  structures in \pkgpandas DataFrames  . . 279:1--279:1
          Bennett Kleinberg and   
               Maximilian Mozes   Web-based text anonymization with
                                  \pkgNode.js: Introducing NETANOS (Named
                                  entity-based Text Anonymization for Open
                                  Science) . . . . . . . . . . . . . . . . 293:1--293:2
               Taylor B. Arnold   \pkgkerasR: R Interface to the Keras
                                  Deep Learning Library  . . . . . . . . . 296:1--296:1
               Mark Padgham and   
             Robin Lovelace and   
         Maëlle Salmon and   
                      Bob Rudis   \pkgosmdata  . . . . . . . . . . . . . . 305:1--305:1

Journal of Open Source Software
Volume 2, Number 15, July, 2017

                 Dominik Moritz   Text detection in screen images with a
                                  Convolutional Neural Network . . . . . . 235:1--235:1
            Daniel Standage and   
                Ali Aliyari and   
              Lisa J. Cohen and   
          Michael R. Crusoe and   
                   Tim Head and   
                 Luiz Irber and   
       Shannon E. K. Joslin and   
             N. B. Kingsley and   
            Kevin D. Murray and   
             Russell Neches and   
              Camille Scott and   
                 Ryan Shean and   
           Sascha Steinbiss and   
                Cait Sydney and   
                 C. Titus Brown   \pkgkhmer release v2.1: software for
                                  biological sequence analysis . . . . . . 272:1--272:2
             Alexander Bock and   
              Emil Axelsson and   
                Karl Bladin and   
             Jonathas Costa and   
                 Gene Payne and   
            Matthew Territo and   
               Joakim Kilby and   
           Masha Kuznetsova and   
              Carter Emmart and   
                Anders Ynnerman   \pkgOpenSpace: An open-source
                                  astrovisualization framework . . . . . . 281:1--281:1
        Bede Constantinides and   
             David L. Robertson   \pkgKindel: indel-aware consensus for
                                  nucleotide sequence alignments . . . . . 282:1--282:2
          Daniele De Vecchi and   
           Fabio Dell'Acqua and   
        Daniel Aurelio Galeazzo   \pkgCLOOPSy --- Copernicus Land cOver
                                  crOwdsourcing Platform for
                                  Sentinel-based mapping . . . . . . . . . 291:1--291:2
             Nima S. Hejazi and   
                 Weixin Cai and   
                Alan E. Hubbard   \pkgbiotmle: Targeted Learning for
                                  Biomarker Discovery  . . . . . . . . . . 295:1--295:4
             Anush Krishnan and   
            Olivier Mesnard and   
                Lorena A. Barba   \pkgcuIBM: a GPU-based immersed boundary
                                  method code  . . . . . . . . . . . . . . 301:1--301:1

Journal of Open Source Software
Volume 2, Number 16, August, 2017

          Paul Francis Harrison   \pkgVaristran: Anscombe's variance
                                  stabilizing transformation for RNA-seq
                                  gene expression data . . . . . . . . . . 257:1--257:1
                   Danny Hermes   Helper for Bézier Curves, Triangles, and
                                  Higher Order Objects . . . . . . . . . . 267:1--267:3
             Pi-Yueh Chuang and   
                Lorena A. Barba   \pkgAmgXWrapper: An interface between
                                  \pkgPETSc and the NVIDIA \pkgAmgX
                                  library  . . . . . . . . . . . . . . . . 280:1--280:1
            Lucas A. Wilson and   
             John M. Fonner and   
              Jason Allison and   
              Oscar Esteban and   
                Harry Kenya and   
                Marshall Lerner   \pkgLauncher: A simple tool for
                                  executing high throughput computing
                                  workloads  . . . . . . . . . . . . . . . 289:1--289:2
           Edmund Noel Dawe and   
         Piti Ongmongkolkul and   
                  Giordon Stark   \pkgroot\_numpy: The interface between
                                  \pkgROOT and \pkgNumPy . . . . . . . . . 307:1--307:2
         Simon J. van Heeringen   \pkggenomepy: download genomes the easy
                                  way  . . . . . . . . . . . . . . . . . . 320:1--320:1
             Konstantin Stadler   The country converter \pkgcoco --- a
                                  Python package for converting country
                                  names between different classification
                                  schemes  . . . . . . . . . . . . . . . . 332:1--332:2
         Maëlle Salmon and   
       Sreekanth Vakacherla and   
              Carles Mil\`a and   
         Julian D. Marshall and   
                  Cathryn Tonne   \pkgrtimicropem: an R package supporting
                                  the analysis of RTI MicroPEM output
                                  files  . . . . . . . . . . . . . . . . . 333:1--333:1
               Mathew W. McLean   \pkgRefManageR: Import and Manage BibTeX
                                  and BibLaTeX References in R . . . . . . 338:1--338:2
                 P. James Joyce   \pkgLcopt --- An interactive tool for
                                  creating fully parameterised Life Cycle
                                  Assessment (LCA) foreground models . . . 339:1--339:1
          Francesco Strozzi and   
       Raoul Jean Pierre Bonnal   \pkgPipengine: an ultra light YAML-based
                                  pipeline execution engine  . . . . . . . 341:1--341:2
        Juanjo Bazán and   
           Oscar Gonzalez-Recio   \pkgNimbus: a Ruby gem to implement
                                  Random Forest algorithms in a genomic
                                  selection context  . . . . . . . . . . . 351:1--351:3
            Thomas Cokelaer and   
    Dimitri Desvillechabrol and   
            Rachel Legendre and   
          Mélissa Cardon   '\pkgSequana': a Set of Snakemake NGS
                                  pipelines  . . . . . . . . . . . . . . . 352:1--352:2
        Sebastiano Ferraris and   
    Dzhoshkun Ismail Shakir and   
     Johannes Van Der Merwe and   
                Willy Gsell and   
                Jan Deprest and   
                Tom Vercauteren   \pkgBruker2nifti: Magnetic Resonance
                                  Images converter from Bruker
                                  \pkgParaVision to \pkgNifti format . . . 354:1--354:2
               Nicholas Tierney   \pkgvisdat: Visualising Whole Data
                                  Frames . . . . . . . . . . . . . . . . . 355:1--355:2
            Alicia N. Schep and   
            Sarah K. Kummerfeld   \pkgiheatmapr: Interactive complex
                                  heatmaps in R  . . . . . . . . . . . . . 359:1--359:1
              Philipp S. Sommer   The \pkgpsyplot interactive
                                  visualization framework  . . . . . . . . 363:1--363:1
           Tanner C. Hobson and   
             Mathieu Doucet and   
         Ricardo M. Ferraz Leal   \pkgDjango Remote Submission . . . . . . 366:1--366:2
             Benjamin J. Morgan   \pkgbsym: A basic symmetry module  . . . 370:1--370:2

Journal of Open Source Software
Volume 2, Number 17, September, 2017

                Sepand Haghighi   \pkgPyrgg: Python Random Graph Generator 331:1--331:2
     Ashlee N. Ford Versypt and   
           Grace K. Harrell and   
            Alexandra N. McPeak   \pkgACEInhibPKPD: An open-source MATLAB
                                  app for a
                                  pharmacokinetic/pharmacodynamic model of
                                  ACE inhibition . . . . . . . . . . . . . 340:1--340:2
     Adrian M. Price-Whelan and   
          Daniel Foreman-Mackey   \pkgschwimmbad: A uniform interface to
                                  parallel processing pools in Python  . . 357:1--357:2
               Marco van Hulten   \pkgComPlot: Comparison Plotter to
                                  visually evaluate ocean model
                                  simulations  . . . . . . . . . . . . . . 368:1--368:4
            Sebastien Binet and   
              Bastian Wieck and   
                David Blyth and   
            Emmanuel Busato and   
       Michaël Ughetto and   
                   Peter Waller   \pkgGo-HEP: libraries for High Energy
                                  Physics analyses in Go . . . . . . . . . 372:1--372:4
                Shane J. Latham   \pkgarray\_split: Multi-dimensional
                                  array partitioning . . . . . . . . . . . 373:1--373:2
                   Jakob Bossek   \pkgmcMST: A Toolbox for the
                                  Multi-Criteria Minimum Spanning Tree
                                  Problem  . . . . . . . . . . . . . . . . 374:1--374:2
      Pradeep Reddy Raamana and   
            Stephen C. Strother   \pkgPython class defining a machine
                                  learning dataset ensuring key-based
                                  correspondence and maintaining integrity 382:1--382:1
        Benjamin W. L. Margolis   \pkgSimuPy: A Python framework for
                                  modeling and simulating dynamical
                                  systems  . . . . . . . . . . . . . . . . 396:1--396:1
             Travis Kessler and   
               John Hunter Mack   \pkgECNet: Large scale machine learning
                                  projects for fuel property prediction    401:1--401:2
                   Michael Kane   \pkgbittrex: An R client for the Bittrex
                                  Crypto-Currency Exchange . . . . . . . . 402:1--402:1
             Adam H. Sparks and   
               Mark Padgham and   
             Hugh Parsonage and   
                Keith Pembleton   \pkgbomrang: Fetch Australian Government
                                  Bureau of Meteorology Data in R  . . . . 411:1--411:2

Journal of Open Source Software
Volume 2, Number 18, October, 2017

        R. Daniel Kortschak and   
               David L. Adelson   \pkgbíogo/ncbi: interfaces to NCBI
                                  services for the Go language . . . . . . 234:1--234:2
Offray Vladimir Luna Cárdenas   \pkgGrafoscopio: A moldable tool for
                                  literate computing and reproducible
                                  research . . . . . . . . . . . . . . . . 251:1--251:2
            Thomas Cokelaer and   
                  Juergen Hasch   \pkg'Spectrum': Spectral Analysis in
                                  Python . . . . . . . . . . . . . . . . . 348:1--348:2
                  Marcin Wojdyr   \pkgUglyMol: a WebGL macromolecular
                                  viewer focused on the electron density   350:1--350:2
           Conrad Sanderson and   
                    Ryan Curtin   \pkggmm\_diag and \pkggmm\_full: C++
                                  classes for multi-threaded Gaussian
                                  mixture models and
                                  Expectation-Maximisation . . . . . . . . 365:1--365:2
             Gabriele Rovigatti   Production Function Estimation in R: The
                                  \pkgprodest Package  . . . . . . . . . . 371:1--371:1
                 Sara Mahar and   
                 Matthew Bellis   \pkghmis: A python tool to visualize and
                                  analyze HMIS data  . . . . . . . . . . . 384:1--384:2
         Adrian M. Price-Whelan   \pkgGala: A Python package for galactic
                                  dynamics . . . . . . . . . . . . . . . . 388:1--388:2
                    Ben Lauwens   \pkgResumableFunctions: C# sharp style
                                  generators for Julia . . . . . . . . . . 400:1--400:2
           Philip Stegmaier and   
              Alexander Kel and   
                Edgar Wingender   \pkggeneXplainR: An R interface for the
                                  geneXplain platform  . . . . . . . . . . 412:1--412:3
                 Tim Folsom and   
                   V. P. Nagraj   \pkghei: Calculate Healthy Eating Index
                                  (HEI) Scores . . . . . . . . . . . . . . 417:1--417:1
Bérénice Batut and   
        Björn Grüning   \pkgENASearch: A Python library for
                                  interacting with ENA's API . . . . . . . 418:1--418:1
          Andrew C. Heusser and   
      Paxton C. Fitzpatrick and   
          Campbell E. Field and   
              Kirsten Ziman and   
              Jeremy R. Manning   \pkgQuail: A Python toolbox for
                                  analyzing and plotting free recall data  424:1--424:2
                 Vanessa Sochat   Singularity Registry: Open Source
                                  Registry for Singularity Images  . . . . 426:1--426:3

Journal of Open Source Software
Volume 2, Number 19, November, 2017

              Kivan Polimis and   
                Ariel Rokem and   
                 Bryna Hazelton   Confidence Intervals for Random Forests
                                  in Python  . . . . . . . . . . . . . . . 124:1--124:4
         Dominique Makowski and   
            Léo Dutriaux   \pkgNeuropsydia.py: A Python Module for
                                  Creating Experiments, Tasks and
                                  Questionnaires . . . . . . . . . . . . . 259:1--259:2
        Natalia C. Clementi and   
            Gilbert Forsyth and   
      Christopher D. Cooper and   
                Lorena A. Barba   \pkgPyGBe-LSPR: Python and GPU
                                  Boundary-integral solver for
                                  electrostatics . . . . . . . . . . . . . 306:1--306:2
      Pradeep Reddy Raamana and   
            Stephen C. Strother   Histogram-weighted Networks for Feature
                                  Extraction, Connectivity and Advanced
                                  Analysis in Neuroscience . . . . . . . . 380:1--380:3
               Yuxuan Zhang and   
                   Jean Bilheux   \pkgImagingReso: A Tool for Neutron
                                  Resonance Imaging  . . . . . . . . . . . 407:1--407:3
                Andrew P. Smith   \pkgUKCensusAPI: python and R interfaces
                                  to the nomisweb UK census data API . . . 408:1--408:1
               Haytham M. Fayek   \pkgMatDL: A Lightweight Deep Learning
                                  Library in MATLAB  . . . . . . . . . . . 413:1--413:2
 Carlos X. Hernández and   
                 Vijay S. Pande   \pkgMDEntropy: Information-Theoretic
                                  Analyses for Molecular Dynamics  . . . . 427:1--427:2
 José Jiménez and   
                  Josep Ginebra   \pkgpyGPGO: Bayesian Optimization for
                                  Python . . . . . . . . . . . . . . . . . 431:1--431:3
           Marcus D. Bloice and   
           Christof Stocker and   
              Andreas Holzinger   \pkgAugmentor: An Image Augmentation
                                  Library for Machine Learning . . . . . . 432:1--432:2
                Philippe Renard   \pkgHytool: an open source MATLAB
                                  toolbox for the interpretation of
                                  hydraulic tests using analytical
                                  solutions  . . . . . . . . . . . . . . . 441:1--441:3
              Henry Kironde and   
         Benjamin D. Morris and   
                 Akash Goel and   
               Andrew Zhang and   
           Akshay Narasimha and   
                Shivam Negi and   
            David J. Harris and   
    Deborah Gertrude Digges and   
                Kapil Kumar and   
            Amritanshu Jain and   
                  Kunal Pal and   
         Kevinkumar Amipara and   
  Prabh Simran Singh Baweja and   
                 Ethan P. White   \pkgRetriever: Data Retrieval Tool . . . 451:1--451:1
                 Carl Boettiger   Generating \pkgCodeMeta Metadata for R
                                  Packages . . . . . . . . . . . . . . . . 454:1--454:1
                George Datseris   \pkgDynamicalBilliards.jl: An
                                  easy-to-use, modular and extendable
                                  Julia package for Dynamical Billiard
                                  systems in two dimensions  . . . . . . . 458:1--458:4

Journal of Open Source Software
Volume 2, Number 20, December, 2017

      Andre Schmeißer and   
            Daniel Burkhart and   
               Dominik Linn and   
         Johannes Schnebele and   
      Manuel Ettmüller and   
             Simone Gramsch and   
                    Walter Arne   \pkgEnsight4Matlab: read, process, and
                                  write files in EnSight\reg Gold format
                                  from C++ or MATLAB\reg . . . . . . . . . 217:1--217:1
              Rohan Dandage and   
             Kausik Chakraborty   \pkgdms2dfe: Comprehensive Workflow for
                                  Analysis of Deep Mutational Scanning
                                  Data . . . . . . . . . . . . . . . . . . 362:1--362:3
                  Ilja Honkonen   High-Dimensional Integrator  . . . . . . 437:1--437:1
           Olivier Delestre and   
Frédéric Darboux and   
      François James and   
               Carine Lucas and   
         Christian Laguerre and   
        Stéphane Cordier   \pkgFullSWOF: Full Shallow-Water
                                  equations for Overland Flow  . . . . . . 448:1--448:1
              Sachin Chitta and   
      Eitan Marder-Eppstein and   
               Wim Meeussen and   
              Vijay Pradeep and   
Adolfo Rodríguez Tsouroukdissian and   
            Jonathan Bohren and   
              David Coleman and   
               Bence Magyar and   
             Gennaro Raiola and   
        Mathias Lüdtke and   
      Enrique Fernandez Perdomo   \pkgros\_control: A generic and simple
                                  control framework for ROS  . . . . . . . 456:1--456:5
                   Ai Okada and   
              Kenichi Chiba and   
              Hiroko Tanaka and   
              Satoru Miyano and   
               Yuichi Shiraishi   A framework for generating interactive
                                  reports for cancer genome analysis . . . 457:1--457:4
               Daniel Suess and   
           Milan Holzäpfel   \pkgmpnum: A matrix product
                                  representation library for Python  . . . 465:1--465:2
               Mark Padgham and   
                Richard Ellison   \pkgbikedata . . . . . . . . . . . . . . 471:1--471:1
              Steve Lockley and   
             Claudio Benghi and   
          Martin \vCerný   \pkgXbim.Essentials: a library for
                                  interoperable building information
                                  applications . . . . . . . . . . . . . . 473:1--473:3
                David J. Harris   An easy-to-use \pkgp5.js $3$D object
                                  picker for visual artists  . . . . . . . 475:1--475:2
                     Sam Albers   \pkgtidyhydat: Extract and Tidy Canadian
                                  Hydrometric Data . . . . . . . . . . . . 511:1--511:4
                  Sinan Shi and   
David Pérez-Suárez and   
               Steve Harris and   
            Niall MacCallum and   
              David Brealey and   
              Mervyn Singer and   
             James Hetherington   Critical care data processing tools  . . 513:1--513:4


Journal of Open Source Software
Volume 3, Number 21, January, 2018

                 Brandon LeBeau   \pkghighlightHTML: CSS Formatting of R
                                  Markdown Documents . . . . . . . . . . . 185:1--185:2
           Gilbert Marzolin and   
                Olivier Gimenez   Fitting a Gamma--Gompertz survival model
                                  to capture-recapture data collected on
                                  free-ranging animal populations  . . . . 216:1--216:3
          Alexander Lindsay and   
                   Kathryn Huff   \pkgMoltres: finite element based
                                  simulation of molten salt reactors . . . 298:1--298:2
             Jason K. Moore and   
         Antonie van den Bogert   \pkgopty: Software for trajectory
                                  optimization and parameter
                                  identification using direct collocation  300:1--300:4
                  Paul B. Govan   \pkgBayesianNetwork: Interactive
                                  Bayesian Network Modeling and Analysis   425:1--425:2
        Lester James V. Miranda   \pkgPySwarms: a research toolkit for
                                  Particle Swarm Optimization in Python    433:1--433:2
             Jiao Y. Y. Lin and   
               Fahima Islam and   
                      Max Kresh   \pkgMultiphonon: Phonon Density of
                                  States tools for Inelastic Neutron
                                  Scattering Powder Data . . . . . . . . . 440:1--440:2
           Nathan Sheffield and   
               V. P. Nagraj and   
                   Vince Reuter   \pkgsimpleCache: R caching for
                                  reproducible, distributed, large-scale
                                  projects . . . . . . . . . . . . . . . . 463:1--463:1
       Markus J. Ankenbrand and   
                Simon Pfaff and   
           Niklas Terhoeven and   
            Musga Qureischi and   
           Maik Gündel and   
      Clemens L. Weiß and   
               Thomas Hackl and   
             Frank Förster   \pkgchloroExtractor: extraction and
                                  assembly of the chloroplast genome from
                                  whole genome shotgun data  . . . . . . . 464:1--464:3
          Anton Rodenhauser and   
             Wilson W. Good and   
               Brian Zenger and   
                  Jess Tate and   
                 Kedar Aras and   
               Brett Burton and   
                 Rob S. MacLeod   \pkgPFEIFER: Preprocessing Framework for
                                  Electrograms Intermittently Fiducialized
                                  from Experimental Recordings . . . . . . 472:1--472:2
             Pablo G. Garay and   
              Jorge A. Vila and   
              Osvaldo A. Martin   \pkgCheSweet: An application to predict
                                  glycan's chemicals shifts  . . . . . . . 488:1--488:2
            Björn Dahlgren   \pkgpyodesys: Straightforward numerical
                                  integration of ODE systems from Python   490:1--490:2
            Pamphile T. Roy and   
               Sophie Ricci and   
              Romain Dupuis and   
               Robin Campet and   
    Jean-Christophe Jouhaud and   
                 Cyril Fournier   \pkgBATMAN: Statistical analysis for
                                  expensive computer codes made easy . . . 493:1--493:2
          René L. Warren   Visualizing genome synteny with
                                  \pkgxmatchview . . . . . . . . . . . . . 497:1--497:4
        William D. McGinnis and   
                Chapman Siu and   
                   Andre S. and   
                    Hanyu Huang   Category Encoders: a
                                  \pkgscikit-learn-contrib package of
                                  transformers for encoding categorical
                                  data . . . . . . . . . . . . . . . . . . 501:1--501:2
            Jeremy R. Coyle and   
                 Nima S. Hejazi   \pkgorigami: A Generalized Framework for
                                  Cross-Validation in R  . . . . . . . . . 512:1--512:3
          Stephanie J. Spielman   \pkgphyphy: Python package for
                                  facilitating the execution and parsing
                                  of HyPhy standard analyses . . . . . . . 514:1--514:1
            R. Daniel Kortschak   \pkgarrgh: a Go interface to the OpenCPU
                                  R server system  . . . . . . . . . . . . 517:1--517:1
            Björn Dahlgren   \pkgpyneqsys: Solve symbolically defined
                                  systems of non-linear equations
                                  numerically  . . . . . . . . . . . . . . 531:1--531:2
Sébastien Boisgérault   \pkgBitstream --- Binary Data for Humans 541:1--541:2
               Joshua T. Karpel   \pkgIDESolver: a general purpose
                                  integro-differential equation solver . . 542:1--542:2
         William Michael Landau   The \pkgdrake R package: a pipeline
                                  toolkit for reproducibility and
                                  high-performance computing . . . . . . . 550:1--550:1

Journal of Open Source Software
Volume 3, Number 22, February, 2018

            Benny Malengier and   
              Pavol Ki\vson and   
             James Tocknell and   
                Claas Abert and   
           Florian Bruckner and   
           Marc-Antonio Bisotti   \pkgODES: a high level interface to ODE
                                  and DAE solvers  . . . . . . . . . . . . 165:1--165:2
              James Hiebert and   
             Alex J. Cannon and   
             Trevor Murdock and   
              Stephen Sobie and   
                  Arelia Werner   \pkgClimDown: Climate Downscaling in R   360:1--360:1
              Danilo Freire and   
         Robert Myles McDonnell   \pkgprisonbrief: An R package that
                                  returns tidy data from the World Prison
                                  Brief website  . . . . . . . . . . . . . 361:1--361:1
             Shadia Mikhael and   
                     Calum Gray   \pkgMasks2Metrics (M2M): A Matlab
                                  Toolbox for Gold Standard Morphometrics  436:1--436:3
             Dominique Makowski   The \pkgpsycho Package: an Efficient and
                                  Publishing-Oriented Workflow for
                                  Psychological Science  . . . . . . . . . 470:1--470:2
             James P. Howard II   Phonetic Algorithms in R . . . . . . . . 480:1--480:2
                Parker Owan and   
             Cameron Devine and   
               W. Tony Piaskowy   \pkgCoreRobotics: An object-oriented C++
                                  library with cross-language wrappers for
                                  cross-platform robot control . . . . . . 489:1--489:2
              Jeongseok Lee and   
            Michael X. Grey and   
                  Sehoon Ha and   
                Tobias Kunz and   
                 Sumit Jain and   
                  Yuting Ye and   
    Siddhartha S. Srinivasa and   
               Mike Stilman and   
                   C. Karen Liu   \pkgDART: Dynamic Animation and Robotics
                                  Toolkit  . . . . . . . . . . . . . . . . 500:1--500:3
             Roderick Bovee and   
                Nick Greenfield   \pkgFinch: a tool adding dynamic
                                  abundance filtering to genomic
                                  MinHashing . . . . . . . . . . . . . . . 505:1--505:2
               Kevin M. Moerman   \pkgGIBBON: The Geometry and Image-Based
                                  Bioengineering add-On  . . . . . . . . . 506:1--506:4
             Robert Gieseke and   
            Sven N. Willner and   
                Matthias Mengel   \pkgPymagicc: A Python wrapper for the
                                  simple climate model MAGICC  . . . . . . 516:1--516:3
                 Vanessa Sochat   The Experiment Factory: Reproducible
                                  Experiment Containers  . . . . . . . . . 521:1--521:4
                 Taha Zaghdoudi   \pkgivporbit: An R package to estimate
                                  the instrumental variables probit model  523:1--523:1
           Niklas Terhoeven and   
          Jörg Schultz and   
                   Thomas Hackl   \pkgreper: Genome-wide identification,
                                  classification and quantification of
                                  repetitive elements without an assembled
                                  genome . . . . . . . . . . . . . . . . . 527:1--527:4
                   Jakob Bossek   \pkggrapherator: A Modular Multi-Step
                                  Graph Generator  . . . . . . . . . . . . 528:1--528:3
                Nicola Demo and   
              Marco Tezzele and   
                Gianluigi Rozza   \pkgPyDMD: Python Dynamic Mode
                                  Decomposition  . . . . . . . . . . . . . 530:1--530:3
                 Matthew Pitkin   \pkgpsrqpy: a python interface for
                                  querying the ATNF pulsar catalogue . . . 538:1--538:2
                Aleksey Bilogur   \pkgMissingno: a missing data
                                  visualization suite  . . . . . . . . . . 547:1--547:4
                Robert Reinecke   \pkgG$^3$M-f a global gradient-based
                                  groundwater modelling framwork . . . . . 548:1--548:2
        Matilda Åslin and   
              Monika Brandt and   
                 Johan Dahlberg   \pkgCheckQC: Quick quality control of
                                  Illumina sequencing runs . . . . . . . . 556:1--556:2
                   Julia Wrobel   \pkgregister: Registration for
                                  Exponential Family Functional Data . . . 557:1--557:2
                 Chi-Lin Yu and   
                 Ching-Fan Sheu   \pkgEFAshiny: An User-Friendly Shiny
                                  Application for Exploratory Factor
                                  Analysis . . . . . . . . . . . . . . . . 567:1--567:2
                      Anonymous   \pkgChebTools: C++11 (and Python) tools
                                  for working with Chebyshev expansions    569:1--569:3
        Stefanie E. LaZerte and   
                     Sam Albers   \pkgweathercan: Download and format
                                  weather data from Environment and
                                  Climate Change Canada  . . . . . . . . . 571:1--571:2
                 James Tocknell   \pkgh5preserve: Thin wrapper around
                                  \pkgh5py, inspired by \pkgcamel  . . . . 581:1--581:2

Journal of Open Source Software
Volume 3, Number 23, March, 2018

          Lincoln A. Mullen and   
                   Jordan Bratt   \pkgUSAboundaries: Historical and
                                  Contemporary Boundaries of the United
                                  States of America  . . . . . . . . . . . 314:1--314:2
               Nuno Fachada and   
              Agostinho C. Rosa   \pkgmicompm: A MATLAB/Octave toolbox for
                                  multivariate independent comparison of
                                  observations . . . . . . . . . . . . . . 430:1--430:1
           David J. Mulryne and   
                John W. Ronayne   \pkgPyTransport: A Python package for
                                  the calculation of inflationary
                                  correlation functions  . . . . . . . . . 494:1--494:2
                   Pierre Morel   \pkgGramm: grammar of graphics plotting
                                  in Matlab  . . . . . . . . . . . . . . . 568:1--568:4
                 Peter Laurinec   \pkgTSrepr R package: Time Series
                                  Representations  . . . . . . . . . . . . 577:1--577:2
                 Michael Hirsch   \pkgPyMap3D: $3$-D coordinate
                                  conversions for terrestrial and geospace
                                  environments . . . . . . . . . . . . . . 580:1--580:2
                 John Mount and   
                     Nina Zumel   The \pkgvtreat R package: a
                                  statistically sound data processor for
                                  predictive modeling  . . . . . . . . . . 584:1--584:2
          Donald E. Willcox and   
                Michael Zingale   \pkgpynucastro: an interface to nuclear
                                  reaction rates and code generator for
                                  reaction network equations . . . . . . . 588:1--588:3
               Sander Wahls and   
        Shrinivas Chimmalgi and   
                 Peter J. Prins   \pkgFNFT: A Software Library for
                                  Computing Nonlinear Fourier Transforms   597:1--597:2
                George Datseris   \pkgDynamicalSystems.jl: A Julia
                                  software library for chaos and nonlinear
                                  dynamics . . . . . . . . . . . . . . . . 598:1--598:5
             Andreas Bender and   
                Alexander Bauer   \pkgcoalitions: Coalition probabilities
                                  in multi-party democracies . . . . . . . 606:1--606:2
         Grega Vrban\vci\vc and   
         Lucija Brezo\vcnik and   
              Uro\vs Mlakar and   
             Du\vsan Fister and   
              Iztok Fister, Jr.   \pkgNiaPy: Python microframework for
                                  building nature-inspired algorithms  . . 613:1--613:3
                    Joe Thorley   \pkgcheckr: An R package for Assertive
                                  Programming  . . . . . . . . . . . . . . 624:1--624:1
            Konstantinos Vantas   \pkghydroscoper: R interface to the
                                  Greek National Data Bank for
                                  Hydrological and Meteorological
                                  Information  . . . . . . . . . . . . . . 625:1--625:2
                 Rory Nolan and   
            Sergi Padilla-Parra   \pkgijtiff: An R package providing TIFF
                                  I/O for ImageJ users . . . . . . . . . . 633:1--633:2
           Alessandro Gasparini   \pkgcomorbidity: An R package for
                                  computing comorbidity scores . . . . . . 648:1--648:3
          Lincoln A. Mullen and   
             Kenneth Benoit and   
                   Os Keyes and   
           Dmitry Selivanov and   
                 Jeffrey Arnold   Fast, Consistent Tokenization of Natural
                                  Language Text  . . . . . . . . . . . . . 655:1--655:3

Journal of Open Source Software
Volume 3, Number 24, April, 2018

            Björn Dahlgren   \pkgChemPy: A package useful for
                                  chemistry written in Python  . . . . . . 565:1--565:2
     Sergio Ibarra-Espinosa and   
              Daniel Schuch and   
       Edmilson Dias de Freitas   \pkgeixport: An R package to export
                                  emissions to atmospheric models  . . . . 607:1--607:4
        Giuseppe Cardellini and   
                    Chris Mutel   \pkgTemporalis: an open source software
                                  for dynamic LCA  . . . . . . . . . . . . 612:1--612:2
        Patrick K. Mogensen and   
       Asbjòrn N. Riseth   \pkgOptim: A mathematical optimization
                                  package for Julia  . . . . . . . . . . . 615:1--615:3
               Daniel Amsel and   
       André Billion and   
         Andreas Vilcinskas and   
             Frank Förster   \pkgmicroPIECE --- microRNA pipeline
                                  enhanced by CLIP experiments . . . . . . 616:1--616:4
               Louise A. Dennis   The MCAPL Framework including the Agent
                                  Infrastructure Layer and Agent Java
                                  Pathfinder . . . . . . . . . . . . . . . 617:1--617:2
              Sebastian Raschka   \pkgMLxtend: Providing machine learning
                                  and data science utilities and
                                  extensions to Python's scientific
                                  computing stack  . . . . . . . . . . . . 638:1--638:2
       Mordechai (Moti) Ben-Ari   \pkgLearnSAT: A SAT Solver for Education 639:1--639:2
               Casey Youngflesh   \pkgMCMCvis: Tools to Visualize,
                                  Manipulate, and Summarize MCMC Output    640:1--640:3
                     Caley Finn   \pkgOpenEPSim: An Open Exclusion Process
                                  Simulation Tool  . . . . . . . . . . . . 650:1--650:2
                  Michael Hucka   \pkgSpiral: splitters for identifiers in
                                  source code files  . . . . . . . . . . . 653:1--653:3
                      Yuan Tang   \pkgautoplotly: An R package for
                                  automatic generation of interactive
                                  visualizations for statistical results   657:1--657:2
               Brian E. J. Rose   \pkgCLIMLAB: a Python toolkit for
                                  interactive, process-oriented climate
                                  modeling . . . . . . . . . . . . . . . . 659:1--659:2
                Nicola Demo and   
              Marco Tezzele and   
                Gianluigi Rozza   \pkgEZyRB: Easy Reduced Basis method . . 661:1--661:3
                    Jasper Ginn   \pkgqualtRics: retrieve survey data
                                  using the Qualtrics API  . . . . . . . . 690:1--690:1
         Júlio Hoffimann   \pkgGeoStats.jl --- High-performance
                                  geostatistics in Julia . . . . . . . . . 692:1--692:4
              Sebastian S. Zeki   \pkgEndoMineR for the extraction of
                                  endoscopic and associated pathology data
                                  from medical reports . . . . . . . . . . 701:1--701:2

Journal of Open Source Software
Volume 3, Number 25, May, 2018

       Benjamin Allévius   \pkgscanstatistics: space-time anomaly
                                  detection using scan statistics  . . . . 515:1--515:2
             Pi-Yueh Chuang and   
            Olivier Mesnard and   
             Anush Krishnan and   
                Lorena A. Barba   \pkgPetIBM: toolbox and applications of
                                  the immersed-boundary method on
                                  distributed-memory architectures . . . . 558:1--558:5
      Ignacio Ferrés and   
                Gregorio Iraola   \pkgPhylen: automatic phylogenetic
                                  reconstruction using the EggNOG database 593:1--593:3
                  Michael Hucka   \pkgNostril: A nonsense string evaluator
                                  written in Python  . . . . . . . . . . . 596:1--596:2
                     Mike Innes   \pkgFlux: Elegant machine learning with
                                  Julia  . . . . . . . . . . . . . . . . . 602:1--602:1
                 Dave Hudak and   
               Doug Johnson and   
               Alan Chalker and   
             Jeremy Nicklas and   
                 Eric Franz and   
            Trey Dockendorf and   
             Brian L. McMichael   Open OnDemand: A web-based client portal
                                  for HPC centers  . . . . . . . . . . . . 622:1--622:2
                Andrew P. Smith   \pkghumanleague: a C++ microsynthesis
                                  package with R and Python interfaces . . 629:1--629:1
              Ryan C. Brown and   
                   Joshua Moser   \pkgHSImage: A Python and C++ library to
                                  allow interaction with ENVI-BIL
                                  hyperspectral images . . . . . . . . . . 630:1--630:2
           Amelia Ortiz-Gil and   
          Jordi Burguet-Castell   Mapelia and friends: create $3$D models
                                  from maps  . . . . . . . . . . . . . . . 660:1--660:2
                   Arjun Chennu   \pkgMicroBenthos: a modeling framework
                                  for microbial benthic ecology  . . . . . 674:1--674:2
          Mikkel Meyer Andersen   \pkgmalan: MAle Lineage ANalysis . . . . 684:1--684:2
              Boaz Blankrot and   
             Clemens Heitzinger   \pkgParticleScattering: Solving and
                                  optimizing multiple-scattering problems
                                  in Julia . . . . . . . . . . . . . . . . 691:1--691:3
             Jacob Anhòj   \pkgqicharts2: Quality Improvement
                                  Charts for R . . . . . . . . . . . . . . 699:1--699:2
          William D. Pearse and   
           Scott A. Chamberlain   \pkgSuppdata: Downloading Supplementary
                                  Data from Published Manuscripts  . . . . 721:1--721:2
            Sepand Haghighi and   
            Masoomeh Jasemi and   
            Shaahin Hessabi and   
              Alireza Zolanvari   \pkgPyCM: Multiclass confusion matrix
                                  library in Python  . . . . . . . . . . . 729:1--729:2
              Stephen D. Turner   \pkgqqman: an R package for visualizing
                                  GWAS results using Q-Q and Manhattan
                                  plots  . . . . . . . . . . . . . . . . . 731:1--731:2
              Ryan G. James and   
     Christopher J. Ellison and   
           James P. Crutchfield   \pkgdit: a Python package for discrete
                                  information theory . . . . . . . . . . . 738:1--738:3
               Richard Izzo and   
             David Steinman and   
              Simone Manini and   
                    Luca Antiga   The Vascular Modeling Toolkit: A Python
                                  Library for the Analysis of Tubular
                                  Structures in Medical Images . . . . . . 745:1--745:5

Journal of Open Source Software
Volume 3, Number 26, June, 2018

                      Anonymous   \pkgkima: Exoplanet detection in radial
                                  velocities . . . . . . . . . . . . . . . 487:1--487:3
              Antoine Cully and   
Konstantinos Chatzilygeroudis and   
          Federico Allocati and   
           Jean-Baptiste Mouret   \pkgLimbo: A Flexible High-performance
                                  Library for Gaussian Processes modeling
                                  and Data-Efficient Optimization  . . . . 545:1--545:3
        Edward W. Doddridge and   
                   Alexey Radul   \pkgAronnax: An idealised isopycnal
                                  ocean model  . . . . . . . . . . . . . . 592:1--592:2
               Laurent Fasnacht   \pkgmmappickle: Python 3 module to store
                                  memory-mapped \pkgnumpy array in
                                  \pkgpickle format  . . . . . . . . . . . 651:1--651:2
                 Tobias C. Wood   \pkgQUIT: QUantitative Imaging Tools . . 656:1--656:2
             Manuel Krebber and   
                Henrik Barthels   \pkgMatchPy: Pattern Matching in Python  670:1--670:2
               Gregory M. Green   \pkgdustmaps: A Python interface for
                                  maps of interstellar dust  . . . . . . . 695:1--695:2
                 Karl Wette and   
              Reinhard Prix and   
               David Keitel and   
             Matthew Pitkin and   
    Christoph Dreissigacker and   
             John T. Whelan and   
                    Paola Leaci   \pkgOctApps: a library of Octave
                                  functions for continuous
                                  gravitational-wave data analysis . . . . 707:1--707:3
             Shahriar Iravanian   \pkgfib-tf: A TensorFlow-based Cardiac
                                  Electrophysiology Simulator  . . . . . . 719:1--719:2
             Ryan R. Curtin and   
                Marcus Edel and   
          Mikhail Lozhnikov and   
          Yannis Mentekidis and   
             Sumedh Ghaisas and   
                Shangtong Zhang   \pkgmlpack 3: a fast, flexible machine
                                  learning library . . . . . . . . . . . . 726:1--726:2
               Inom Mirzaev and   
      Drew F. K. Williamson and   
                 Jacob G. Scott   \pkgegtplot: A Python Package for
                                  Three-Strategy Evolutionary Games  . . . 735:1--735:4
           Alessandro Gasparini   \pkgrsimsum: Summarise results from
                                  Monte Carlo simulation studies . . . . . 739:1--739:3
             James Bourbeau and   
          Zigfried Hampel-Arias   \pkgPyUnfold: A Python package for
                                  iterative unfolding  . . . . . . . . . . 741:1--741:3
          Mikkel Meyer Andersen   Discrete Laplace mixture model with
                                  applications in forensic genetics  . . . 748:1--748:3
         Daniel G. A. Smith and   
                   Johnnie Gray   \pkgopt\_einsum --- A Python package for
                                  optimizing contraction order for
                                  einsum-like expressions  . . . . . . . . 753:1--753:3
            Daniel Lüdecke   \pkgsjmisc: Data and Variable
                                  Transformation Functions . . . . . . . . 754:1--754:2
               Hajk-Georg Drost   \pkgPhilentropy: Information Theory and
                                  Distance Quantification with R . . . . . 765:1--765:4
             Jeroen F. J. Laros   General binary file parser . . . . . . . 766:1--766:1
            Daniel Lüdecke   \pkgggeffects: Tidy Data Frames of
                                  Marginal Effects from Regression Models  772:1--772:5
            Adam J. Jackson and   
             Alex M. Ganose and   
               Anna Regoutz and   
          Russell G. Egdell and   
               David O. Scanlon   \pkgGalore: Broadening and weighting for
                                  simulation of photoelectron spectroscopy 773:1--773:6
                 Vanessa Sochat   \pkgHelpMe Command Line Helper Utility   775:1--775:3
             David H. Hagan and   
              Andrew Tolmie and   
                  Jakub Trochim   \pkgpy-opc: operate the Alphasense
                                  OPC-N2 from a raspberry pi or other
                                  popular microcontrollers/microcomputers  782:1--782:2
           Christoph Molnar and   
       Giuseppe Casalicchio and   
                   Bernd Bischl   \pkgiml: An R package for Interpretable
                                  Machine Learning . . . . . . . . . . . . 786:1--786:2
         Shaun P. Wilkinson and   
                  Simon K. Davy   \pkgphylogram: an R package for
                                  phylogenetic analysis with nested lists  790:1--790:2

Journal of Open Source Software
Volume 3, Number 27, July, 2018

                 Brandon LeBeau   \pkgpdfsearch: Search Tools for PDF
                                  Files  . . . . . . . . . . . . . . . . . 668:1--668:2
            Sepand Haghighi and   
               Kasra Askari and   
              Sarmin Hamidi and   
          Mohammad Mahdi Rahimi   \pkgOPEM: Open Source PEM Cell
                                  Simulation Tool  . . . . . . . . . . . . 676:1--676:4
          Russell Y. Neches and   
                  Camille Scott   \pkgSuchTree: Fast, thread-safe
                                  computations with phylogenetic trees . . 678:1--678:3
            Bryan Brancotte and   
        Christophe Blanchet and   
    Hervé Ménager   A reusable tree-based web-visualization
                                  to browse EDAM ontology, and contribute
                                  to it  . . . . . . . . . . . . . . . . . 698:1--698:4
     Ashlee N. Ford Versypt and   
             James D. Crall and   
                   Biswadip Dey   \pkgBeeNestABM: An open-source
                                  agent-based model of spatiotemporal
                                  distribution of bumblebees in nests  . . 718:1--718:2
           Hilary J. Oliver and   
               Matthew Shin and   
                 Oliver Sanders   \pkgCylc: A Workflow Engine for Cycling
                                  Systems  . . . . . . . . . . . . . . . . 737:1--737:2
                 Amirsina Torfi   \pkgSpeechPy --- A Library for Speech
                                  Processing and Recognition . . . . . . . 749:1--749:5
               Ruud van der Ham   \pkgsalabim: discrete event simulation
                                  and animation in Python  . . . . . . . . 767:1--767:2
         Vyas Ramasubramani and   
              Sharon C. Glotzer   \pkgrowan: A Python package for working
                                  with quaternions . . . . . . . . . . . . 787:1--787:3
         Robert W. Schlegel and   
               Albertus J. Smit   \pkgheatwaveR: A central algorithm for
                                  the detection of heatwaves and
                                  cold-spells  . . . . . . . . . . . . . . 821:1--821:2
                     Evan Odell   \pkgnomisr: Access Nomis UK Labour
                                  Market Data  . . . . . . . . . . . . . . 859:1--859:2

Journal of Open Source Software
Volume 3, Number 28, August, 2018

            Jarvist Moore Frost   \pkgPolaronMobility.jl: Implementation
                                  of the Feynman variational polaron model 566:1--566:2
            Kirill Tsyganov and   
         Andrew James Perry and   
      Stuart Kenneth Archer and   
                   David Powell   \pkgRNAsik: A Pipeline for complete and
                                  reproducible RNA-seq analysis that runs
                                  anywhere with speed and ease . . . . . . 583:1--583:3
               Momar G-O Hughes   \pkgMCycle: A Python package for $1$D
                                  sizing and analysis of thermodynamic
                                  power cycles . . . . . . . . . . . . . . 710:1--710:2
        Federico Reghenzani and   
           Giuseppe Massari and   
             William Fornaciari   \pkgchronovise: Measurement-Based
                                  Probabilistic Timing Analysis framework  711:1--711:3
             Alex M. Ganose and   
            Adam J. Jackson and   
               David O. Scanlon   \pkgsumo: Command-line tools for
                                  plotting and analysis of periodic ab
                                  initio calculations  . . . . . . . . . . 717:1--717:3
              David Topping and   
              Paul Connolly and   
                  Jonathan Reid   \pkgPyBox: An automated box-model
                                  generator for atmospheric chemistry and
                                  aerosol simulations  . . . . . . . . . . 755:1--755:2
                Lucy D. Whalley   \pkgeffmass: An effective mass package   797:1--797:2
            Andrew P. Smith and   
                    Tom Russell   \pkgukpopulation: unified national and
                                  subnational population estimates and
                                  projections, including variants  . . . . 803:1--803:2
         Nathan J. Goldbaum and   
             John A. ZuHone and   
            Matthew J. Turk and   
             Kacper Kowalik and   
                  Anna L. Rosen   \pkgunyt: Handle, manipulate, and
                                  convert data with units in Python  . . . 809:1--809:11
            Jean-Philippe Coene   \pkgsigmajs: An R \pkghtmlwidget
                                  interface to the \pkgsigma.js
                                  visualization library  . . . . . . . . . 814:1--814:2
             Jason K. Moore and   
                   Mont Hubbard   \pkgskijumpdesign: A Ski Jump Design
                                  Tool for Specified Equivalent Fall
                                  Height . . . . . . . . . . . . . . . . . 818:1--818:3
          Marcus D. Sherman and   
                  Ryan E. Mills   \pkgBAMnostic: an OS-agnostic toolkit
                                  for genomic sequence analysis  . . . . . 826:1--826:2
             Shawn David Taylor   \pkgpyPhenology: A python framework for
                                  plant phenology modelling  . . . . . . . 827:1--827:2
             Philip D. Waggoner   The \pkghhi Package: Streamlined
                                  Calculation and Visualization of
                                  Herfindahl--Hirschman Index Scores . . . 828:1--828:5
     Christopher Ostrouchov and   
               Yanwen Zhang and   
               William J. Weber   \pkgpysrim: Automation, Analysis, and
                                  Plotting of SRIM Calculations  . . . . . 829:1--829:3
                    David Wiley   \pkgRISE: An R package for RISE analysis 846:1--846:1
       Vincent Arel-Bundock and   
            Nils Enevoldsen and   
                   C. J. Yetman   \pkgcountrycode: An R package to convert
                                  country names and country codes  . . . . 848:1--848:2
                   Will Handley   \pkgfgivenx: A Python package for
                                  functional posterior plotting  . . . . . 849:1--849:4
               Steven G. Murray   \pkgpowerbox: A Python package for
                                  creating structured fields with
                                  isotropic power spectra  . . . . . . . . 850:1--850:2
            Brett M. Morris and   
        Trevor Dorn-Wallenstein   \pkgaesop: ARC Echelle Spectroscopic
                                  Observation Pipeline . . . . . . . . . . 854:1--854:1
            Raoul R. Wadhwa and   
      Drew F. K. Williamson and   
              Andrew Dhawan and   
                 Jacob G. Scott   \pkgTDAstats: R pipeline for computing
                                  persistent homology in topological data
                                  analysis . . . . . . . . . . . . . . . . 860:1--860:3
              Michael T. Porter   \pkgjs-emass: A flexible JavaScript
                                  implementation of the \pkgemass
                                  algorithm  . . . . . . . . . . . . . . . 869:1--869:1
            Andrew T. Jones and   
             Hien D. Nguyen and   
          Geoffrey J. McLachlan   \pkglogKDE: log-transformed kernel
                                  density estimation . . . . . . . . . . . 870:1--870:3
                 Pierre de Buyl   \pkgtidynamics: A tiny package to
                                  compute the dynamics of stochastic and
                                  molecular simulations  . . . . . . . . . 877:1--877:4
                 Vanessa Sochat   \pkgContainershare: Open Source Registry
                                  to build, test, deploy with CircleCI . . 878:1--878:3
                  Thomas Klebel   \pkgjstor: Import and Analyse Data from
                                  Scientific Texts . . . . . . . . . . . . 883:1--883:2
           Jared M. Andrews and   
           Mohamed El-Alawi and   
           Jacqueline E. Payton   \pkgGenotify: Fast, lightweight gene
                                  lookup and summarization . . . . . . . . 885:1--885:4
              Benjamin Williams   Combining a Probability and a
                                  Non-Probability Sample in a
                                  Capture--Recapture Setting . . . . . . . 886:1--886:2
    Anwar O. Nunez-Elizalde and   
               James S. Gao and   
             Tianjiao Zhang and   
                Jack L. Gallant   \pkgcottoncandy: scientific python
                                  package for easy cloud storage . . . . . 890:1--890:2
             David N. Sousa and   
          João R. Daniel   \pkgbor: An R Package for Transforming
                                  Behavioral Observation Records into Data
                                  Matrices . . . . . . . . . . . . . . . . 909:1--909:4
                 Simon Dirmeier   \pkgdatastructures: An R package for
                                  organisation and storage of data . . . . 910:1--910:2

Journal of Open Source Software
Volume 3, Number 29, September, 2018

           Lionel Roubeyrie and   
        Sébastien Celles   \pkgWindrose: A Python \pkgMatplotlib,
                                  \pkgNumpy library to manage wind and
                                  pollution data, draw windrose  . . . . . 268:1--268:5
           David P. Fleming and   
                Jake VanderPlas   \pkgapproxposterior: Approximate
                                  Posterior Distributions in Python  . . . 781:1--781:2
                   Johnnie Gray   \pkgquimb: A python package for quantum
                                  information and many-body calculations   819:1--819:3
          Stefan Pfenninger and   
                 Bryn Pickering   \pkgCalliope: a multi-scale energy
                                  systems modelling framework  . . . . . . 825:1--825:2
             Leland McInnes and   
                 John Healy and   
             Nathaniel Saul and   
         Lukas Großberger   \pkgUMAP: Uniform Manifold Approximation
                                  and Projection . . . . . . . . . . . . . 861:1--861:2
               Palash Goyal and   
                 Emilio Ferrara   \pkgGEM: A Python package for graph
                                  embedding methods  . . . . . . . . . . . 876:1--876:2
        William F. Holmgren and   
         Clifford W. Hansen and   
               Mark A. Mikofski   \pkgpvlib python: a python package for
                                  modeling solar energy systems  . . . . . 884:1--884:3