scholarly journals revtools: An R package to support article screening for evidence synthesis

2018 ◽  
Author(s):  
Martin J. Westgate
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Evidence Synthesis ◽  
R Package ◽  
Software Tools ◽  
Free Access ◽  
Bibliographic Data ◽  
Meta Analyses ◽  
Low Prevalence ◽  
User Friendly

AbstractThe field of evidence synthesis is growing rapidly, with a corresponding increase in the number of software tools and workflows to support the construction of systematic reviews, systematic maps, and meta-analyses. Despite much progress, however, a number of problems remain including slow integration of new statistical or methodological approaches into user-friendly software, low prevalence of open-source software, and poor integration among distinct software tools. These issues hinder the utility and transparency of new methods to the research community. Here I present revtools, an R package to support article screening during evidence synthesis projects. It provides tools for the import and de-duplication of bibliographic data, screening of articles by title or abstract, and visualization of article content using topic models. The software is entirely open-source and combines command-line scripting for experienced programmers with custom-built user interfaces for casual users, with further methods to support article screening to be added over time. Revtools provides free access to novel methods in an open-source environment, and represents a valuable step in expanding the capacity of R to support evidence synthesis projects.

Geopsy: A User-Friendly Open-Source Tool Set for Ambient Vibration Processing

2020 ◽  
Vol 91 (3) ◽  
pp. 1878-1889 ◽  
Author(s):  
Marc Wathelet ◽  
Jean-Luc Chatelain ◽  
Cécile Cornou ◽  
Giuseppe Di Giulio ◽  
Bertrand Guillier ◽  
...  
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Site Characterization ◽  
Ambient Vibration ◽  
The European Union ◽  
Vibration Data ◽  
Single Station ◽  
Characterization Studies ◽  
Single Trace ◽  
User Friendly

Abstract Ambient vibrations are nowadays considerably used worldwide for numerous types of engineering applications and scientific research. Geopsy and its companion tools are part of that landscape. Since the first release of the program package in 2005, as outcome of the European Union project Site Effects aSsessment from AMbient noisE, Geopsy has become a mature multiplatform open-source package (released under GNU Public License version 3) that has already been recognized as a reference tool for analyzing ambient vibration data in the context of site characterization studies. The community of users has grown from a core group of researchers up to thousands of seismologists and engineers on every career level and on all continents. The versatility of geopsy allows for the processing of all kinds of data needed in site characterization studies, that is, from single station single trace to three-component array recordings. In all of the aforementioned cases, the steps from field acquisition to the production of publication-ready figures are covered and supported by user-friendly graphical user interfaces or corresponding command-line tools for the automation of the complete processing chain. To avoid black-box usage, a number of lower-level tools guarantee maximum flexibility in accessing and controlling processing results at any stage of the analysis.

scholarly journals cmvdrg - An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping

2020 ◽  
Author(s):  
Oscar J Charles ◽  
Cristina Venturini ◽  
Judith Breuer
Keyword(s):  
Drug Resistance ◽  
Open Source ◽  
Human Cytomegalovirus ◽  
Antiviral Drug ◽  
R Package ◽  
Effective Vaccine ◽  
Analysis Tool ◽  
Resistance Mutations ◽  
Drug Resistance Genotyping ◽  
User Friendly

AbstractThe prevention and treatment of HCMV infection is based on the utilization of antiviral therapies as HCMV lacks an effective vaccine. The rise of drug resistance is therefore an increasing patient threat. We identified the need for an open source and comprehensive HCMV resistance mutations database, to support the research community in this area. Here we present “Cytomegalovirus Drug Resistance Genotyping” (cmvdrg), a freely available database contained within an easily accessible R package, which provides a succinct extraction of literature material in the form of a text file database. Additionally, cmvdrg includes methods for calling resistance in common sequencing files and an optional user-friendly web interface.AvailabilityThe cmvdrg package is freely available under the GNU GPL v3 license at https://github.com/ucl-pathgenomics/cmvdrg,One Sentence SummaryCurrently data regarding Human Cytomegalovirus resistant mutations are contained in unconnected literature sources, here we present an exhaustive open source database and analysis tool for the community.

scholarly journals ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun-Hui Gao ◽  
Guangchuang Yu ◽  
Peng Cai
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
R Package ◽  
Venn Diagram ◽  
Free Access ◽  
High Quality ◽  
Venn Diagrams ◽  
Label Edge ◽  
The Cost

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Satisfactory results can be obtained with minimal configurations. Furthermore, we designed comprehensive objects to store the entire data of the Venn diagram, which allowed free access to both intersection values and Venn plot sub-elements, such as set label/edge and region label/filling. Therefore, high customization of every Venn plot sub-element can be fulfilled without increasing the cost of learning when the user is familiar with ggplot2 methods. To date, ggVennDiagram has been cited in more than 10 publications, and its source code repository has been starred by more than 140 GitHub users, suggesting a great potential in applications. The package is an open-source software released under the GPL-3 license, and it is freely available through CRAN (https://cran.r-project.org/package=ggVennDiagram).

Interfacing the Modifiable Multitasking Environment with ACT-R for Computational Cognitive Modeling of Complex Tasks

2018 ◽  
Vol 62 (1) ◽  
pp. 316-320
Author(s):  
Leslie M. Blaha ◽  
Leif Carlsen ◽  
Tim Halverson ◽  
Brad Reynolds
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Cognitive Modeling ◽  
Cognitive Architecture ◽  
Software Tools ◽  
Graphical User Interfaces ◽  
Complex Tasks ◽  
Software Packages ◽  
Baseline Task ◽  
Computational Cognitive Modeling

We demonstrate a set of software tools designed to facilitate computational cognitive modeling of multitasking performance. The Modifiable Multitasking Environment (ModME) offers a flexible, browser-based platform for creating multitasking experiments. Simplified Interfacing for Modeling Cognition–JavaScript (SIMCog-JS) provides communication between the browser-based experiments in ModME and the Java implementation of the ACT-R cognitive architecture. The baseline configuration of these software packages enables an ACT-R model to perform pilot-like multitasking in the modified Multi-Attribute Task Battery, which is implemented as the baseline task available in ModME. We show how this combination facilitates the development of models for assessing multitasking workload. In this demonstration, we will explain the software packages and allow attendees to interact with system elements, particularly the ModME graphical user interfaces. All software is available open source for attendees to try themselves.

scholarly journals Opening the black box of high resolution fish tracking using yaps

2019 ◽  
Author(s):  
Henrik Baktoft ◽  
Karl Ø. Gjelland ◽  
Finn Økland ◽  
Jennifer S. Rehage ◽  
Jonathan R. Rodemann ◽  
...  
Keyword(s):  
High Resolution ◽  
Open Source ◽  
R Package ◽  
Black Box ◽  
Data Sets ◽  
Important Process ◽  
Complex Process ◽  
Fish Tracking ◽  
User Friendly ◽  
Closed Source

AbstractThe R package yaps was introduced in 2017 as a transparent open source alternative to closed source manufacturer-provided solutions to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters.Although yaps is open source and transparent, the process from raw detections to final tracks has proved to be challenging for many potential users, effectively preventing most users from accessing the benefits of using yaps. Especially, the very important process of synchronizing the hydrophone arrays have proven to be an obstacle for many potential users.To make yaps more approachable to the wider fish tracking community, we have developed and added user-friendly functions assisting users in the complex process of synchronizing the data.Here, we introduce these functions and a six-step protocol intended to provide users with an example workflow that can be used as a template enabling users to apply yaps to their own data. Using example data collected by an array of Vemco VR2 hydrophones, the protocol walks the user through the entire process from raw data to final tracks. Example data sets and complete code for reproducing results are provided.

scholarly journals Using Open Source Tools for Analysis of the Mutation Rate of African Cassava Mosaic Virus

2018 ◽  
Vol 2 (1) ◽  
pp. 44-56
Author(s):  
Grey Chibawe ◽  
Lillian Mzyece ◽  
Mayumbo Nyirenda ◽  
Jackson Phiri
Keyword(s):  
Higher Education ◽  
Open Source ◽  
Mosaic Virus ◽  
Life Sciences ◽  
Software Tools ◽  
African Cassava Mosaic Virus ◽  
User Friendly ◽  
Cassava Mosaic Virus ◽  
Analyze Data

Popular tools used in studies in life sciences are often costly. This often pauses challenges to researchers in spite of the fact that research continues to be a key to the successful systematic development of new knowledge and a fundamental aspect to the usefulness of all higher education. Particularly, higher education also aims to advance, create and disseminate knowledge through research. Such critical studies like mutation studies therefore require affordable and fast results yielding software. In such research, open source software tools become handy in place of expensive proprietary tools. In order to provide alternative software tools for research, we decided to use a case study of the mutation of the African Cassava Mosaic Virus (ACMV) done by researchers in Zambia. The study of ACMV mutation is hampered by fragmented and non-user-friendly tools, which are currently available. A number of the tools used also depend on network connection, especially the Internet, to access and analyze data. To help alleviate this problem this research proposes the use of open source libraries in biopython to generate cost efficient and user-friendly solutions. Additionally, we propose the use of an open standard using XML as a standard protocol to share data between applications or stages in genomic data analysis of the ACMV. In our strife to provide open source solutions we analysed various tools and noted that biopython is quite popular. During our study of biopython our initial results show that it’s possible to use free tools to analyze data in the life sciences and consequently reduce the time and cost required to analyze ACMV. Based on this case study we propose the adoption of such open source libraries in order to make research much more affordable for scientists in the life sciences for researches that operate within a constrained budget.

scholarly journals iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

Megataxa ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
MIGUEL VENCES ◽  
AURÉLIEN MIRALLES ◽  
SOPHIE BROUILLET ◽  
JACQUES DUCASSE ◽  
ALEXANDER FEDOSOV ◽  
...  
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Species Delimitation ◽  
Statistical Tests ◽  
Future Perspective ◽  
User Friendliness ◽  
Morphometric Analyses ◽  
Data Files ◽  
Set Up ◽  
User Friendly

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)

A Review of Meta-Analysis Packages in R

2016 ◽  
Vol 42 (2) ◽  
pp. 206-242 ◽  
Author(s):  
Joshua R. Polanin ◽  
Emily A. Hennessy ◽  
Emily E. Tanner-Smith
Keyword(s):  
Open Source ◽  
Meta Analysis ◽  
R Package ◽  
Statistical Technique ◽  
Effect Sizes ◽  
Online Search ◽  
Multiple Primary ◽  
R Packages ◽  
Meta Analyses ◽  
Analysis Models

Meta-analysis is a statistical technique that allows an analyst to synthesize effect sizes from multiple primary studies. To estimate meta-analysis models, the open-source statistical environment R is quickly becoming a popular choice. The meta-analytic community has contributed to this growth by developing numerous packages specific to meta-analysis. The purpose of this study is to locate all publicly available meta-analytic R packages. We located 63 packages via a comprehensive online search. To help elucidate these functionalities to the field, we describe each of the packages, recommend applications for researchers interested in using R for meta-analyses, provide a brief tutorial of two meta-analysis packages, and make suggestions for future meta-analytic R package creators.

scholarly journals DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments

2018 ◽  
Vol 35 (15) ◽  
pp. 2690-2691 ◽  
Author(s):  
Céline Trébeau ◽  
Jacques Boutet de Monvel ◽  
Fabienne Wong Jun Tai ◽  
Christine Petit ◽  
Raphaël Etournay
Keyword(s):  
User Interfaces ◽  
Dna Barcode ◽  
R Package ◽  
Supplementary Information ◽  
Minimal Distance ◽  
Source Codes ◽  
Dna Library ◽  
Core Facilities ◽  
User Friendly ◽  
Multiplex Sequencing

Abstract Summary Using adequate DNA barcodes is essential to unambiguously identify each DNA library within a multiplexed set of libraries sequenced using next-generation sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one to design single or dual-barcoding multiplex experiments by imposing desired constraints on the barcodes (including sequencer chemistry, barcode pairwise minimal distance and nucleotide content), while optimizing barcode frequency usage, thereby allowing one to both facilitate the demultiplexing step and spare expensive library-preparation kits. The package comes with a user-friendly interface and a web app developed in Java and Shiny (https://dnabarcodecompatibility.pasteur.fr), respectively, with the aim to help bridge the expertise of core facilities with the experimental needs of non-experienced users. Availability and implementation DNABarcodeCompatibility can be easily extended to fulfil specific project needs. The source codes of the R-package and its user interfaces are publicly available along with documentation at [https://github.com/comoto-pasteur-fr] under the GPL-2 licence. Supplementary information Supplementary data are available at Bioinformatics online.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

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