scholarly journals Identifying home locations in human mobility data: an open-source R package for comparison and reproducibility

2021 ◽  
Author(s):  
Qingqing Chen ◽  
Ate Poorthuis

Identifying meaningful locations, such as home or work, from human mobility data has become an increasingly common prerequisite for geographic research. Although location-based services (LBS) and other mobile technology have rapidly grown in recent years, it can be challenging to infer meaningful places from such data, which - compared to conventional datasets – can be devoid of context. Existing approaches are often developed ad-hoc and can lack transparency and reproducibility. To address this, we introduce an R software package for inferring home locations from LBS data. The package implements pre-existing algorithms and provides building blocks to make writing algorithmic ‘recipes’ more convenient. We evaluate this approach by analyzing a de-identified LBS dataset from Singapore that aims to balance ethics and privacy with the research goal of identifying meaningful locations. We show that ensemble approaches, combining multiple algorithms, can be especially valuable in this regard as the resulting patterns of inferred home locations closely correlate with the distribution of residential population. We hope this package, and others like it, will contribute to an increase in use and sharing of comparable algorithms, research code and data. This will increase transparency and reproducibility in mobility analyses and further the ongoing discourse around ethical big data research.

2020 ◽  
Vol 5 ◽  
pp. 252
Author(s):  
Jim R. Broadbent ◽  
Christopher N. Foley ◽  
Andrew J. Grant ◽  
Amy M. Mason ◽  
James R. Staley ◽  
...  

The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added to the package or updated in recent years. These features can be divided into four categories: robust methods for Mendelian randomization, methods for multivariable Mendelian randomization, functions for data visualization, and the ability to load data into the package seamlessly from the PhenoScanner web-resource. We provide examples of the graphical output produced by the data visualization commands, as well as syntax for obtaining suitable data and performing a Mendelian randomization analysis in a single line of code.


2014 ◽  
Vol 13 ◽  
pp. CIN.S13495 ◽  
Author(s):  
Ying Hu ◽  
Chunhua Yan ◽  
Chih-Hao Hsu ◽  
Qing-Rong Chen ◽  
Kelvin Niu ◽  
...  

Summary OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization. Availability and Implementation OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html . An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic—2.0 license.


2020 ◽  
Vol 5 ◽  
pp. 252
Author(s):  
Jim R. Broadbent ◽  
Christopher N. Foley ◽  
Andrew J. Grant ◽  
Amy M. Mason ◽  
James R. Staley ◽  
...  

The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added to the package or updated in recent years. These features can be divided into four categories: robust methods for Mendelian randomization, methods for multivariable Mendelian randomization, functions for data visualization, and the ability to load data into the package seamlessly from the PhenoScanner web-resource. We provide examples of the graphical output produced by the data visualization commands, as well as syntax for obtaining suitable data and performing a Mendelian randomization analysis in a single line of code.


Entropy ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. 863 ◽  
Author(s):  
Jiří Tomčala

Approximate Entropy and especially Sample Entropy are recently frequently used algorithms for calculating the measure of complexity of a time series. A lesser known fact is that there are also accelerated modifications of these two algorithms, namely Fast Approximate Entropy and Fast Sample Entropy. All these algorithms are effectively implemented in the R software package TSEntropies. This paper contains not only an explanation of all these algorithms, but also the principle of their acceleration. Furthermore, the paper contains a description of the functions of this software package and their parameters, as well as simple examples of using this software package to calculate these measures of complexity of an artificial time series and the time series of a complex real-world system represented by the course of supercomputer infrastructure power consumption. These time series were also used to test the speed of this package and to compare its speed with another R package pracma. The results show that TSEntropies is up to 100 times faster than pracma and another important result is that the computational times of the new Fast Approximate Entropy and Fast Sample Entropy algorithms are up to 500 times lower than the computational times of their original versions. At the very end of this paper, the possible use of this software package TSEntropies is proposed.


2021 ◽  
Author(s):  
Finnbar Lee ◽  
Nick Young

The New Zealand Freshwater Fish Database (NZFFD) is a repository of more than 155,000 records of freshwater fish observations from around New Zealand, maintained by the National Institute of Water and Atmospheric Research (NIWA). Records from the NZFFD can be downloaded using a web interface. The statistical computing language R is now widely used for data wrangling, analysis, and visualisation. Here, we present nzffdr, an open source R software package that: i) allows users to query and download data from the New Zealand Freshwater Fish Database directly in R, ii) provides functions to clean imported data, iii) facilitates the addition of information such as species names and Department of Conservation threat classification status, and iv) a workflow for visualising information from the NZFFD. The nzffdr package aims to standardise, simplify, and speed up a workflow likely already used in an ad hoc manner by scientists across New Zealand and abroad.


2016 ◽  
Author(s):  
David Barner

Perceptual representations – e.g., of objects or approximate magnitudes –are often invoked as building blocks that children combine with linguisticsymbols when they acquire the positive integers. Systems of numericalperception are either assumed to contain the logical foundations ofarithmetic innately, or to supply the basis for their induction. Here Ipropose an alternative to this general framework, and argue that theintegers are not learned from perceptual systems, but instead arise toexplain perception as part of language acquisition. Drawing oncross-linguistic data and developmental data, I show that small numbers(1-4) and large numbers (~5+) arise both historically and in individualchildren via entirely distinct mechanisms, constituting independentlearning problems, neither of which begins with perceptual building blocks.Specifically, I propose that children begin by learning small numbers(i.e., *one, two, three*) using the same logical resources that supportother linguistic markers of number (e.g., singular, plural). Several yearslater, children discover the logic of counting by inferring the logicalrelations between larger number words from their roles in blind countingprocedures, and only incidentally associate number words with perception ofapproximate magnitudes, in an *ad hoc* and highly malleable fashion.Counting provides a form of explanation for perception but is not causallyderived from perceptual systems.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shaobin Wang ◽  
Yun Tong ◽  
Yupeng Fan ◽  
Haimeng Liu ◽  
Jun Wu ◽  
...  

AbstractSince spring 2020, the human world seems to be exceptionally silent due to mobility reduction caused by the COVID-19 pandemic. To better measure the real-time decline of human mobility and changes in socio-economic activities in a timely manner, we constructed a silent index (SI) based on Google’s mobility data. We systematically investigated the relations between SI, new COVID-19 cases, government policy, and the level of economic development. Results showed a drastic impact of the COVID-19 pandemic on increasing SI. The impact of COVID-19 on human mobility varied significantly by country and place. Bi-directional dynamic relationships between SI and the new COVID-19 cases were detected, with a lagging period of one to two weeks. The travel restriction and social policies could immediately affect SI in one week; however, could not effectively sustain in the long run. SI may reflect the disturbing impact of disasters or catastrophic events on the activities related to the global or national economy. Underdeveloped countries are more affected by the COVID-19 pandemic.


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