Converting Raw Accelerometer Data to Activity Counts Using Open-Source Code: Implementing a MATLAB Code in Python and R, and Comparing the Results to ActiLife

2021 ◽  
pp. 1-7
Author(s):  
Ruben Brondeel ◽  
Yan Kestens ◽  
Javad Rahimipour Anaraki ◽  
Kevin Stanley ◽  
Benoit Thierry ◽  
...  
Keyword(s):  
Open Source ◽  
Pearson Correlation ◽  
Vertical Axis ◽  
Accelerometer Data ◽  
Accelerometer Sensor ◽  
Interclass Correlation ◽  
Acceleration Data ◽  
The Right ◽  
Pearson Correlations ◽  
Closed Source

Background: Closed-source software for processing and analyzing accelerometer data provides little to no information about the algorithms used to transform acceleration data into physical activity indicators. Recently, an algorithm was developed in MATLAB that replicates the frequently used proprietary ActiLife activity counts. The aim of this software profile was (a) to translate the MATLAB algorithm into R and Python and (b) to test the accuracy of the algorithm on free-living data. Methods: As part of the INTErventions, Research, and Action in Cities Team, data were collected from 86 participants in Victoria (Canada). The participants were asked to wear an integrated global positioning system and accelerometer sensor (SenseDoc) for 10 days on the right hip. Raw accelerometer data were processed in ActiLife, MATLAB, R, and Python and compared using Pearson correlation, interclass correlation, and visual inspection. Results: Data were collected for a combined 749 valid days (>10 hr wear time). MATLAB, Python, and R counts per minute on the vertical axis had Pearson correlations with the ActiLife counts per minute of .998, .998, and .999, respectively. All three algorithms overestimated ActiLife counts per minute, some by up to 2.8%. Conclusions: A MATLAB algorithm for deriving ActiLife counts was implemented in R and Python. The different implementations provide similar results to ActiLife counts produced in the closed source software and can, for all practical purposes, be used interchangeably. This opens up possibilities to comparing studies using similar accelerometers from different suppliers, and to using free, open-source software.

scholarly journals Star Coordinate Dimension Arrangement using Euclidean Distance and Pearson Correlation

2018 ◽  
Vol 12 (1) ◽  
pp. 348
Author(s):  
Noor Elaiza Abdul Khalid ◽  
Izyan Izzati Kamsani
Keyword(s):  
Data Analysis ◽  
Prior Knowledge ◽  
Euclidean Distance ◽  
Pearson Correlation ◽  
Visualization Technique ◽  
Hidden Information ◽  
Correlation Data ◽  
The Right ◽  
Pearson Correlations

<span>Star Coordinate (SC) is a circular visualization technique that maps k-dimensional data. Its interactive features allow user to manipulate projections to search for hidden information. Without prior knowledge of relationship between dimensions users will be blindly searching for clusters. This paper proposes dimension rearrangement using Euclidean Distance and Pearson Correlations to reveal the clusters in SC. The methodology consists of four phases; Calculate the distance between individual attributes against a dependent attribute using Euclidean distance; Pearson correlation is used to obtain the correlation data attributes; Sort the correlation values in ascending order; finally, attributes table are reordered with the positive values to the right and negative values to the left according to the correlation value. The resulting tables are applied to produce the SC. This method is successful in producing clusters that makes it easier for the users to further manipulate the SC for their data analysis.</span>

CARL: a running recognition algorithm for free-living accelerometer data

2021 ◽  
Author(s):  
John J Davis IV ◽  
Marcin Straczkiewicz ◽  
Jaroslaw Harezlak ◽  
Allison H Gruber
Keyword(s):  
Physical Activity ◽  
Confidence Interval ◽  
Open Source ◽  
Recognition Algorithm ◽  
Physical Activities ◽  
Great Promise ◽  
Accelerometer Data ◽  
Free Living ◽  
Acceleration Data ◽  
Wearable Accelerometers

Abstract Wearable accelerometers hold great promise for physical activity epidemiology and sports biomechanists. However, identifying and extracting data from specific physical activities, such as running, remains challenging. Objective: To develop and validate an algorithm to identify bouts of running in raw, free-living accelerometer data from devices worn at the wrist or torso (waist, hip, chest). Approach: The CARL (continuous amplitude running logistic) classifier identifies acceleration data with amplitude and frequency characteristics consistent with running. The CARL classifier was trained on data from 31 adults wearing accelerometers on the waist and wrist, then validated on free-living data from 30 new, unseen subjects plus 166 subjects from previously-published datasets using different devices, wear locations, and sample frequencies. Main Results: On free-living data, the CARL classifier achieved mean accuracy (F1 score) of 0.984 (95% confidence interval 0.962-0.996) for data from the waist and 0.994 (95% CI 0.991-0.996) for data from the wrist. In previously-published datasets, the CARL classifier identified running with mean accuracy (F1 score) of 0.861 (95% CI 0.836-0.884) for data from the chest, 0.911 (95% CI 0.884-0.937) for data from the hip, 0.916 (95% CI 0.877-0.948) for data from the waist, and 0.870 (95% CI 0.834-0.903) for data from the wrist. Misclassification primarily occurred during activities with similar torso acceleration profiles to running, such as rope jumping and elliptical machine use. Significance: The CARL classifier can accurately identify bouts of running as short as three seconds in free-living accelerometry data. An open-source implementation of the CARL classifier is available at <<GITHUBURL>>.

scholarly journals The pirate from Koenigsberg: why closed source software is not worth of copyright protection

2016 ◽  
Author(s):  
Maria Chiara Pievatolo
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Copyright Protection ◽  
Private Property ◽  
Human Beings ◽  
Property A ◽  
The Public ◽  
Works Of Art ◽  
The Right ◽  
Closed Source

According to Kant, property applies only to touchable things, among which he includes the works of art. Forthe very principle of private property, a legitimate purchaser has the right to replicate and to share themwithout restrictions.Kant recognizes copyright only on written texts, by conceiving them as speeches that exclusively authorizedspokespersons - the publishers - may convey to the public in the name of their authors. The rights of theauthorized publishers, however, are justified only if they help the public to get the texts.In a Kantian environment, open source software would be worth of copyright protection, because it can beconceived as a speech meant to human beings. On the contrary, Kant would treat closed source programs asworks of art, without according them copyright protection, because, as none is allowed to read and tounderstand them, they cannot be conceived as a speeches meant to the public. Closed source programs are likesealed books that no one is allowed to read: why do we keep on taking for granted that they are worth ofcopyright protection?

scholarly journals Examining concurrent validity between COMLEX-USA Level 2-Cognitive Evaluation and COMLEX-USA Level 2-Performance Evaluation

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Brandon Craig ◽  
Xiaolin Wang ◽  
Jeanne Sandella ◽  
Tsung-Hsun Tsai ◽  
David Kuo ◽  
...  
Keyword(s):  
Performance Evaluation ◽  
Concurrent Validity ◽  
Pearson Correlation ◽  
The United States ◽  
National Board ◽  
Cognitive Evaluation ◽  
Competency Domain ◽  
Medical Examiners ◽  
Pearson Correlations ◽  
Level 2

Abstract Context The Comprehensive Osteopathic Medical Licensing Examination of the United States of America (COMLEX-USA) is a three level examination used as a pathway to licensure for students in osteopathic medical education programs. COMLEX-USA Level 2 includes a written assessment of Fundamental Clinical Sciences for Osteopathic Medical Practice (Level 2-Cognitive Evaluation [L2-CE]) delivered in a computer based format and separate performance evaluation (Level 2-Performance Evaluation [L2-PE]) administered through live encounters with standardized patients. L2-PE was designed to augment L2-CE. It is expected that the two examinations measure related yet distinct constructs. Objectives To explore the concurrent validity of L2-CE with L2-PE. Methods First attempt test scores were obtained from the National Board of Osteopathic Medical Examiners database for 6,639 candidates who took L2-CE between June 2019 and May 2020 and matched to the students’ L2-PE scores. The sample represented all colleges of osteopathic medicine and 97.5% of candidates who took L2-CE during the complete 2019–2020 test cycle. We calculated disattenuated correlations between the total score for L2-CE, the L2-CE scores for the seven competency domains (CD1 through CD7), and the L2-PE scores for the Humanistic Domain (HM) and Biomedical/Biomechanical Domain (BM). All scores were on continuous scales. Results Pearson correlations ranged from 0.10 to 0.88 and were all statically significant (p<0.01). L2-CE total score was most strongly correlated with CD2 (0.88) and CD3 (0.85). Pearson correlations between the L2-CE competency domain subscores ranged from 0.17 to 0.70, and correlations which included either HM or BM ranged from 0.10 to 0.34 with the strongest of those correlations being between BM and L2-CE total score (0.34) as well as between HM and BM (0.28).The largest increase between corresponding Pearson and disattenuated correlations was for pairs of scores with lower reliabilities such as CD5 and CD6, which had a Pearson correlation of 0.17 and a disattenuated correlation of 0.68. The smallest increase in correlations was observed in pairs of scores with larger reliabilities such as L2-CE total score and HM, which had a Pearson correlation of 0.23 and a disattenuated correlation of 0.28. The reliability of L2-CE was 0.87, 0.81 for HM, and 0.73 for BM. The reliabilities for the L2-CE competency domain scores ranged from 0.22 to 0.74. The small to moderate correlations between the L2-CE total score and the two L2-PE support the expectation that these examinations measure related but distinct constructs. The correlations between L2-PE and L2-CE competency domain subscores reflect the distribution of items defined by the L2-PE blueprint, providing evidence that the examinations are performing as designed. Conclusions This study provides evidence supporting the validity of the blueprints for constructing COMLEX-USA Levels 2-CE and 2-PE examinations in concert with the purpose and nature of the examinations.

scholarly journals QVigourMap: A GIS Open Source Application for the Creation of Canopy Vigour Maps

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 952
Author(s):  
Lia Duarte ◽  
Ana Cláudia Teodoro ◽  
Joaquim J. Sousa ◽  
Luís Pádua
Keyword(s):  
Open Source ◽  
Precision Agriculture ◽  
Vegetation Indices ◽  
Data Interpretation ◽  
Vegetation Monitoring ◽  
Distribution Maps ◽  
Monitoring Process ◽  
Multi Temporal ◽  
The Creation ◽  
The Right

In a precision agriculture context, the amount of geospatial data available can be difficult to interpret in order to understand the crop variability within a given terrain parcel, raising the need for specific tools for data processing and analysis. This is the case for data acquired from Unmanned Aerial Vehicles (UAV), in which the high spatial resolution along with data from several spectral wavelengths makes data interpretation a complex process regarding vegetation monitoring. Vegetation Indices (VIs) are usually computed, helping in the vegetation monitoring process. However, a crop plot is generally composed of several non-crop elements, which can bias the data analysis and interpretation. By discarding non-crop data, it is possible to compute the vigour distribution for a specific crop within the area under analysis. This article presents QVigourMaps, a new open source application developed to generate useful outputs for precision agriculture purposes. The application was developed in the form of a QGIS plugin, allowing the creation of vigour maps, vegetation distribution maps and prescription maps based on the combination of different VIs and height information. Multi-temporal data from a vineyard plot and a maize field were used as case studies in order to demonstrate the potential and effectiveness of the QVigourMaps tool. The presented application can contribute to making the right management decisions by providing indicators of crop variability, and the outcomes can be used in the field to apply site-specific treatments according to the levels of vigour.

MORPHOMETRIC ANATOMY AND INTRAORGAN TOPOGRAPHY OF THE CORONARY ORIFICES IN HEART OF ADULT HUMAN

2020 ◽  
pp. 40-47
Author(s):  
Андрей Аркадьевич Якимов ◽  
Евгения Германовна Дмитриева
Keyword(s):  
Coronary Artery ◽  
Blood Supply ◽  
Coronary Sinus ◽  
Left Coronary Artery ◽  
Rare Variants ◽  
Vertical Axis ◽  
Aortic Valves ◽  
Sinotubular Junction ◽  
Adult Human ◽  
The Right

Цель - выявить варианты строения и внутриорганной топографии устьев венечных артерий у взрослого человека при разных типах кровоснабжения желудочкового комплекса сердца. Материал и методы. На вскрытых через некоронарные синусы аорты 65 препаратах клапанов аорты взрослых людей изучили положение устьев венечных артерий, штангенциркулем измеряли минимальный и максимальный диаметры каждого устья, определяли их форму по соотношению диаметров. Результаты. Для устьев обеих артерий типичной была округлая, реже овальная форма. В большинстве случаев левая венечная артерия начиналась в центральной трети, правая - в центральной или задней трети «своего» синуса на уровне верхнего края полулунной заслонки или между ним и синотубулярным соединением. Локализация устьев в пределах синусов, на уровне синотубулярного соединения или выше него была редкой для обеих артерий. В 20 % случаев в правом синусе аорты спереди от устья правой венечной артерии имелось устье конусной артерии. Выводы. Типичные и редкие варианты формы правого и левого устьев, варианты их положения по вертикальной оси аорты одинаковы, варианты их положения по горизонтали различны. Зависимость вариантов формы и положения устьев от типа кровоснабжения желудочков сердца не выявлена. Objective - to reveal common and rare variants of the anatomy and intraorganic topography of the coronary orifices in normal hearts of adult human with regard to patterns of cardiac ventricular blood supply. Material and methods. On 65 specimens of aortic valves opened through non-coronary sinus, the minimal and maximal diameters of each orifice were measured with a caliper, the shape of the orifices was determined according to the ratio of the diameters, and the position of the orifices was studied. Results. The orifices of both right and left coronary arteries were mostly found to be round, less frequently oval. In most cases, the left coronary artery arose from the central third and the right artery arose from the central or posterior third of corresponding sinus at the level of the upper edge of the semilunar cusp or between the edge and the sinotubular junction. The localization of the arterial orifice within the sinuses at the level of sinotubular junction or above it was uncommon for the both arteries. In 20 % of cases, the conal artery arose with its own orifice in front of the mouth of the right coronary artery. Conclusions. Typical and rare shapes of the coronary orifices, variants of their position regarding to vertical axis of the aorta are the same, whereas variants of their position in horizontal axis are different. There is no relationship between variants of form of the orifices, position of the orifices and types of blood supply of heart ventricles.

Improvement of the visual warning system for various driving and road conditions in road transportation

2017 ◽  
Vol 232 (2) ◽  
pp. 175-187 ◽  
Author(s):  
Güray Tonguç ◽  
İsmail Hakkı Akçay ◽  
Habib Gürbüz
Keyword(s):  
Warning System ◽  
Weather Conditions ◽  
The Other ◽  
Accelerometer Data ◽  
Road Transportation ◽  
Accelerometer Sensor ◽  
The Road ◽  
Information Displays ◽  
Driving Conditions ◽  
Vehicle Information

This study aims to identify the potential adverse driving conditions which result from driver behavior, road surfaces and weather conditions for vehicles during a cruise, and to inform the drivers of the other vehicles moving on the same route. Adverse driving condition scenarios were developed via acceleration data in lateral, longitudinal and vertical directions gathered by using an accelerometer sensor placed at the gravity center of the test vehicles. The drivers were warned through the symbols designed according to the developed scenarios in different shapes and colors, displayed on an information screen showing the position of the vehicle. Three different software programs were used for gathering and evaluating the accelerometer data, storing scenario-specific symbols on the internet and transferring these symbols to the other vehicle information displays. The road tests were performed in conditions present in Turkey. It was observed that the vehicle drivers were alerted with the warning symbols which were designed for dangerous road and driving conditions with a latency of approximately 6s on Google maps which appeared on the driver information screen.

scholarly journals Moving Forward With Accelerometer-Assessed Physical Activity: Two Strategies to Ensure Meaningful, Interpretable, and Comparable Measures

2018 ◽  
Vol 30 (4) ◽  
pp. 450-456 ◽  
Author(s):  
Alex V. Rowlands
Keyword(s):  
Physical Activity ◽  
Black Box ◽  
Data Sets ◽  
Accelerometer Data ◽  
Future Health ◽  
The Past ◽  
Acceleration Data ◽  
Night And Day ◽  
Very High ◽  
Made In

Significant advances have been made in the measurement of physical activity in youth over the past decade. Monitors and protocols promote very high compliance, both night and day, and raw measures are available rather than “black box” counts. Consequently, many surveys and studies worldwide now assess children’s physical behaviors (physical activity, sedentary behavior, and sleep) objectively 24 hours a day, 7 days a week using accelerometers. The availability of raw acceleration data in many of these studies is both an opportunity and a challenge. The richness of the data lends itself to the continued development of innovative metrics, whereas the removal of proprietary outcomes offers considerable potential for comparability between data sets and harmonizing data. Using comparable physical activity outcomes could lead to improved precision and generalizability of recommendations for children’s present and future health. The author will discuss 2 strategies that he believes may help ensure comparability between studies and maximize the potential for data harmonization, thereby helping to capitalize on the growing body of accelerometer data describing children’s physical behaviors.

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