diff --git a/R/app_ui.R b/R/app_ui.R index d344bfdc..b4ecc1e6 100644 --- a/R/app_ui.R +++ b/R/app_ui.R @@ -32,7 +32,7 @@ app_ui <- function(request) { tags$style(".main-header {vertical-align: middle;}"), tags$style(".main-header .logo {vertical-align: middle;}") ), - title = span(img(src="www/favicon.png", width = 30), "activAnalyzer 1.0.3"), titleWidth = 237 + title = span(img(src="www/favicon.png", width = 30), "activAnalyzer 1.0.4"), titleWidth = 237 ), shinydashboardPlus::dashboardSidebar( tags$style(HTML(".sidebar-menu li a {font-size: 17px;}")), diff --git a/R/plot_data_with_intensity.R b/R/plot_data_with_intensity.R index 75fafc63..2a013d7c 100644 --- a/R/plot_data_with_intensity.R +++ b/R/plot_data_with_intensity.R @@ -75,6 +75,22 @@ plot_data_with_intensity <- function(data, x = .data[[col_time]], y = .data[[metric]]) ) + + geom_rect(aes( + xmin = hms::as_hms(0), + xmax = hms::as_hms(valid_wear_time_start), + ymin = -Inf, + ymax = Inf), + color = "grey", + fill = "grey" + ) + + geom_rect(aes( + xmin = hms::as_hms(valid_wear_time_end), + xmax = hms::as_hms("23:59:59"), + ymin = -Inf, + ymax = Inf), + color = "grey", + fill = "grey" + ) + scale_x_time(breaks = hms::hms(seq(3600, 23*3600, 2*3600)), expand = c(0, 0), labels = format_hm diff --git a/joss/paper.md b/joss/paper.md index cc7723ce..89d66501 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -1,12 +1,14 @@ --- title: 'activAnalyzer: An app to analyze ActiGraph accelerometer data and to implement the use of the PROactive Physical Activity in COPD instruments' tags: - - R - physical activity - sedentary behaviour - accelerometer - - PROactive questionnaires + - actigraph - COPD + - PROactive instruments + - R + - Shiny authors: - name: Pierre-Yves de Müllenheim orcid: 0000-0001-9157-7371 @@ -20,22 +22,32 @@ affiliations: - name: Hôpital Saint Philibert, GHICL, France index: 2 date: 05 July 2022 +bibliography: references.bib --- # Summary -Physical activity is a behaviour related to many health outcomes. Accelerometry is commonly accepted as a more accurate method than questionnaires for measuring physical activity. ActiGraph devices have been the most used accelerometers in the scientific literature. Moreover, some research groups have developed specific frameworks to assess patients with specific conditions, as th D-PPAC and C-PPAC instruments developped by the PROactive consortium group for assessing physical activity in COPD patients. +Physical activity is a behaviour related to many health outcomes [@whoWHOGuidelinesPhysical2020]. To measure physical activity, researchers have increasingly used accelerometry during the past two decades to limit the influence of psychosocial bias in outcomes related to questionnaires use [@baumannPitfallsAccelerometerbasedMeasurement2018] and thus to use more valid methods for getting results [@hallalEnergyExpenditureCompared2013; @colbertComparativeValidityPhysical2011;@gardnerAssessmentFreelivingDaily1998]. Accelerometry has also become a way to access a diversity of metrics that cannot be easily (or not at all) obtained using questionnaires [@keadleEvaluationAccelerometerderivedMetrics2017; @backesAdvancedAnalyticalMethods2022]. + +ActiGraph devices have been the most used accelerometers in the scientific literature [@bassettAccelerometerbasedPhysicalActivity2015a]. ActiGraph accelerometers, along with its software companion (ActiLife), now allow to get movement date expressed in either *physical activity counts* or in *G-force* units. + +Moreover, some research groups have developed specific frameworks to assess patients with specific conditions, as th D-PPAC and C-PPAC instruments developped by the PROactive consortium group for assessing physical activity in COPD patients. -- Importantance of actigraph and actilife sofware +- Importance of actigraph and actilife sofware - problems for wide dissemination and use by clinicians, students, and some researchers; existence of programming interface but not accessible for non skilled users - # Statement of need +several packages : ggir, other... # A description of how this software compares to other commonly-used packages in this research area. # A list of key references including a link to the software archive. +# Usage + + + # Acknowledgements # References diff --git a/joss/references.bib b/joss/references.bib new file mode 100644 index 00000000..3f363e19 --- /dev/null +++ b/joss/references.bib @@ -0,0 +1,352 @@ + +@article{armstrongBehaviouralModificationInterventions2021, + title = {Behavioural Modification Interventions alongside Pulmonary Rehabilitation Improve {{COPD}} Patients’ Experiences of Physical Activity}, + author = {Armstrong, Matthew and Hume, Emily and McNeillie, Laura and Chambers, Francesca and Wakenshaw, Lynsey and Burns, Graham and Marshall, Karen Heslop and Vogiatzis, Ioannis}, + date = {2021-04}, + journaltitle = {Respir Med}, + volume = {180}, + pages = {106353}, + issn = {09546111}, + doi = {10.1016/j.rmed.2021.106353}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0954611121000597}, + urldate = {2022-06-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\VBI2R6BQ\\Armstrong et al. - 2021 - Behavioural modification interventions alongside p.pdf} +} + +@article{backesAdvancedAnalyticalMethods2022, + title = {Advanced Analytical Methods to Assess Physical Activity Behavior Using Accelerometer Time Series: A Scoping Review}, + shorttitle = {Advanced Analytical Methods to Assess Physical Activity Behavior Using Accelerometer Time Series}, + author = {Backes, Anne and Gupta, Tripti and Schmitz, Susanne and Fagherazzi, Guy and Hees, Vincent and Malisoux, Laurent}, + date = {2022-01}, + journaltitle = {Scand J Med Sci Sports}, + volume = {32}, + number = {1}, + pages = {18--44}, + issn = {0905-7188, 1600-0838}, + doi = {10.1111/sms.14085}, + url = {https://onlinelibrary.wiley.com/doi/10.1111/sms.14085}, + urldate = {2022-07-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\IBSIS9PB\\Backes et al. - 2022 - Advanced analytical methods to assess physical act.pdf} +} + +@article{baumannPitfallsAccelerometerbasedMeasurement2018, + title = {Pitfalls in Accelerometer-Based Measurement of Physical Activity: The Presence of Reactivity in an Adult Population}, + shorttitle = {Pitfalls in Accelerometer-Based Measurement of Physical Activity}, + author = {Baumann, S. and Groß, S. and Voigt, L. and Ullrich, A. and Weymar, F. and Schwaneberg, T. and Dörr, M. and Meyer, C. and John, U. and Ulbricht, S.}, + date = {2018-03}, + journaltitle = {Scand J Med Sci Sports}, + volume = {28}, + number = {3}, + pages = {1056--1063}, + issn = {09057188}, + doi = {10.1111/sms.12977}, + url = {https://onlinelibrary.wiley.com/doi/10.1111/sms.12977}, + urldate = {2022-07-10}, + langid = {english} +} + +@article{bowlerRealworldUseRescue2019, + title = {Real-World Use of Rescue Inhaler Sensors, Electronic Symptom Questionnaires and Physical Activity Monitors in {{COPD}}}, + author = {Bowler, Russell and Allinder, Matthew and Jacobson, Sean and Miller, Andrew and Miller, Bruce and Tal-Singer, Ruth and Locantore, Nicholas}, + date = {2019-02}, + journaltitle = {BMJ Open Resp Res}, + volume = {6}, + number = {1}, + pages = {e000350}, + issn = {2052-4439}, + doi = {10.1136/bmjresp-2018-000350}, + url = {https://bmjopenrespres.bmj.com/lookup/doi/10.1136/bmjresp-2018-000350}, + urldate = {2022-06-15}, + abstract = {Background Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterised by airflow obstruction and other morbidities such as respiratory symptoms, reduced physical activity and frequent bronchodilator use. Recent advances in personal digital monitoring devices can permit continuous collection of these data in COPD patients, but the relationships among them are not well understood. Methods 184 individuals from a single centre of the COPDGene cohort agreed to participate in this 3-week observational study. Each participant used a smartphone to complete a daily symptom diary (EXAcerbations of Chronic pulmonary disease Tool, EXACT), wore a wrist-worn accelerometer to record continuously physical activity and completed the Clinical Visit PROactive Physical Activity in COPD questionnaire. 58 users of metered dose inhalers for rescue (albuterol) were provided with an inhaler sensor, which time stamped each inhaler actuation. Results Rescue inhaler use was strongly correlated with E-RS:COPD score, while step counts were correlated with neither rescue use nor E-RS:COPD score. Frequent, unpatterned inhaler use pattern was associated with worse respiratory symptoms and less physical activity compared with frequent inhaler use with a regular daily pattern. There was a strong week-by-week correlation among measurements, suggesting that 1\,week of monitoring is sufficient to characterise stable patients with COPD. Discussion The study highlights the interaction and relevance of personal real-time monitoring of respiratory symptoms, physical activity and rescue medication in patients with COPD. Additionally, visual displays of longitudinal data may be helpful for disease management to help drive conversations between patients and caregivers and for risk-based monitoring in clinical trials.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\R45Y6HD6\\Bowler et al. - 2019 - Real-world use of rescue inhaler sensors, electron.pdf} +} + +@software{changShinyWebApplication2021, + title = {Shiny: {{Web Application Framework}} for {{R}}. {{R}} Package}, + author = {Chang, Winston and Cheng, Joe and Allaire, JJ and Sievert, Carson and Schloerke, Barret and Xie, Yihui and Allen, Jeff and McPherson, Jonathan and Dipert, Alan}, + date = {2021}, + url = {https://CRAN.R-project.org/package=shiny}, + version = {1.17.1} +} + +@article{choiAssessmentWearNonwear2012, + title = {Assessment of Wear/Nonwear Time Classification Algorithms for Triaxial Accelerometer}, + author = {Choi, Leena and Ward, Suzanne Capen and Schnelle, John F. and Buchowski, Maciej S.}, + date = {2012-10}, + journaltitle = {Med Sci Sports Exerc}, + volume = {44}, + number = {10}, + pages = {2009--2016}, + issn = {0195-9131}, + doi = {10.1249/MSS.0b013e318258cb36}, + url = {https://journals.lww.com/00005768-201210000-00023}, + urldate = {2022-06-15}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\JML8K736\\Choi et al. - 2012 - Assessment of WearNonwear Time Classification Alg.pdf} +} + +@article{colbertComparativeValidityPhysical2011, + title = {Comparative Validity of Physical Activity Measures in Older Adults}, + author = {Colbert, Lisa H. and Matthews, Charles E. and Havighurst, Thomas C. and Kim, Kyungmann and Schoeller, Dale A.}, + date = {2011-05}, + journaltitle = {Med Sci Sports Exerc}, + volume = {43}, + number = {5}, + pages = {867--876}, + issn = {0195-9131}, + doi = {10.1249/MSS.0b013e3181fc7162}, + url = {https://journals.lww.com/00005768-201105000-00018}, + urldate = {2022-07-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\53ITCPWM\\Colbert et al. - 2011 - Comparative Validity of Physical Activity Measures.pdf} +} + +@article{demeyerObjectivelyMeasuredPhysical2021, + title = {Objectively Measured Physical Activity in Patients with {{COPD}}: Recommendations from an International {{Task Force}} on Physical Activity}, + shorttitle = {Objectively {{Measured Physical Activity}} in {{Patients}} with {{COPD}}}, + author = {Demeyer, Heleen and Mohan, Divya and Burtin, Chris and Vaes, Anouk and Heasley, Matthew and Bowler, Russell P. and Casaburi, Richard and Cooper, Christopher B. and Corriol-Rohou, Solange and Frei, Anja and Hamilton, Alan and Hopkinson, Nicholas S. and Karlsson, Niklas and Man, William D-C. and Moy, Marilyn L. and Pitta, Fabio and Polkey, Michael I. and Puhan, Milo and Rennard, Stephen I. and Rochester, Carolyn L. and Rossiter, Harry B. and Sciurba, Frank and Singh, Sally and Tal-Singer, Ruth and Vogiatzis, Ioannis and Watz, Henrik and Lummel, Rob Van and Wyatt, Jeremy and Merrill, Debora D. and Spruit, Martijn A. and Garcia-Aymerich, Judith and Troosters, Thierry}, + date = {2021}, + journaltitle = {J COPD F}, + volume = {8}, + number = {4}, + pages = {528--550}, + issn = {2372952X}, + doi = {10.15326/jcopdf.2021.0213}, + url = {https://journal.copdfoundation.org/jcopdf/id/1359/Objectively-Measured-Physical-Activity-in-Patients-with-COPD-Recommendations-from-an-International-Task-Force-on-Physical-Activity}, + urldate = {2022-06-15}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\UYCBQA92\\Demeyer et al. - 2021 - Objectively Measured Physical Activity in Patients.pdf} +} + +@article{dobbelsPROactiveInnovativeConceptual2014, + title = {The {{PROactive}} Innovative Conceptual Framework on Physical Activity}, + author = {Dobbels, Fabienne and de Jong, Corina and Drost, Ellen and Elberse, Janneke and Feridou, Chryssoula and Jacobs, Laura and Rabinovich, Roberto and Frei, Anja and Puhan, Milo A. and de Boer, Willem I. and van der Molen, Thys and Williams, Kate and Pinnock, Hillary and Troosters, Thierry and Karlsson, Niklas and Kulich, Karoly and Rüdell, Katja and {the PROactive consortium}}, + options = {useprefix=true}, + date = {2014-11}, + journaltitle = {Eur Respir J}, + volume = {44}, + number = {5}, + pages = {1223--1233}, + issn = {0903-1936, 1399-3003}, + doi = {10.1183/09031936.00004814}, + url = {http://erj.ersjournals.com/lookup/doi/10.1183/09031936.00004814}, + urldate = {2022-06-15}, + abstract = {Although physical activity is considered an important therapeutic target in chronic obstructive pulmonary disease (COPD), what “physical activity” means to COPD patients and how their perspective is best measured is poorly understood. We designed a conceptual framework, guiding the development and content validation of two patient reported outcome (PRO) instruments on physical activity (PROactive PRO instruments). 116 patients from four European countries with diverse demographics and COPD phenotypes participated in three consecutive qualitative studies (63\% male, age mean± sd 66±9 years, 35\% Global Initiative for Chronic Obstructive Lung Disease stage III–IV). 23 interviews and eight focus groups (n = 54) identified the main themes and candidate items of the framework. 39 cognitive debriefings allowed the clarity of the items and instructions to be optimised. Three themes emerged, i.e. impact of COPD on amount of physical activity, symptoms experienced during physical activity, and adaptations made to facilitate physical activity. The themes were similar irrespective of country, demographic or disease characteristics. Iterative rounds of appraisal and refinement of candidate items resulted in 30 items with a daily recall period and 34 items with a 7-day recall period. For the first time, our approach provides comprehensive insight on physical activity from the COPD patients’ perspective. The PROactive PRO instruments’ content validity represents the pivotal basis for empirically based item reduction and validation.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\4N9ZGRA5\\Dobbels et al. - 2014 - The PROactive innovative conceptual framework on p.pdf} +} + +@software{fayGolemFrameworkRobust2022, + title = {Golem: {{A Framework}} for {{Robust Shiny Applications}}}, + author = {Fay, Colin and Guyader, Vincent and Rochette, Sébastien and Girard, Cervan}, + date = {2022}, + version = {0.3.2} +} + +@article{garcia-aymerichValidityResponsivenessDaily2021, + title = {Validity and Responsiveness of the {{Daily-}} and {{Clinical}} Visit-{{PROactive Physical Activity}} in {{COPD}} ({{D-PPAC}} and {{C-PPAC}}) Instruments}, + author = {Garcia-Aymerich, Judith and Puhan, Milo A and Corriol-Rohou, Solange and de Jong, Corina and Demeyer, Heleen and Dobbels, Fabienne and Erzen, Damijan and Frei, Anja and Gimeno-Santos, Elena and Hopkinson, Nicholas S and Ivanoff, Nathalie and Karlsson, Niklas and Louvaris, Zafeiris and Polkey, Michael I and Rabinovich, Roberto A and Scuri, Mario and Tabberer, Maggie and Vogiatzis, Ioannis and Troosters, Thierry}, + options = {useprefix=true}, + date = {2021-03}, + journaltitle = {Thorax}, + volume = {76}, + number = {3}, + pages = {228--238}, + issn = {0040-6376, 1468-3296}, + doi = {10.1136/thoraxjnl-2020-214554}, + url = {https://thorax.bmj.com/lookup/doi/10.1136/thoraxjnl-2020-214554}, + urldate = {2022-06-10}, + abstract = {Background The Daily-PROactive and Clinical visit-PROactive Physical Activity (D-PPAC and C-PPAC) instruments in chronic obstructive pulmonary disease (COPD) combines questionnaire with activity monitor data to measure patients’ experience of physical activity. Their amount, difficulty and total scores range from 0 (worst) to 100 (best) but require further psychometric evaluation. Objective To test reliability, validity and responsiveness, and to define minimal important difference (MID), of the D-PPAC and C-PPAC instruments, in a large population of patients with stable COPD from diverse severities, settings and countries. Methods We used data from seven randomised controlled trials to evaluate D-PPAC and C-PPAC internal consistency and construct validity by sex, age groups, COPD severity, country and language as well as responsiveness to interventions, ability to detect change and MID. Results We included 1324 patients (mean (SD) age 66 (8) years, forced expiratory volume in 1 s 55 (17)\% predicted). Scores covered almost the full range from 0 to 100, showed strong internal consistency after stratification and correlated as a priori hypothesised with dyspnoea, health-related quality of life and exercise capacity. Difficulty scores improved after pharmacological treatment and pulmonary rehabilitation, while amount scores improved after behavioural physical activity interventions. All scores were responsive to changes in self-reported physical activity experience (both worsening and improvement) and to the occurrence of COPD exacerbations during follow-up. The MID was estimated to 6 for amount and difficulty scores and 4 for total score. Conclusions The D-PPAC and C-PPAC instruments are reliable and valid across diverse COPD populations and responsive to pharmacological and non-pharmacological interventions and changes in clinically relevant variables.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\AGXQHEZR\\Garcia-Aymerich et al. - 2021 - Validity and responsiveness of the Daily- and Clin.pdf} +} + +@article{gardnerAssessmentFreelivingDaily1998, + title = {Assessment of Free-Living Daily Physical Activity in Older Claudicants: Validation against the Doubly Labeled Water Technique}, + shorttitle = {Assessment of {{Free-Living Daily Physical Activity}} in {{Older Claudicants}}}, + author = {Gardner, A. W. and Poehlman, E. T.}, + date = {1998-07-01}, + journaltitle = {The Journals of Gerontology Series A: Biological Sciences and Medical Sciences}, + volume = {53A}, + number = {4}, + pages = {M275-M280}, + issn = {1079-5006, 1758-535X}, + doi = {10.1093/gerona/53A.4.M275}, + url = {https://academic.oup.com/biomedgerontology/article-lookup/doi/10.1093/gerona/53A.4.M275}, + urldate = {2022-07-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\D4YNDAB3\\Gardner et Poehlman - 1998 - Assessment of Free-Living Daily Physical Activity .pdf} +} + +@article{gimeno-santosPROactiveInstrumentsMeasure2015, + title = {The {{PROactive}} Instruments to Measure Physical Activity in Patients with Chronic Obstructive Pulmonary Disease}, + author = {Gimeno-Santos, Elena and Raste, Yogini and Demeyer, Heleen and Louvaris, Zafeiris and de Jong, Corina and Rabinovich, Roberto A. and Hopkinson, Nicholas S. and Polkey, Michael I. and Vogiatzis, Ioannis and Tabberer, Maggie and Dobbels, Fabienne and Ivanoff, Nathalie and de Boer, Willem I. and van der Molen, Thys and Kulich, Karoly and Serra, Ignasi and Basagaña, Xavier and Troosters, Thierry and Puhan, Milo A. and Karlsson, Niklas and Garcia-Aymerich, Judith}, + options = {useprefix=true}, + date = {2015-10}, + journaltitle = {Eur Respir J}, + volume = {46}, + number = {4}, + pages = {988--1000}, + issn = {0903-1936, 1399-3003}, + doi = {10.1183/09031936.00183014}, + url = {http://erj.ersjournals.com/lookup/doi/10.1183/09031936.00183014}, + urldate = {2022-06-14}, + abstract = {No current patient-centred instrument captures all dimensions of physical activity in chronic obstructive pulmonary disease (COPD). Our objective was item reduction and initial validation of two instruments to measure physical activity in COPD. Physical activity was assessed in a 6-week, randomised, two-way cross-over, multicentre study using PROactive draft questionnaires (daily and clinical visit versions) and two activity monitors. Item reduction followed an iterative process including classical and Rasch model analyses, and input from patients and clinical experts. 236 COPD patients from five European centres were included. Results indicated the concept of physical activity in COPD had two domains, labelled “amount” and “difficulty”. After item reduction, the daily PROactive instrument comprised nine items and the clinical visit contained 14. Both demonstrated good model fit (person separation index {$>$}0.7). Confirmatory factor analysis supported the bidimensional structure. Both instruments had good internal consistency (Cronbach's α{$>$}0.8), test–retest reliability (intraclass correlation coefficient ≥0.9) and exhibited moderate-to-high correlations (r{$>$}0.6) with related constructs and very low correlations (r{$<$}0.3) with unrelated constructs, providing evidence for construct validity. Daily and clinical visit “PROactive physical activity in COPD” instruments are hybrid tools combining a short patient-reported outcome questionnaire and two activity monitor variables which provide simple, valid and reliable measures of physical activity in COPD patients.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\JVKM44WX\\Gimeno-Santos et al. - 2015 - The PROactive instruments to measure physical acti.pdf} +} + +@article{hallalEnergyExpenditureCompared2013, + title = {Energy {{Expenditure}} Compared to Physical Activity Measured by Accelerometry and Self-Report in Adolescents: A Validation Study}, + shorttitle = {Energy {{Expenditure Compared}} to {{Physical Activity Measured}} by {{Accelerometry}} and {{Self-Report}} in {{Adolescents}}}, + author = {Hallal, Pedro C. and Reichert, Felipe F. and Clark, Valerie L. and Cordeira, Kelly L. and Menezes, Ana M. B. and Eaton, Simon and Ekelund, Ulf and Wells, Jonathan C.}, + editor = {Votruba, Susanne Breuer}, + date = {2013-11-04}, + journaltitle = {PLoS One}, + volume = {8}, + number = {11}, + pages = {e77036}, + issn = {1932-6203}, + doi = {10.1371/journal.pone.0077036}, + url = {https://dx.plos.org/10.1371/journal.pone.0077036}, + urldate = {2022-07-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\H5547JSS\\Hallal et al. - 2013 - Energy Expenditure Compared to Physical Activity M.pdf} +} + +@article{keadleEvaluationAccelerometerderivedMetrics2017, + title = {An Evaluation of Accelerometer-Derived Metrics to Assess Daily Behavioral Patterns}, + author = {Keadle, Sarah Kozey and Sampson, Joshua N. and Li, Haocheng and Lyden, Kate and Matthews, Charles E. and Carroll, Raymond J.}, + date = {2017-01}, + journaltitle = {Med Sci Sports Exerc}, + volume = {49}, + number = {1}, + pages = {54--63}, + issn = {0195-9131}, + doi = {10.1249/MSS.0000000000001073}, + url = {https://journals.lww.com/00005768-201701000-00007}, + urldate = {2022-07-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\4YN6F6UZ\\Keadle et al. - 2017 - An Evaluation of Accelerometer-derived Metrics to .pdf} +} + +@article{korenyPatternsPhysicalActivity2021, + title = {Patterns of Physical Activity Progression in Patients with {{COPD}}}, + author = {Koreny, Maria and Demeyer, Heleen and Benet, Marta and Arbillaga-Etxarri, Ane and Balcells, Eva and Barberan-Garcia, Anael and Gimeno-Santos, Elena and Hopkinson, Nicholas S. and De Jong, Corina and Karlsson, Niklas and Louvaris, Zafeiris and Polkey, Michael I. and Puhan, Milo A. and Rabinovich, Roberto A. and Rodríguez-Roisin, Robert and Vall-Casas, Pere and Vogiatzis, Ioannis and Troosters, Thierry and Garcia-Aymerich, Judith and Arbillaga-Etxarri, Ane and Benet, Marta and Delgado, Anna and Garcia-Aymerich, Judith and Gimeno-Santos, Elena and Torrent-Pallicer, Jaume and Vilaró, Jordi and Barberan-Garcia, Anael and Rodriguez-Roisín, Robert and Balcells, Eva and Chiaradía, Diego A Rodríguez and Marín, Alicia and Ortega, Pilar and Celorrio, Nuria and Monteagudo, Mónica and Montellà, Nuria and Muñoz, Laura and Toran, Pere and Simonet, Pere and Jané, Carme and Martín-Cantera, Carlos and Borrell, Eulàlia and Vall-Casas, Pere and Ivanoff, Nathalie and Karlsson, Niklas and Corriol-Rohou, Solange and Jarrod, Ian and Erzen, Damijen and Brindicci, Caterina and Higenbottam, Tim and Scuri, Mario and McBride, Paul and Kamel, Nadia and Tabberer, Margaret and Troosters, Thierry and Dobbels, Fabienne and Garcia-Aymerich, Judith and de Boer, Pim and Kulich, Karoly and Glendenning, Alastair and Rudell, Katja and Wilson, Frederick J. and Polkey, Michael I. and Hopkinson, Nick S. and Vogiatzis, Ioannis and Nikai, Enkeleida and van der Molen, Thys and De Jong, Corina and Rabinovich, Roberto A. and MacNee, Bill and Puhan, Milo A. and Frei, Anja}, + options = {useprefix=true}, + date = {2021-03}, + journaltitle = {Arch Bronconeumol}, + volume = {57}, + number = {3}, + pages = {214--223}, + issn = {03002896}, + doi = {10.1016/j.arbres.2020.08.001}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0300289620302805}, + urldate = {2022-06-10}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\4CHPN684\\Koreny et al. - 2021 - Patterns of Physical Activity Progression in Patie.pdf} +} + +@article{miguelesAccelerometerDataCollection2017, + title = {Accelerometer {{Data Collection}} and {{Processing Criteria}} to {{Assess Physical Activity}} and {{Other Outcomes}}: {{A Systematic Review}} and {{Practical Considerations}}}, + shorttitle = {Accelerometer {{Data Collection}} and {{Processing Criteria}} to {{Assess Physical Activity}} and {{Other Outcomes}}}, + author = {Migueles, Jairo H. and Cadenas-Sanchez, Cristina and Ekelund, Ulf and Delisle Nyström, Christine and Mora-Gonzalez, Jose and Löf, Marie and Labayen, Idoia and Ruiz, Jonatan R. and Ortega, Francisco B.}, + date = {2017-09}, + journaltitle = {Sports Med}, + volume = {47}, + number = {9}, + pages = {1821--1845}, + issn = {0112-1642, 1179-2035}, + doi = {10.1007/s40279-017-0716-0}, + url = {http://link.springer.com/10.1007/s40279-017-0716-0}, + urldate = {2022-06-15}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\976M4CBU\\Migueles et al. - 2017 - Accelerometer Data Collection and Processing Crite.pdf} +} + +@article{philipMovingSingingLung2020, + title = {Moving Singing for Lung Health Online in Response to {{COVID-19}}: Experience from a Randomised Controlled Trial}, + shorttitle = {Moving Singing for Lung Health Online in Response to {{COVID-19}}}, + author = {Philip, Keir EJ and Lewis, Adam and Jeffery, Edmund and Buttery, Sara and Cave, Phoene and Cristiano, Daniele and Lound, Adam and Taylor, Karen and Man, William D-C and Fancourt, Daisy and Polkey, Michael I and Hopkinson, Nicholas S}, + date = {2020-11}, + journaltitle = {BMJ Open Resp Res}, + volume = {7}, + number = {1}, + pages = {e000737}, + issn = {2052-4439}, + doi = {10.1136/bmjresp-2020-000737}, + url = {https://bmjopenrespres.bmj.com/lookup/doi/10.1136/bmjresp-2020-000737}, + urldate = {2022-06-10}, + abstract = {Introduction Singing for lung health (SLH) is a popular arts-in-health activity for people with long-term respiratory conditions. Participants report biopsychosocial benefits, however, research on impact is limited. The ‘SLH: Improving Experiences of Lung Disease trial’, a randomised controlled, single (assessor) blind, trial of 12 weeks SLH versus usual care for people with chronic obstructive pulmonary disease (COPD) (n=120) was setup to help to address this. The first group (n=18, nine singing and nine controls) started face-to-face (five sessions) before changing to online delivery (seven sessions) due to COVID-19-related physical distancing measures. As such, the experience of this group is here reported as a pilot study to inform further research in this area. Methods We conducted semistructured interviews and thematic analysis regarding barriers, facilitators and key considerations for transitioning from face-to-face to online delivery. Pilot quantitative outcomes include attendance, premeasures and postmeasures of quality of life and disease impact (Short Form 36 Health Survey, COPD Assessment Test score), breathlessness (Medical Research Council breathlessness scale, Dyspnoea-12), depression (Patient Health Questionnaire-9, PHQ-9), anxiety (Generalised Anxiety Disorder-7), balance confidence (Activity specific Balance Confidence, ABC scale) and physical activity (clinical visit PROactive physical activity in COPD tool, combining subjective rating and actigraphy). Results Attendance was 69\% overall, (90\% of the face-to-face sessions, 53\% online sessions). Analysis of semistructured interviews identified three themes regarding participation in SLH delivered face to face and online, these where (1) perceived benefits; (2) digital barriers (online) and (3) digital facilitators (online). Findings were summarised into key considerations for optimising transitioning singing groups from face-to-face to online delivery. Pilot quantitative data suggested possible improvements in depression (treatment effect −4.78 PHQ-9 points, p{$<$}0.05, MCID 5) and balance confidence (treatment effect +17.21 ABC scale points, p=0.04, MCID 14.2). Discussion This study identifies key considerations regarding the adaptation of SLH from face-to-face to online delivery. Pilot data suggest online group singing for people with COPD may deliver benefits related to reducing depression and improved balance confidence.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\GZ3Q5X23\\Philip et al. - 2020 - Moving singing for lung health online in response .pdf} +} + +@software{rcoreteamLanguageEnvironmentStatistical2022, + title = {R: {{A}} Language and Environment for Statistical Computing. {{R Foundation}} for {{Statistical Computing}}, {{Vienna}}, {{Austria}}.}, + author = {R Core Team}, + date = {2022}, + url = {https://www.R-project.org/} +} + +@article{sorianoPrevalenceAttributableHealth2020, + title = {Prevalence and Attributable Health Burden of Chronic Respiratory Diseases, 1990–2017: A Systematic Analysis for the {{Global Burden}} of {{Disease Study}} 2017}, + shorttitle = {Prevalence and Attributable Health Burden of Chronic Respiratory Diseases, 1990–2017}, + author = {Soriano, Joan B and Kendrick, Parkes J and Paulson, Katherine R and Gupta, Vinay and Abrams, Elissa M and Adedoyin, Rufus Adesoji and Adhikari, Tara Ballav and Advani, Shailesh M and Agrawal, Anurag and Ahmadian, Elham and Alahdab, Fares and Aljunid, Syed Mohamed and Altirkawi, Khalid A and Alvis-Guzman, Nelson and Anber, Nahla Hamed and Andrei, Catalina Liliana and Anjomshoa, Mina and Ansari, Fereshteh and Antó, Josep M and Arabloo, Jalal and Athari, Seyyede Masoume and Athari, Seyyed Shamsadin and Awoke, Nefsu and Badawi, Alaa and Banoub, Joseph Adel Mattar and Bennett, Derrick A and Bensenor, Isabela M and Berfield, Kathleen S Sachiko and Bernstein, Robert S and Bhattacharyya, Krittika and Bijani, Ali and Brauer, Michael and Bukhman, Gene and Butt, Zahid A and Cámera, Luis Alberto and Car, Josip and Carrero, Juan J and Carvalho, Felix and Castañeda-Orjuela, Carlos A and Choi, Jee-Young Jasmine and Christopher, Devasahayam J and Cohen, Aaron J and Dandona, Lalit and Dandona, Rakhi and Dang, Anh Kim and Daryani, Ahmad and de Courten, Barbora and Demeke, Feleke Mekonnen and Demoz, Gebre Teklemariam and De Neve, Jan-Walter and Desai, Rupak and Dharmaratne, Samath Dhamminda and Diaz, Daniel and Douiri, Abdel and Driscoll, Tim Robert and Duken, Eyasu Ejeta and Eftekhari, Aziz and Elkout, Hajer and Endries, Aman Yesuf and Fadhil, Ibtihal and Faro, Andre and Farzadfar, Farshad and Fernandes, Eduarda and Filip, Irina and Fischer, Florian and Foroutan, Masoud and Garcia-Gordillo, M.A. and Gebre, Abadi Kahsu and Gebremedhin, Ketema Bizuwork and Gebremeskel, Gebreamlak Gebremedhn and Gezae, Kebede Embaye and Ghoshal, Aloke Gopal and Gill, Paramjit Singh and Gillum, Richard F and Goudarzi, Houman and Guo, Yuming and Gupta, Rajeev and Hailu, Gessessew Bugssa and Hasanzadeh, Amir and Hassen, Hamid Yimam and Hay, Simon I and Hoang, Chi Linh and Hole, Michael K and Horita, Nobuyuki and Hosgood, H Dean and Hostiuc, Mihaela and Househ, Mowafa and Ilesanmi, Olayinka Stephen and Ilic, Milena D and Irvani, Seyed Sina Naghibi and Islam, Sheikh Mohammed Shariful and Jakovljevic, Mihajlo and Jamal, Amr A and Jha, Ravi Prakash and Jonas, Jost B and Kabir, Zubair and Kasaeian, Amir and Kasahun, Gebremicheal Gebreslassie and Kassa, Getachew Mullu and Kefale, Adane Teshome and Kengne, Andre Pascal and Khader, Yousef Saleh and Khafaie, Morteza Abdullatif and Khan, Ejaz Ahmad and Khan, Junaid and Khubchandani, Jagdish and Kim, Young-Eun and Kim, Yun Jin and Kisa, Sezer and Kisa, Adnan and Knibbs, Luke D and Komaki, Hamidreza and Koul, Parvaiz A and Koyanagi, Ai and Kumar, G Anil and Lan, Qing and Lasrado, Savita and Lauriola, Paolo and La Vecchia, Carlo and Le, Tham Thi and Leigh, James and Levi, Miriam and Li, Shanshan and Lopez, Alan D and Lotufo, Paulo A and Madotto, Fabiana and Mahotra, Narayan B and Majdan, Marek and Majeed, Azeem and Malekzadeh, Reza and Mamun, Abdullah A and Manafi, Navid and Manafi, Farzad and Mantovani, Lorenzo Giovanni and Meharie, Birhanu Geta and Meles, Hagazi Gebre and Meles, Gebrekiros Gebremichael and Menezes, Ritesh G and Mestrovic, Tomislav and Miller, Ted R and Mini, Gk and Mirrakhimov, Erkin M and Moazen, Babak and Mohammad, Karzan Abdulmuhsin and Mohammed, Shafiu and Mohebi, Farnam and Mokdad, Ali H and Molokhia, Mariam and Monasta, Lorenzo and Moradi, Masoud and Moradi, Ghobad and Morawska, Lidia and Mousavi, Seyyed Meysam and Musa, Kamarul Imran and Mustafa, Ghulam and Naderi, Mehdi and Naghavi, Mohsen and Naik, Gurudatta and Nair, Sanjeev and Nangia, Vinay and Nansseu, Jobert Richie and Nazari, Javad and Ndwandwe, Duduzile Edith and Negoi, Ruxandra Irina and Nguyen, Trang Huyen and Nguyen, Cuong Tat and Nguyen, Huong Lan Thi and Nixon, Molly R and Ofori-Asenso, Richard and Ogbo, Felix Akpojene and Olagunju, Andrew T and Olagunju, Tinuke O and Oren, Eyal and Ortiz, Justin R and Owolabi, Mayowa O and P A, Mahesh and Pakhale, Smita and Pana, Adrian and Panda-Jonas, Songhomitra and Park, Eun-Kee and Pham, Hai Quang and Postma, Maarten J and Pourjafar, Hadi and Poustchi, Hossein and Radfar, Amir and Rafiei, Alireza and Rahim, Fakher and Rahman, Mohammad Hifz Ur and Rahman, Muhammad Aziz and Rawaf, Salman and Rawaf, David Laith and Rawal, Lal and Reiner Jr., Robert C and Reitsma, Marissa Bettay and Roever, Leonardo and Ronfani, Luca and Roro, Elias Merdassa and Roshandel, Gholamreza and Rudd, Kristina E and Sabde, Yogesh Damodar and Sabour, Siamak and Saddik, Basema and Safari, Saeed and Saleem, Komal and Samy, Abdallah M and Santric-Milicevic, Milena M and Sao Jose, Bruno Piassi and Sartorius, Benn and Satpathy, Maheswar and Savic, Miloje and Sawhney, Monika and Sepanlou, Sadaf G and Shaikh, Masood Ali and Sheikh, Aziz and Shigematsu, Mika and Shirkoohi, Reza and Si, Si and Siabani, Soraya and Singh, Virendra and Singh, Jasvinder A and Soljak, Michael and Somayaji, Ranjani and Soofi, Moslem and Soyiri, Ireneous N and Tefera, Yonatal Mesfin and Temsah, Mohamad-Hani and Tesfay, Berhe Etsay and Thakur, Jarnail Singh and Toma, Alemayehu Toma and Tortajada-Girbés, Miguel and Tran, Khanh Bao and Tran, Bach Xuan and Tudor Car, Lorainne and Ullah, Irfan and Vacante, Marco and Valdez, Pascual R and van Boven, Job F M and Vasankari, Tommi Juhani and Veisani, Yousef and Violante, Francesco S and Wagner, Gregory R and Westerman, Ronny and Wolfe, Charles D A and Wondafrash, Dawit Zewdu and Wondmieneh, Adam Belay and Yonemoto, Naohiro and Yoon, Seok-Jun and Zaidi, Zoubida and Zamani, Mohammad and Zar, Heather J and Zhang, Yunquan and Vos, Theo}, + options = {useprefix=true}, + date = {2020-06}, + journaltitle = {Lancet Respir Med}, + volume = {8}, + number = {6}, + pages = {585--596}, + issn = {22132600}, + doi = {10.1016/S2213-2600(20)30105-3}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2213260020301053}, + urldate = {2022-06-15}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\IHUXTYGT\\Soriano et al. - 2020 - Prevalence and attributable health burden of chron.pdf} +} + +@article{vaesChangesPhysicalActivity2014, + title = {Changes in Physical Activity and All-Cause Mortality in {{COPD}}}, + author = {Vaes, Anouk W. and Garcia-Aymerich, Judith and Marott, Jacob L. and Benet, Marta and Groenen, Miriam T.J. and Schnohr, Peter and Franssen, Frits M.E. and Vestbo, Jørgen and Wouters, Emiel F.M. and Lange, Peter and Spruit, Martijn A.}, + date = {2014-11}, + journaltitle = {Eur Respir J}, + volume = {44}, + number = {5}, + pages = {1199--1209}, + issn = {0903-1936, 1399-3003}, + doi = {10.1183/09031936.00023214}, + url = {http://erj.ersjournals.com/lookup/doi/10.1183/09031936.00023214}, + urldate = {2022-06-15}, + abstract = {Little is known about changes in physical activity in subjects with chronic obstructive pulmonary disease (COPD) and its impact on mortality. Therefore, we aimed to study changes in physical activity in subjects with and without COPD and the impact of physical activity on mortality risk. Subjects from the Copenhagen City Heart Study with at least two consecutive examinations were selected. Each examination included a self-administered questionnaire and clinical examination. 1270 COPD subjects and 8734 subjects without COPD (forced expiratory volume in 1 s 67±18 and 91±15\% predicted, respectively) were included. COPD subjects with moderate or high baseline physical activity who reported low physical activity level at follow-up had the highest hazard ratios of mortality (1.73 and 2.35, respectively; both p{$<$}0.001). In COPD subjects with low baseline physical activity, no differences were found in survival between unchanged or increased physical activity at follow-up. In addition, subjects without COPD with low physical activity at follow-up had the highest hazard ratio of mortality, irrespective of baseline physical activity level (p≤0.05). A decline to low physical activity at follow-up was associated with an increased mortality risk in subjects with and without COPD. These observational data suggest that it is important to assess and encourage physical activity in the earliest stages of COPD in order to maintain a physical activity level that is as high as possible, as this is associated with better prognosis.}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\MNQYEGRP\\Vaes et al. - 2014 - Changes in physical activity and all-cause mortali.pdf} +} + +@article{vaidyaTranslationCulturalAdaptation2020, + title = {Translation and Cultural Adaptation of {{PROactive}} Instruments for {{COPD}} in French and Influence of Weather and Pollution on Its Difficulty Score}, + author = {Vaidya, Trija and Thomas-Ollivier, Véronique and Hug, François and Bernady, Alain and Le Blanc, Camille and de Bisschop, Claire and Chambellan, Arnaud}, + options = {useprefix=true}, + date = {2020-03}, + journaltitle = {Int J Chron Obstruct Pulmon Dis}, + volume = {Volume 15}, + pages = {471--478}, + issn = {1178-2005}, + doi = {10.2147/COPD.S214410}, + url = {https://www.dovepress.com/translation-and-cultural-adaptation-of-proactive-instruments-for-copd--peer-reviewed-article-COPD}, + urldate = {2022-06-14}, + langid = {english}, + file = {C\:\\Users\\pydemullenheim\\Zotero\\storage\\CC94RYWK\\Vaidya et al. - 2020 - Translation and Cultural Adaptation of PROactive I.pdf} +} + +@book{whoWHOGuidelinesPhysical2020, + title = {{{WHO}} Guidelines on Physical Activity and Sedentary Behaviour}, + author = {WHO}, + date = {2020}, + publisher = {{Geneva: World Health Organization}} +} + +