BEGIN:VCALENDAR VERSION:2.0 PRODID:-//PR Stats - ECPv6.15.20//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-ORIGINAL-URL:https://prstats.org X-WR-CALDESC:Events for PR Stats REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/London BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20241027T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20250330T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20251026T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20260329T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20261025T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;VALUE=DATE:20251006 DTEND;VALUE=DATE:20251011 DTSTAMP:20260419T153431 CREATED:20240613T132140Z LAST-MODIFIED:20260408T111745Z UID:10000460-1759708800-1760140799@prstats.org SUMMARY:Bioacoustics Data Analysis (BIAC05) DESCRIPTION:Joint Species Distribution Modelling (JSDM) using HMSC: A Hierarchical Modelling Approach (JSDM01)\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Event Date \nMonday\, October 6th\, 2025\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Format\nThis is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link\, a good internet connection is essential. \nTime Zone\nTIME ZONE – UK (GMT) local time – however all sessions will be recorded and made available allowing attendees from different time zones to follow. \nPlease email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you. \n \n \n \n \n \n \n \n \n \n \n About this course\n The study of animal acoustic signals is a central tool for many fields in behavior\, ecology\, evolution and biodiversity monitoring. The accessibility of recording equipment and growing availability of open-access acoustic libraries provide an unprecedented opportunity to study animal acoustic signals at large temporal\, geographic and taxonomic scales. However\, the diversity of analytical methods and the multidimensionality of these signals posts significant challenges to conduct analyses that can quantify biologically meaningful variation. The recent development of acoustic analysis tools in the R programming environment provides a powerful means for overcoming these challenges\, facilitating the gathering and organization of large acoustic data sets and the use of more elaborated analyses that better fit the studied acoustic signals and associated biological questions. The course will introduce students on the basic concepts in animal acoustic signal research as well as hands-on experience on analytical tools in R. \nBy the end of the course\, participants should be able to: \n\nUnderstand the basic concepts of bioacoustics and how animal acoustic signals are analyzed\nGain proficiency in handling and manipulating acoustic data in R\, including working with ‘wave’ objects and other audio formats\nDevelop skills in building and interpreting spectrograms using Fourier transform techniques and the seewave package in R\nImport Raven Pro annotations into R and refine these annotations with warbleR functions\nUnderstand how to quantify the structure of acoustic signals through various approaches\nGain experience in quality control of recordings and annotations\, ensuring data integrity and accuracy\nCompare different methods for quantifying acoustic signal structure and understand the implications of each approach\n\n \n \n \n \n \n Intended Audiences\n \nAcademics and post-graduate students conducting research in bioacoustics\, animal behavior\, ecology\, or related fields\nApplied researchers and analysts in public\, private\, or non-profit organizations who require robust\, reproducible\, and flexible tools for analyzing acoustic data\nCurrent R users seeking to expand their knowledge into the field of bioacoustics and learn how to utilize specialized packages for acoustic analysis\nWildlife biologists\, and conservationists interested in leveraging bioacoustic methods for species monitoring and behavioral studies\nData scientists and programmers interested in applying their coding skills to the analysis of animal acoustic signals\n\n \n \n \n \n \n Venue\n Delivered remotely \n \n \n \n \n \n Course Details\n Time Zone – UK (GMT) local time \nAvailability – 20 places \nDuration – 5 days\, 4 hours per day \nContact hours – Approx. 20 hours \nECT’s – Equal to 2 ECT’s \nLanguage – English \n \n \n \n \n \n Teaching Format\n Introductory lectures on the concepts and refreshers on R usage. Intermediate-level lectures interspersed with hands-on mini practicals and longer projects. Data sets for computer practicals will be provided by the instructors\, but participants are welcome to bring their own data. \n \n \n \n \n \n \n Assumed quantitative knowledge\n A basic understanding of statistical concepts. Specifically\, generalised linear regression models\, statistical significance\, hypothesis testing. \n \n \n \n \n \n Assumed computer background\n Familiarity with R. Ability to import/export data\, manipulate data frames\, fit basic statistical models & generate simple exploratory and diagnostic plots. \n \n \n \n \n \n Equipment and software requirements\n \nA laptop computer with a working version of R or RStudio is required. R and RStudio are both available as free and open source software for PCs\, Macs\, and Linux computers. R may be downloaded by following the links here https://www.r-project.org/. RStudio may be downloaded by following the links here: https://www.rstudio.com/. \n\n\nAll the R packages that we will use in this course will be possible to download and install during the workshop itself as and when they are needed\, and a full list of required packages will be made available to all attendees prior to the course. \n\n\nA working webcam is desirable for enhanced interactivity during the live sessions\, we encourage attendees to keep their cameras on during live zoom sessions. \n\n\nAlthough not strictly required\, using a large monitor or preferably even a second monitor will improve he learning experience \n\n\nDownload R \n\n\nDownload RStudio \n\n\nDownload Zoom \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tickets \n \n \n \n \n \n \n The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities. \n\n\n\n \n \n HMSC01 ONLINE\n \n HMSC01 ONLINE\n\n \n \n \n \n £\n 450.00\n \n \n\n \n Unlimited \n \n \n Open the ticket description.\n More \n \n Close the ticket description.\n Less \n \n \n\n \n \n Decrease ticket quantity for HMSC01 ONLINE\n -\n \n \n Quantity \n \n\n \n Increase ticket quantity for HMSC01 ONLINE\n +\n \n \n \n \n\n \n \n Quantity: \n 0\n\n \n \n Total: \n \n \n \n £\n 0.00\n \n \n\n \n Get Tickets\n \n\n \n \n \n\n \n \n\n \n \n\n \n\n\n\n\n\n \n\n\n \n \n \n \n \n \n \n \n \n \n \n PLEASE READ – CANCELLATION POLICY \nCancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered\, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.\n \n \n \n \n \n \n\n\nIf you are unsure about course suitability\, please get in touch by email to find out more oliverhooker@prstatistics.com \n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Programme\n \n \n \n \n \n \n \n \n \n \n Monday 6th\n Day 1 – Classes from 13:30 – 17:30 \nIntroduction \n\nHow animal acoustic signals look like?An overview of the variety of acoustic signals produced by animals\, with examples from different species. This includes visualizing sound waves and spectrograms to understand their structure and complexity.\nAnalytical workflow in bioacoustics researchIntroduction to the step-by-step process involved in bioacoustic research\, from recording anddata collection to analysis and interpretation. This session will outline the typical workflow\,emphasizing the importance of each step.\nAdvantages of programmingDiscussion on the benefits of using programming languages like R for bioacoustic analysis\,including reproducibility\, efficiency\, and the ability to handle large datasets. This will highlighthow programming can enhance research capabilities.\n\n  \nWhat is sound? \n\nSound as a time seriesExplanation of how sound can be represented as a time series\, with each point in the seriesrepresenting the sound pressure level at a given moment in time. This forms the basis for further analysis and manipulation.\nSound as a digital objectDiscussion on the digitization of sound\, including sampling rates\, bit depth\, and the conversion of analog sound waves into digital formats that can be analyzed using software.\nAcoustic data in RIntroduction to handling and analyzing acoustic data in R. This includes importing sound files\, basic data exploration\, and visualization techniques.\n‘wave’ object structureExplanation of the ‘wave’ object in R\, its structure\, and the information it contains. This isessential for understanding how to manipulate and analyze sound data in R.\n‘wave’ object manipulationsTechniques for manipulating ‘wave’ objects\, including trimming\, concatenating\, and modifying sound files. Practical exercises will be provided to reinforce these concepts.\nAdditional formatsOverview of other audio file formats (e.g.\, MP3\, FLAC) and how they can be converted and used in R for bioacoustic analysis.\n\n \n \n \n \n \n Tuesday 7th\n Day 2 – Classes from 13:30 – 17:30 \nBuilding spectrograms \n\nFourier transformExplanation of the Fourier transform and its application in converting time-domain signals intofrequency-domain representations. This is the foundation for creating spectrograms.\nBuilding a spectrogramStep-by-step guide on how to construct spectrograms\, including parameter selection (e.g.\,window size\, overlap) and interpretation of the resulting visual representations.\nCharacteristics and limitationsDiscussion on the strengths and limitations of spectrograms\, including resolution trade-offs and potential artifacts. Participants will learn to critically evaluate spectrograms.\nSpectrograms in RPractical session on generating and customizing spectrograms in R using the seewave package.\nParticipants will create spectrograms from their own data.Package seewave\nExplore\, modify and measure ‘wave’ objectsHands-on exploration of the seewave package\, focusing on functions for modifying andmeasuring 'wave' objects. This includes exercises on filtering\, re-sampling\, and extracting acoustic features.\nSpectrograms and oscillogramsCreating and interpreting both spectrograms and oscillograms in R. Participants will learn tovisualize sound data in different ways to highlight various aspects of the signal.\nFiltering and re-samplingTechniques for filtering (e.g.\, band-pass\, high-pass) and re-sampling sound files to focus onspecific frequency ranges or standardize sampling rates.\nAcoustic measurementsUsing the seewave package to perform detailed acoustic measurements\, such as peak frequency\, dominant frequency\, and frequency range. Practical examples will be provided.\n\n \n \n \n \n \n Wednesday 8th\n Day 3 – Classes from 13:30 – 17:30 \nAnnotations \n\nIntroduction to the Raven Pro InterfaceA guided tour of the Raven Pro software\, its main features\, and interface elements. Participants will learn how to navigate the software efficiently.\nIntroduction to selections and measurementsInstruction on how to make selections within sound files and take basic measurements such as duration and frequency using Raven Pro.\nSaving\, retrieving\, and exporting selection tablesHow to save\, retrieve\, and export selection tables in Raven Pro for further analysis. This session will cover best practices for data management and organization.\nUsing annotationsTechniques for annotating sound files in Raven Pro\, including the use of labels and notes to mark significant events or features within the recordings.\n\n  \nQuantifying acoustic signal structure \n\nSpectro-temporal measurements (spectro_analysis())Introduction to the spectro_analysis() function in R for extracting spectro-temporalmeasurements from audio recordings. Participants will learn to describe acoustic signals in terms of their temporal and spectral characteristics.\nParameter descriptionDetailed explanation of key acoustic parameters\, such as duration\, frequency range\, andamplitude\, and how they are used to describe sound signals.\nHarmonic contentTechniques for analyzing the harmonic content of signals\, including identifying harmonic series and measuring harmonic-to-noise ratios.\nCepstral coefficients (mfcc_stats())Introduction to Mel-frequency cepstral coefficients (MFCCs) and their use in characterizing the timbral properties of sound signals. Participants will use the mfcc_stats() function to extract MFCCs.\nCross-correlation (cross_correlation())Explanation of cross-correlation techniques for comparing sound signals. Participants will use cross_correlation() to measure the similarity between different recordings.\nDynamic time warping (freq_DTW())Introduction to dynamic time warping (DTW) and its application in aligning and comparing time-series data. The freq_DTW() function will be used to compare sound signals.\nSignal-to-noise ratio (sig2noise())Techniques for calculating the signal-to-noise ratio (SNR) of recordings\, which is crucial forassessing the quality of sound data.\nInflections (inflections())Identifying and measuring inflections in sound signals\, which can indicate changes in pitch or other dynamic features.\nParameters at other levels (song_analysis())Exploring acoustic parameters at higher hierarchical levels\, such as entire songs or sequences of vocalizations\, using the song_analysis() function.\n\n \n \n \n \n \n Thursday 9th\n Day 4 – Classes from 13:30 – 17:30 \nQuality control in recordings and annotations \n\nCreate catalogsCompiling catalogs of annotated sound files\, which can be used for further analysis or asreference materials.\nCheck and modify sound file format (check_wavs()\, info_wavs()\, duration_wavs()\,mp32wav() y fix_wavs())Techniques for checking and modifying sound file formats using various functions in R. Thisincludes converting files\, checking file integrity\, and fixing common issues.\nTuning spectrogram parameters (tweak_spectro())Adjusting spectrogram parameters to optimize the visualization and analysis of sound signals.Participants will use tweak_spectro() to fine-tune their spectrograms.\nDouble-checking selection tables (check_sels()\, spectrograms()\, full_spectrograms() &catalog())Methods for verifying and refining selection tables\, ensuring that all annotations are accurate and comprehensive.\nRe-adjusting selections (tailor_sels())Techniques for re-adjusting selections in response to quality control checks\, ensuring that allannotations are precise and correctly positioned.Characterizing hierarchical levels in acoustic signals\nCreating ‘song’ spectrograms (full_spectrograms()\, spectrograms())Building spectrograms that represent entire songs or sequences of vocalizations\, providing ahigher-level view of acoustic patterns.\n‘Song’ parameters (song_analysis())Measuring and analyzing parameters at the song level\, such as song duration\, number ofelements and element rate\, using the song_analysis() function.\n\n \n \n \n \n \n Friday 10th\n Day 5 – Classes from 13:30 – 17:30 \nChoosing the right method for quantifying structure \n\nCompare different methods for quantifying structure (compare_methods())Comparing various methods for quantifying acoustic signal structure. Participants will usecompare_methods() to evaluate different approaches.Quantifying acoustic spaces\nIntro to PhenotypeSpaceIntroduction to the concept of acoustic spaces and the PhenotypeSpace framework\, which allows for the visualization and comparison of acoustic diversity.\nQuantifying space sizeTechniques for measuring the size of acoustic spaces\, which can provide insights into thevariability and complexity of vocalizations.\nComparing sub-spacesMethods for comparing different sub-spaces within the overall acoustic space\, allowing for the analysis of variations between species\, populations\, or other groups.\nEach of these topics will be covered with detailed explanations\, practical examples\, and hands-on exercises to ensure that participants gain a comprehensive understanding of bioacoustics research using the R platform.\n\n \n \n \n \n \n \n Course Instructor\n \n*\nDr. Marcelo Araya Salas\nWorks at – Neuroscience Research Center\, Universidad de Costa Rica \nMarcelo Araya-Salas works at the intersection of scientific programming and evolutionary behavioral ecology\, focusing on the evolution of behavior and the factors influencing it across cultural and evolutionary timescales. His research primarily examines the communication systems of neotropical species using single-species behavioral studies\, comparative phylogenetic methods\, and advanced data analysis techniques. He has developed several computational tools for biological data analysis\, including the R packages warbleR\, Rraven and baRulho which simplify the manipulation of annotated acoustic data and the quantification of structure and degradation of animal sounds. \nResearchGate \nGoogle Scholar \nWork Homepage \nPersonal Homepage URL:https://prstats.org/course/bioacoustics-data-analysis-biac05/ LOCATION:Delivered remotely (United Kingdom)\, Western European Time\, United Kingdom CATEGORIES:All Live Courses,Home Courses,Live Online Courses ATTACH;FMTTYPE=image/jpeg:https://prstats.org/wp-content/uploads/2024/06/BIACO5.jpg GEO:55.378051;-3.435973 END:VEVENT BEGIN:VEVENT DTSTART;VALUE=DATE:20251006 DTEND;VALUE=DATE:20251018 DTSTAMP:20260419T153431 CREATED:20251205T152336Z LAST-MODIFIED:20260408T112951Z UID:10000570-1759708800-1760745599@prstats.org SUMMARY:Introduction to Snakemake (SNKM01) DESCRIPTION:Joint Species Distribution Modelling (JSDM) using HMSC: A Hierarchical Modelling Approach (JSDM01)\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Event Date \nTuesday\, November 18th\, 2025\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Format\nThis is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link\, a good internet connection is essential. \nTime Zone\nTIME ZONE – UK (GMT) local time – however all sessions will be recorded and made available allowing attendees from different time zones to follow. \nPlease email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you. \n \n \n \n \n \n \n \n \n \n \n About this course\n This course is aimed towards researchers analysing field observations\, who are often faced by data heterogeneities due to field sampling protocols changing from one project to another\, or through time over the lifespan of projects\, or trying to combine legacy data sets with new data collected by recording units. \nSuch heterogeneities can bias analyses when data sets are integrated inadequately or can lead to information loss when filtered and standardized to common standards. Accounting for these issues is important for better inference regarding status and trend of species and communities. \nAnalysis of such ‘messy’ data sets need to feel comfortable with manipulating the data\, need a full understanding the mechanics of the models being used (i.e. critically interpreting the results and acknowledging assumptions and limitations)\, and should be able to make informed choices when faced with methodological challenges. \nThe course emphasizes critical thinking and active learning through hands on programming exercises. We will use publicly available data sets to demonstrate the data manipulation and analysis. We will use freely available and open-source R packages. \nThe expected outcome of the course is a solid foundation for further professional development via increased confidence in applying these methods for field observations. \nBy the end of the course\, participants should be able to: \n\nUnderstand basic statistical concepts related to detection error\nWork with field collected data and data from automated recording units (ARU)\nKnow packages such as unmarked\, detect\, bSims\nCritically evaluate modelling options and assumptions using simulations\nFit N-mixture\, distance sampling\, and time-removal models to data\n\n \n \n \n \n \n Intended Audiences\n \nAcademics and post-graduate students working on projects related to avian data\nApplied researchers and analysts in public\, private or third-sector organizations who need the reproducibility\, speed and flexibility of a programming language such as R for analysing point count data arising from avian field surveys\n\n \n \n \n \n \n Venue\n Delivered remotely \n \n \n \n \n \n Course Details\n Time Zone – UK (GMT) local time \nAvailability – 25 places \nDuration – 3 days\, 4 hours per day \nContact hours – Approx. 12 hours \nECT’s – Equal to 1 ECT \nLanguage – English \n \n \n \n \n \n Teaching Format\n Introductory lectures on the concepts and refreshers on R usage. Intermediate-level lectures interspersed with hands-on mini practicals and longer projects. Data sets for computer practicals will be provided by the instructors\, but participants are welcome to bring their own data. \n \n \n \n \n \n \n Assumed quantitative knowledge\n A basic understanding of statistical\, mathematical and physical concepts. Specifically\, generalised linear regression models\, including mixed models; basic knowledge of calculus. \n \n \n \n \n \n Assumed computer background\n Familiarity with R\, ability to import/export data\, manipulate data frames\, fit basic statistical models (up to GLM) and generate simple exploratory and diagnostic plots. \n \n \n \n \n \n Equipment and software requirements\n \nA laptop computer with a working version of R or RStudio is required. R and RStudio are both available as free and open source software for PCs\, Macs\, and Linux computers. R may be downloaded by following the links here https://www.r-project.org/. RStudio may be downloaded by following the links here: https://www.rstudio.com/. \n\n\nAll the R packages that we will use in this course will be possible to download and install during the workshop itself as and when they are needed\, and a full list of required packages will be made available to all attendees prior to the course. \n\n\nA working webcam is desirable for enhanced interactivity during the live sessions\, we encourage attendees to keep their cameras on during live zoom sessions. \n\n\nAlthough not strictly required\, using a large monitor or preferably even a second monitor will improve he learning experience \n\n\nDownload R \n\n\nDownload RStudio \n\n\nDownload Zoom \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tickets \n \n \n \n \n \n \n The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities. \n\n\n\n \n \n HMSC01 ONLINE\n \n HMSC01 ONLINE\n\n \n \n \n \n £\n 450.00\n \n \n\n \n Unlimited \n \n \n Open the ticket description.\n More \n \n Close the ticket description.\n Less \n \n \n\n \n \n Decrease ticket quantity for HMSC01 ONLINE\n -\n \n \n Quantity \n \n\n \n Increase ticket quantity for HMSC01 ONLINE\n +\n \n \n \n \n\n \n \n Quantity: \n 0\n\n \n \n Total: \n \n \n \n £\n 0.00\n \n \n\n \n Get Tickets\n \n\n \n \n \n\n \n \n\n \n \n\n \n\n\n\n\n\n \n\n\n \n \n \n \n \n \n \n \n \n \n \n PLEASE READ – CANCELLATION POLICY \nCancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered\, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.\n \n \n \n \n \n \n\n\nIf you are unsure about course suitability\, please get in touch by email to find out more oliverhooker@prstatistics.com \n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Programme\n \n \n \n \n \n \n \n \n \n \n Tuesday 18th\n Day 1 – Classes from 13:30 – 17:30 \nIntroduction \n\nIntroduction and background\nReview of field sampling techniques\nIntroduction to agent-based simulations\nOverview of regression techniques\nNaïve estimates of occupancy and abundance\nMultiple visits and N-mixture models\n\n \n \n \n \n \n Wednesday 19th\n Day 2 – Classes from 13:30 – 17:30 \nIntroduction to modelling \n\nBird behaviour\nTime-removal models\nObservation process\nDistance sampling\nCombining removal and distance sampling (QPAD)\n\n \n \n \n \n \n Thursday 20th\n Day 3 – Classes from 13:30 – 17:30 \nDifferent approaches \n\nSingle visit-based approaches (N-mixture and SQPAD)\nAnalysing data from recording units\nMulti-species models and using species traits and phylogeny\nDealing with roadside and other biases\nClosing remarks\n\n \n \n \n \n \n \n Course Instructor\n \nDr. Peter Solymos \nPéter is an ecologist and R programmer. He has worked with continental scale data sets and developed statistical techniques for estimating population density from messy data sets. He is the author of numerous well-known R packages\, including detect\, dclone\, vegan\, and ResourceSelection. He works currently as a data scientist helping utility companies improving their outage and impact prevention practices\, and is an adjunct professor at the University of Alberta in Edmonton\, Canada. \nGoogle Scholar \nWork Homepage \nPersonal Homepage URL:https://prstats.org/course/introduction-to-snakemake-snkm01/ LOCATION:Delivered remotely (United Kingdom)\, Western European Time Zone\, United Kingdom CATEGORIES:All Live Courses,Home Courses,Live Online Courses ATTACH;FMTTYPE=image/jpeg:https://prstats.org/wp-content/uploads/2025/09/SNKM01-1.jpg GEO:53.1423672;-7.6920536 END:VEVENT BEGIN:VEVENT DTSTART;VALUE=DATE:20251020 DTEND;VALUE=DATE:20251031 DTSTAMP:20260419T153431 CREATED:20251210T184910Z LAST-MODIFIED:20260408T111541Z UID:10000571-1760918400-1761868799@prstats.org SUMMARY:Path Analysis\, Structural Equations\, and Causal Inference for Biologists (PSCB03) DESCRIPTION:Joint Species Distribution Modelling (JSDM) using HMSC: A Hierarchical Modelling Approach (JSDM01)\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Event Date \nMonday\, October 20th\, 2025\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Format\nThis is a ‘LIVE COURSE’ – the instructors will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link\, a good internet connection is essential. \nCOURSE PROGRAM\nTIME ZONE – Quebec (Canada) local time – however all sessions will be recorded and made available allowing attendees from different time zones to follow. \nPlease email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you). \n \n \n \n \n \n \n \n \n \n \n About This Course\n This course\, based primarily on my 2016 book\, teaches you how to use path analysis and structural equations modelling to test causal hypotheses using observational data that is typical of research in ecology and evolution. It is taught in half-day sessions so that you can practice individually after each half-day session. You will learn how to conduct these tests\, why (andwhen) they are justified\, and how to interpret the results. The first few lectures will primarily present the theory but practical sessions will become more prominent later in the course. Thepractical work will be based on R and RStudio. Students will receive R script\, datasets\, and a list of R packages to install. It is highly recommended that each student have a copy of my 2016 book for the course\, but not essential. \n\nBy the end of the course\, participants should be able to: Understand the logical relationships between d-separation\, data\, and causal hypotheses. Know when to use piecewise SEM\, when to use covariance- based SEM\, and the advantages/disadvantages and assumptions of each Be able to construct\, test\, and interpret measurement models involving latent variables Be able to construct and identify equivalent models Be able to incorporate nested or mixed models\, multigroup models\, and non-normal distributions into SEM\n\nParticipants are encouraged to bring their own data\, as there will be opportunities throughout the course to plan\, analyze\, and receive feedback on structural equation models. \n \n \n \n \n \n Intended Audiences\n Scientists generally\, and ecologists specifically\, who want to test hypotheses concerning cause-and-effect relationships involving several variables\, especially involving observational data. \n \n \n \n \n \n Venue\n Delivered remotely \n \n \n \n \n \n Course Details\n Time Zone – Quebec (Canada) local time \nAvailability – TBC \nDuration – 9 days\, 4 hours per day \nContact hours – Approx. 35 hours \nECT’s – Equal to 3 ECT’s \nLanguage – English \n \n \n \n \n \n Teaching Format\n This course involves a mixture of theory and practical work. Data and analytical approaches will be presented in a lecture format to explain key concepts. Statistical analyses will then be presented using R. All R script that the instructor uses during these sessions will be shared with participants\, and R script will be presented and explained. \n \n \n \n \n \n Assumed quantative knowledge\n \nExperience in using R and RStudio for statistical analysis.\nA basic understanding of statistical inference and regression methods.\nA familiarity of more advanced regression models (mixed models\, generalized linear models) is an asset but is not essential.\n\n \n \n \n \n \n Assumed computer background\n Proficiency with R programming language\, including: importing/exporting data; manipulating data in the R environment; constructing and evaluating basic statistical models (e.g.\, lm()).\n \n \n \n \n \n Equipment and software requirements\n \nA laptop computer with a working version of R or RStudio is required. R and RStudio are both available as free and open source software for PCs\, Macs\, and Linux computers. R may be downloaded by following the links here https://www.r-project.org/. RStudio may be downloaded by following the links here: https://www.rstudio.com/. \n\n\nAll the R packages that we will use in this course will be possible to download and install during the workshop itself as and when they are needed\, and a full list of required packages will be made available to all attendees prior to the course. \n\n\nA working webcam is desirable for enhanced interactivity during the live sessions\, we encourage attendees to keep their cameras on during live zoom sessions. \n\n\nAlthough not strictly required\, using a large monitor or preferably even a second monitor will improve he learning experience \n\n\nDownload R \n\n\nDownload RStudio \n\n\nDownload Zoom \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tickets \n \n \n \n \n \n \n The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities. \n\n\n\n \n \n HMSC01 ONLINE\n \n HMSC01 ONLINE\n\n \n \n \n \n £\n 450.00\n \n \n\n \n Unlimited \n \n \n Open the ticket description.\n More \n \n Close the ticket description.\n Less \n \n \n\n \n \n Decrease ticket quantity for HMSC01 ONLINE\n -\n \n \n Quantity \n \n\n \n Increase ticket quantity for HMSC01 ONLINE\n +\n \n \n \n \n\n \n \n Quantity: \n 0\n\n \n \n Total: \n \n \n \n £\n 0.00\n \n \n\n \n Get Tickets\n \n\n \n \n \n\n \n \n\n \n \n\n \n\n\n\n\n\n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \nPLEASE READ – CANCELLATION POLICY \n\n\nCancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered\, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited \n\n \n \n \n \n \n \nIf you are unsure about course suitability\, please get in touch by email to find out more oliverhooker@prstatistics.com \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n COURSE PROGRAMME\n \n \n \n \n \n \n \n \n \n \n Monday 20th\n Day 1 – Classes from 08:30 – 12:30 \nCausal inference using experiments vs. observations (4h) \n\nRandomised experiments are the gold standard\nLimitations on randomised experiments\nThe logic of controlled experiments\nLimitations of controlled experiments\nPhysical control vs. observational control DAGs\, d-separation and data (2h)\\nTranslating from the language of causality to the language of statistics\nDirected acyclic graphs (DAGS) and d-separation\nD-separation and statistical conditioning\nThe difference between experimental control and statistical conditioning\nThe logic of causal inference using d-separation\n\n \n \n \n \n \n Tuesday 21st\n Day 2 – Classes from 08:30 – 12:30 \nPath analysis using piecewise structural equation modelling (1h30) \n\nD-separation basis sets of a DAG\nThe steps in conducting a piecewise SEM\nRejecting or provisionally accepting your path model\nPath coefficients as measures of direct causal effect\nDecomposing causal effects\n\nPractical work (2h) \n \n \n \n \n \n Wednesday 22nd\n Day 3 – Classes from 08:30 – 12:30 \nPath analysis using piecewiseSEM (2h30) \n\nThe piecewiseSEM library in R\n\nPractical work (1h) \n  \n \n \n \n \n \n Thursday 23rd\n Day 4 – Classes from 08:30 – 12:30 \nEquivalent models and AIC statistics (2h) \n\nStatistical power in SEM\nProvisionally accepting a causal hypothesis\nWhat is a “d-separation equivalent” DAG\nRules for identifying equivalent models\nAIC statistic to compare between non-equivalent models\nHow to interpret AIC statistics\n\nPractical work (1h30) \n \n \n \n \n \n Friday 24th\n Day 5 – Classes from 08:30 – 12:30 \nCovariance-based path analysis (2h) \n\nTranslating the DAG into “structural equations”\nThe model-predicted covariance matrix\nAn intuitive explanation of maximum likelihood estimating\nEstimating the free parameters via ML\nThe concept of “degrees of freedom”\nThe ML chi-squared statistic of model fit\nRejecting (or not) your SE model\n\nCovariance-based path analysis using lavaan (1h30) \n \n \n \n \n \n Monday 27th\n Day 6 – Classes from 08:30 – 12:30 \nLatent variables and measurement models (3h) \n\nRemoving latent variables from a DAG\nDAGs and MAGs\nDAG.to.MAG() function\nWhen you can’t remove a latent: measurement models\nMeasurement models and ML estimation\nFixing the scale of a latent variable\nMeasurement models and minimum degrees of freedom\nMeasurement models in lavaan\nEmpirical example: measuring soil fertility\n\n \n \n \n \n \n Tuesday 28th\n Day 7 – Classes from 08:30 – 12:30 \nPractical using measurement models (1h) \nThe full structural equation model (2h30) \n\nModel identification: structural and empirical\nComposite variables and composite latents\nConsequences and solutions for small sample sizes\nConsequences and solutions for non-normal data\nMeasures of approximate fit\nMissing data\nReporting results in publications\n\n \n \n \n \n \n Wednesday 29th\n Day 8 – Classes from 08:30 – 12:30 \nMultigroup models (2h) \n\nWhat is causal heterogeneity?\nThe concept of nested models\nHow to fit multigroup models in lavaan\n\nPractical: putting everything together (1h30) \n \n \n \n \n \n Thursday 30th\n Day 9 – Classes from 08:30 – 12:30 \nPractical and group presentations of results \n \n \n \n \n \n \n \n \n Bill Shipley\n \n Bill Shipley is an experienced researcher and teacher in plant ecology and statistical ecology.  He has published four scientific monographs and over 170 peer-reviewed papers. URL:https://prstats.org/course/path-analysis-structural-equations-and-causal-inference-for-biologists-pscb03/ LOCATION:Delivered remotely (United Kingdom)\, Western European Time Zone\, United Kingdom CATEGORIES:All Live Courses,Home Courses,Live Online Courses ATTACH;FMTTYPE=image/jpeg:https://prstats.org/wp-content/uploads/2023/12/PCSB03.jpg GEO:53.1423672;-7.6920536 END:VEVENT BEGIN:VEVENT DTSTART;VALUE=DATE:20251020 DTEND;VALUE=DATE:20251101 DTSTAMP:20260419T153431 CREATED:20250714T090844Z LAST-MODIFIED:20260413T142343Z UID:10000482-1760918400-1761955199@prstats.org SUMMARY:Bayesian Multilevel Modelling using brms for Ecologists (BMME01) DESCRIPTION:Joint Species Distribution Modelling (JSDM) using HMSC: A Hierarchical Modelling Approach (JSDM01)\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Event Date \nMonday\, December 1st\, 2025\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Course Format\nThis is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link\, a good internet connection is essential. \nTime Zone\nTIME ZONE – Portugal (GMT+1) local time – however all sessions will be recorded and made available allowing attendees from different time zones to follow. \nPlease email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you). \n \n \n \n \n \n \n \n \n \n \n About This Course\n Have you built an Ecological Niche Model? If yes\, you have already encountered challenges on data preparation\, or have struggled with issues in models fitting and accuracy. This course will teach you how to overcome these challenges and improve the accuracy of your ecological niche models. By the end of 5-day practical course\, you will have the capacity to filter records and select your variables with variance inflation factor; to test effect of Maxent regularization parameter in models performance; to validate models performance and accuracy; to perform MESS analysis\, null models\, and mechanistic models\, as well as to build your “virtual species”. \nEcological niche\, species distribution\, habitat distribution\, or climatic envelope models are different names for mechanistic and correlative models\, which are empirical or mathematical approaches to the ecological niche of a species. These methods relate different types of ecogeographical variables (environmental\, topographical\, human) to species physiological data or geographical locations\, in order to identify the factors limiting and defining the species' niche. ENMs have become popular because of their efficiency in the design and implementation of conservation management. \nBy the end of 5-day practical course should be able to: \n\nfilter records and select your variables with variance inflation factor;\ntest the effect of Maxent regularization parameter in models performance;\nvalidate models performance and accuracy;\nperform MESS analysis\, null models\, and mechanistic models\, as well as to build your “virtual species”.\n\nStudents will learn to use functions implemented in the packages “usdm”; “dismo”; “ENMEval”; “SDMvspecies”; “spThin”; and “NicheMapper” among others. \n \n \n \n \n \n Intended Audiences\n This course is orientated to PhD and MSc students\, as well as other students and researchers working on biogeography\, spatial ecology\, or related disciplines\, with experience in ecological niche models. \n \n \n \n \n \n Venue\n Delivered remotely\n \n \n \n \n \n Course Details\n Time Zone – Portugal (GMT+!) local time \nAvailability – 24 places \nDuration – 5 days\, 7 hours a day \nContact hours – Approx. 35 hours \nECT’s – Equal to 3ECT’s \nLanguage – English \n \n \n \n \n \n Teaching Format\n The course will be mainly practical\, with some theoretical lectures. All modelling processes and calculations will be performed with R\, the free software environment for statistical computing and graphics (http://www.r-project.org/). Students will learn to use functions implemented in the packages “usdm”; “dismo”; “ENMEval”; “SDMvspecies”; “spThin”; and “NicheMapper” among others. \n \n \n \n \n \n Assumed quantitative knowledge\n A basic understanding of ecological niche models and biogeography in general is required\, thus we will assume the attendees know how to run an ecological niche model. \n \n \n \n \n \n Assumed computer background\n Solid knowledge in Geographical Information Systems and R statistical package is necessary. It is also essential to have experience in ecological niche models. We will focus exclusively on advanced methods. If you need an introductory course on ecological niche models\, please consider attending our basic course on PRStatistics (www.prstats.org). \n \n \n \n \n \n Equipment and software requirements\n \nA laptop computer with a working version of R or RStudio is required. R and RStudio are both available as free and open source software for PCs\, Macs\, and Linux computers. R may be downloaded by following the links here https://www.r-project.org/. RStudio may be downloaded by following the links here: https://www.rstudio.com/. \n\n\nAll the R packages that we will use in this course will be possible to download and install during the workshop itself as and when they are needed\, and a full list of required packages will be made available to all attendees prior to the course. \n\n\nA working webcam is desirable for enhanced interactivity during the live sessions\, we encourage attendees to keep their cameras on during live zoom sessions. \n\n\nAlthough not strictly required\, using a large monitor or preferably even a second monitor will improve he learning experience \n\n\nDownload R \n\n\nDownload RStudio \n\n\nDownload Zoom \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tickets \n \n \n \n \n \n \n The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities. \n\n\n\n \n \n HMSC01 ONLINE\n \n HMSC01 ONLINE\n\n \n \n \n \n £\n 450.00\n \n \n\n \n Unlimited \n \n \n Open the ticket description.\n More \n \n Close the ticket description.\n Less \n \n \n\n \n \n Decrease ticket quantity for HMSC01 ONLINE\n -\n \n \n Quantity \n \n\n \n Increase ticket quantity for HMSC01 ONLINE\n +\n \n \n \n \n\n \n \n Quantity: \n 0\n\n \n \n Total: \n \n \n \n £\n 0.00\n \n \n\n \n Get Tickets\n \n\n \n \n \n\n \n \n\n \n \n\n \n\n\n\n\n\n \n\n\n \n \n \n \n \n \n \n \n \n \n \n PLEASE READ – CANCELLATION POLICY \nCancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered\, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.\n \n \n \n \n \n \nIf you are unsure about course suitability\, please get in touch by email to find out more oliverhooker@prstatistics.com \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n COURSE PROGRAMME\n  \n \n \n \n \n \n \n \n \n \n \n Monday 1st\n Day 1 – Classes from 09:30 to 17:30 \n\nENM guide: how to model\nENM R packages.\nSources of environmental variables using geodata package.\nGetting species records with geodata package.\n\n \n \n \n \n \n Tuesday 2nd\n Day 2 – Classes from 09:30 to 17:30 \n\nVariable selection with variance inflation factor (VIF) and usdm packages.\nChoosing the correct study area.\nFiltering records using usdm/spThin packages.\nChoosing pseudo-absences with Biomod2 package.\n\n \n \n \n \n \n Wednesday 3rd\n Day 3 – Classes from 09:30 to 17:30 \n\nSplit records in training and test with ENMeval package.\nTest effect of Maxent regularization parameter.<.li>\nComparing correlative models with AIC\, with ENMeval package.\n\n \n \n \n \n \n Thursday 4th\n Day 4 – Classes from 09:30 to 17:30 \n\nMESS practice with Biomod2 package.\nValidate models null models.\nVirtualSpecies virtualspecies packages.\n\n \n \n \n \n \n Friday 5th\n Day 5 – Classes from 09:30 to 17:30 \n\nMechanistic model NicheMapper packages.\n\n \n \n \n \n \n \n \n \n Dr. Neftali Sillero\n \n Neftalí Sillero works in the analysis and identification of biodiversity spatial patterns\, from species to populations and individuals. For this\, he uses four powerful tools to better understand how space influence biodiversity: Geographical Information Systems\, Remote Sensing\, Ecological Niche Modelling\, and Spatial Statistics. His main areas of research are: application of new technologies on species’ distributions atlases\, ecological modelling of species’ ranges\, identification of biogeographical regions and species’ chorotypes\, mapping and modelling road-kill hotspots\, and spatial analyses of home ranges. \nHe has more than 10 years’ experience working in ecological niche models. He has authored >70 peer reviewed publications and he is since 2007 Chairman of the Mapping Committee of the Societas Herpetologica Europaea\, where he is the PI of the NA2RE project (www.na2re.ismai.pt)\, the New Atlas of Amphibians and Reptiles of Europe \nPersonal website \nWork Webpage \nResearchGate \nGoogleScholar \n \n \n \n \n \n \n \n \n \n \n \n \n Teaches\n \nEcological Niche Modelling Using R (ENMR)\nAdvanced Ecological Niche Modelling Using R (ANMR)\nGIS And Remote Sensing Analyses With R (GARM)\n\n \n \n \n \n \n Teaches\n \nEcological Niche Modelling Using R (ENMR)\nAdvanced Ecological Niche Modelling Using R (ANMR)\nGIS And Remote Sensing Analyses With R (GARM)\n\n \n \n \n \n \n \n \n \n Dr. Salvador Arenas-Castro\n \n Dr. Salvador Arenas-Castro is a broad-spectrum ecologist with interesting in differentintegrative perspective of the fundamental ecology\, macroecology and biogeographywith their both application and relationship to climate and land management. He is alsoexploring other research sources in agroecology\, forestry\, spatial ecology\, andecoinformatics\, all addressed by explicitly considering the spatial component ofecological processes\, mainly applying spatially explicit modelling approaches\, GIS andremote sensing techniques. Please check his webpage for further information:https://salvadorarenascastro.wordpress.com \nGoogle Scholar: https://scholar.google.com/citations?user=UAYiB5UAAAAJ&hl=es&oi=aoResearchGate: https://www.researchgate.net/profile/Salvador-Arenas-Castro URL:https://prstats.org/course/bayesian-multilevel-modelling-using-brms-for-ecologists-bmme01/ LOCATION:Delivered remotely (United Kingdom)\, Western European Time Zone\, United Kingdom CATEGORIES:Home Courses,Live Online Courses ATTACH;FMTTYPE=image/jpeg:https://prstats.org/wp-content/uploads/2025/07/BMME01-1.jpg GEO:53.1423672;-7.6920536 END:VEVENT END:VCALENDAR