[MARMAM] New Online Training Course: An Introduction To Integrating QGIS/GIS And R For Spatial Analysis - 6th to 8th May 2020
We will be running a new online training course called 'An Introduction To Integrating QGIS/GIS and R For Spatial Analysis' between the 6th and 8th of May 2020. It will be held via the Zoom video-conferencing platform. This course is aimed at those who wish to learn how to use and integrate QGIS (the leading freely available GIS software package) and R (the leading freely available data analysis software package) for spatial analysis. It will be taught by Dr. Colin D. MacLeod, the author of 'An Introduction To Integrating QGIS And R for Spatial Analysis [1]' (Pictish Beast Publications) and a renowned expert in using GIS in biological and ecological research. He is also a co-author of the recenntly publised 'An Introduction To Basic Statistics For Biologists Using R [2]', which is a practical guide to carrying out the analysis of biological data in R. The course assumes no prior knowledge of either QGIS/GIS or R, and so is open to complete beginners as well as those how know how to use one of these software packages, and wish to learn how to integrate it with the other. Attendance will be limited to a maximum of 16 people. The course for this three day course will cost GBP 395 per person (with a discounted rate of GBP 300 for students, the unwaged and those working for registered charities). To book a place, or for more information, visit http://gisinecology.com/online-course-an-introduction-to-integrating-qgis-gis-and-r-for-spatial-analysis/ or email i...@gisinecology.com. GIS and statistical analysis are two of the most fundamental software tools for marine mammalogists wishing to conduct spatial analyses, which is, itself, a cornerstone for the management and conservation of marine mammal species. However, GIS and statistical analyses have their own sets of software packages, and sometimes it can be difficult to know how to integrate the two. This course will provide an introduction to the integration of QGIS (the leading freely available GIS software package) and R (the leading data analysis software packages used by biologists) to create a combined tool set that makes the most of the strengths of each of these individual software packages. It will consist of a series of background sessions on using GIS and R for spatial analysis, mixed in with practical sessions where you will learn how to use QGIS, how to use R, and how to integrate two to complete a spatial analysis project. This last part will include working through an example project, starting with creating a high quality map for publication through creating raster data layers of environmental variables, joining data together based on their spatial relationships and analysing the combined data set using R (including creating summary statistics, conducting linear regressions and conducting generalised additive modelling - GAMs). While it will primarily be based around QGIS, this course is taught using software-independent approach, and it is also open to those who wish to learn how to use ArcGIS to do biological GIS. When you attend this course you will receive a free copy of An Introduction To Integrating QGIS And R for Spatial Analysis [1] (GIS For Biologists Workbooks) as the practical exercises in that course are based on the ones contained in that book. NOTE: If you wish to use ArcGIS software for this course, alternative materials will be provided for the practical sessions. == GIS IN ECOLOGY - Providing Training, Advice And Consultancy On The Use Of GIS In Ecology Web: www.GISinEcology.com Email: i...@gisinecology.com Need to ask a question about using GIS? Try the GIS In Ecology Forum: www.GISinEcology.com/GIS_in_Ecology_forum.htm Books From GIS In Ecology Staff: GIS For Biologists: A Practical Introduction For Undergraduates; RRP: £24.99 An Introduction To Using GIS In Marine Biology; RRP: £44.99 An Introduction To Using GIS In Marine Biology: Supplementary Workbook One - Creating Maps Of Species Distribution; RRP: £19:99 If you wish to purchase these books, visit: http://www.gisinecology.com/Book_Shop.htm To help the environment, please do not print out this email unless it is unavoidable. == Links: -- [1] http://gisinecology.com/an-introduction-to-integrating-qgis-and-r-for-spatial-analysis-gis-for-biologists-workbooks-series/ [2] http://gisinecology.com/stats-for-biologists-1___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] MARMAM submission, New Publication: What’s in a whisker? High-throughput analysis of twenty-eight C19 and C21 steroids in mammalian whiskers by ultra-performance convergence chromatography-ta
Dear Marmamers, My co-authors and I are pleased to announce our new publication in *Journal of Chromatography B*. Lübcker N, Bloem LM, du Toit T, Swart P, de Bruyn PN, Swart AC, Millar RP. What’s in a whisker? High-throughput analysis of twenty-eight C19 and C21 steroids in mammalian whiskers by ultra-performance convergence chromatography-tandem mass spectrometry. Journal of Chromatography B. 2020 Mar 15;1141:122028. https://doi.org/10.1016/j.jchromb.2020.122028 Please take care and shout if I can be of assistance. *Highlights* • We developed a high-throughput assay to quantify 28 steroids from single whiskers. •This UPC2-MS/MS method enabled the first quantification of a suite of steroids detectable in mammalian whiskers. •Sensitive and accurate quantification method at reduced cost and time. •Whiskers provides biomatrix for longitudinal steroid hormones monitoring. •Applicable to free-ranging mammals with cryptic life cycles. *Abstract* Obtaining longitudinal endocrinological data from free-ranging animals remains challenging. Steroid hormones can be extracted sequentially from non-invasively sampled biologically inert keratinous tissues, such as feathers, nails, hair and whiskers. However, uncertainty regarding the type and levels of steroids incorporated into such tissues complicates their utility in wildlife studies. Here, we developed a novel, comprehensive method to analyze fourteen C19 and fourteen C21 steroids deposited chronologically along the length of seal whiskers in a single, 6-minute chromatographic step, using ultra-performance convergence chromatography-tandem mass spectrometry. The limits of detection and quantification ranged from 0.01 to 2 ng/mL and from 0.1 to 10 ng/mL, respectively. The accuracy and precision were within acceptable limits for steroids at concentrations ≥2 ng/mL. The recovery (mean = 107.5% at 200 ng/mL), matrix effect and process efficiency of steroids evaluated, using blanked whisker matrix samples, were acceptable. The method was applied to the analysis of steroid hormone levels in adult female whisker segments obtained from southern elephant seals (Mirounga leonina), n = 10, and two fur seal species, Antarctic fur seals (Arctocephalus gazella; n = 5) and subantarctic fur seals (Arctocephalus tropicalis; n = 5), sampled between 2012 and 2017. In the whisker subsamples analyzed (n = 71), the median concentration of steroid hormones detected above the LOQ ranged from 2.0 to 273.7 pg/mg. This was the first extraction of multiple C19 and C21 steroids, including their C11-oxy metabolites, from the whiskers of mammals. Measuring hormones sequentially along the whisker lengths can contribute to our understanding of the impact of stress associated with environmental/climate changes that affect the health, survival of organisms, as well as to delineate the reproductive cycles of free-living mammals with cryptic life stages. https://www.researchgate.net/publication/339227340_What's_in_a_whisker_High-throughput_analysis_of_twenty-eight_C19_and_C21_steroids_in_mammalian_whiskers_by_ultra-performance_convergence_chromatography-tandem_mass_spectrometry Thank you Sincerely, Nico Lubcker PhD. Zoology Candidate Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria https://www.researchgate.net/profile/Nico_Luebcker marionseals.com/people/ ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] MARMAM submission, New Publication: Fasting affects amino acid nitrogen isotope values: a new tool for identifying nitrogen balance of free-ranging mammals
Dear Marmamers, My co-authors and I are pleased to announce our new publication in *Oecologia*. Lübcker, N., Whiteman, J.P., Millar, R.P. et al. Fasting affects amino acid nitrogen isotope values: a new tool for identifying nitrogen balance of free-ranging mammals. Oecologia (2020). https://doi.org/10.1007/s00442-020-04645-5 Please take care of yourselves and each other during this difficult time. Abstract Changes in the nutritional status of free-ranging animals have a strong influence on individual fitness, yet it remains challenging to monitor longitudinally. Nitrogen (δ15N) and carbon (δ13C) isotope values measured chronologically along the length of metabolically inert keratinous tissues can be used as a nutritional biomarker to retrospectively reconstruct the foraging ecology and eco-physiology of consumers. We quantitatively describe the physiological effects of fasting on amino acid metabolism using sequentially measured bulk tissue and amino acid δ15N values along the length of whiskers sampled from free-ranging juvenile, subadults, adult female, and male southern elephant seals (SES; Mirounga leonina) on Marion Island in the Southern Ocean. For both juveniles and adult females, whisker segments representing fasting had significantly higher bulk tissue δ15N values of 0.6 ± 0.5‰ and 1.3–1.8‰, respectively, in comparison to segments unaffected by fasting. We also found a large increase (2–6‰) in δ15N values for most glucogenic amino acids and a simultaneous depletion (2–3‰) of alanine in segments reflecting fasting, which enabled us to accurately predict (74%) the nutritional status of our model species. We hypothesize that the glucose-alanine cycle is the mechanism driving the observed depletion of alanine δ15N values during fasting. We demonstrated that keratinaceous tissues can be used as a longitudinal nutritional biomarker to detect changes in the nitrogen balance of an individual. Moreover, it is evident that physiological factors have an important influence on tissue δ15N values and can lead to erroneous bulk tissue or amino acid isotope-based reconstructions of foraging habits. https://www.researchgate.net/publication/340684991_Fasting_affects_amino_acid_nitrogen_isotope_values_a_new_tool_for_identifying_nitrogen_balance_of_free-ranging_mammals Thank you Sincerely, Nico Lubcker PhD. Zoology Candidate Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria https://www.researchgate.net/profile/Nico_Luebcker marionseals.com/people/ ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] ONLINE COURSE – Python for data science, machine learning, and scientific computing
ONLINE COURSE – Python for data science, machine learning, and scientific computing (PDMS02) This course will be delivered live https://www.psstatistics.com/course/python-for-data-science-machine-learning-and-scientific-computing-pdms02/ Dates 4 - 8 May 2020 Time zone - UK (GMT) Please email oliverhoo...@psstatistics.com with any questions Course Overview: Python is one of the most widely used and highly valued programming languages in the world, and is especially widely used in data science, machine learning, and in other scientific computing applications. This course provides both a general introduction to programming with Python and a comprehensive introduction to using Python for data science, machine learning, and scientific computing. The skills learnt will be of value to any marine a mammal researcher handling large data sets. The major topics that we will cover include the following: the fundamentals of general purpose programming in Python; using Jupyter notebooks as a reproducible interactive Python programming environment; numerical computing using numpy; data processing and manipulations using pandas; data visualization using matplotlib, seaborn, ggplot, bokeh, altair, etc; symbolic mathematics using sympy; data science and machine learning using scikit-learn, keras, and tensorflow; Bayesian modelling using PyMC3 and PyStan; high performance computing with Cython, Numba, IPyParallel, Dask. Overall, this course aims to provide a solid introduction to Python generally as a programming language, and to its principal tools for doing data science, machine learning, and scientific computing. (Note that this course will focus on Python 3 exclusively given that Python 2 has now reached it end of life). Monday 4th – Classes from 09:30 to 17:30 • Topic 1: The What and Why of Python. In order to provide some general background and context, we will describe Python where came from, what its major design principles and intended use was originally, and where and how it is now currently used. We will see that Python is now extremely widely used, especially in powering the web, in data science and machine learning, and system level programming. Here, we also compare and contrast Python and R, given that both are extremely widely used in data science. • Topic 2: Installing and setting up Python. There are many ways to write and execute code in Python. Which to use depends on personal preference and the type of programming that is being done. Here, we will explore some of the commonly used Integrated Development Environments (IDE) for Python, which include Spyder and PyCharm. Here, we will also mention and briefly describe Jupyter notebooks, which are widely used for scientific applications of Python, and are an excellent tool for doing reproducible interactive work. We will cover Jupyter more extensively starting on Day 3. Also as part of this topic, we will describe how to use virtual environments and package installers such as pip and conda. • Topic 3: Introduction to Python: Data Structures. We will begin our coverage of programming with Python by introducing its different data structures.and operations on data structures This will begin with the elementary data types such as integers, floats, Booleans, and strings, and the common operations that can be applied to these data types. We will then proceed to the so-called collection data structures, which primarily include lists, dictionaries, tuples, and sets. • Topic 4: Introduction to Python: Programming. Having introduced Python’s data types, we will now turn to how to program in Python. We will begin with iteration, such as the for and while loops. We will then cover conditionals and functions. Tuesday 5th – Classes from 09:30 to 17:30 • Topic 5: Modules, packages, and imports. Python is extended by hundreds of thousands of additional packages. Here, we will cover how to install and import these packages, and also how to write our own modules and packages. • Topic 6: Numerical programming with numpy. Although not part of Python’s official standard library, the numpy package is the part of the de facto standard library for any scientific and numerical programming. Here we will introduce numpy, especially numpy arrays and their built in functions (i.e. “methods”). • Topic 7: Data processing with pandas. The pandas library provides means to represent and manipulate data frames. Like numpy, pandas can be see as part of the de facto standard library for data oriented uses of Python. • Topic 8: Object Oriented Programming. Python is an object oriented language and object oriented programming in Python is extensively used in anything beyond the very simplest types of programs. Moreover, compared to other languages, object oriented programming in Python is relatively easy to learn. Here, we provide a comprehensive introduction to object oriented programming in Python. • Topic 9: Other Python programming features. In this section, we will cover some important
[MARMAM] Request: Survey on difficulties and abuse faced by early career marine environmentalists
Dear MARMAM Subscribers, Me and my colleagues are preparing a report on the situation of early career marine environmentalists. We want to understand the nature and extent of the hardships faced by these starting in our field, with a special focus on time and monetary investment in work and education. Marine mammalogy is one of the fields with many "work opportunities" abusing current legal regulations, thus it is extremely important to document this situation. The aim of the report, which we will make publicly available, is to show clearly the most burning issues and help to solve them. We hope to shed some light on the various forms of abuse experienced by young marine professionals, but all stories are valid, and we also ask people who have never faced any hardships to share their experiences. We are mostly interested in the experiences of current students, PhD candidates and those who graduated within the last 5 years. There is no deadline, though we hope to close the questionnaire at the beginning of May 2020. Link to survey: https://forms.gle/TC6ruUc8E82vut3p8 Thank you for your time and honesty, Anna N Osiecka ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Bottlenose dolphin project research in Venezuela. Interns and volunteer program 2020.
BOTTLENOSE DOLPHIN PROJECT RESEARCH IN VENEZUELA. INTERNS AND VOLUNTEER PROGRAM 2020. BACKGROUND: The Laboratory of Ecosystems and Global Change (LEGC) of the Venezuelan Institute of Scientific Research (IVIC, www.ivic.gob.ve) invites the second season of internships-volunteering (2020) in the study of coastal dolphins. LEGC is a scientific team that among its research lines on the fauna of coastal and riparian ecosystems, it has established the first one on aquatic mammals in Venezuela. On the other hand, Provita is an important NGO that contributes to the research and conservation in Venezuela. This research will begin with a project focused on sociobiology (social structure, social networks and bioacoustics) of resident groups of the coastal bottlenose dolphin (Tursiops truncatus) in the central coast of Venezuela. This, after an experience of 5 years in that locality studying ecological aspects of T. truncatus ( https://doi.org/10.1007/s13364-018-0401-1). The coast of Aragua not only home this species, but also the Bryde's whale (Balaenoptera edeni), the common dolphin (Delphinus sp.) and the spinner dolphin (Stenella longirostris). Of which basic information is collected too. LEGC interns and volunteers are young, hard-working who are willing to contribute to research by learning as they experience fieldwork in teams, field techniques for collecting and processing data and methodologies. All team members and interns share academic space, housing in the Institute, housework in the study area, knowledge and experience in a friendly and multicultural environment. The internship consists of three weeks: The first week of theoretical-practical introduction (24 theoretical hours and 16 practicals hours) at the IVIC Ecology Center ( www.ivic.gob.ve/es/investigacion-3/centros-31/ecologia-316). The second week of seven field surveys for data collection (42 h) on the Cata Bay (Aragua state) and the third week for data processing and analysis at the IVIC Ecology Center (40 h). The volunteering consist of the second and third weeks. WHERE: Theory: LEGC, Center of Ecology (IVIC) Miranda State, Caracas (10 23 N - 66 58 W). Practice: Cata Bay, western coast of the (rain forest) National Park Henry Pittier, Aragua state (central coast of Venezuela) 150 km from Caracas (DC) (10 29 N - 67 44 W). PROGRAM: Interns (Three weeks), Volunteers (Two weeks). 1st WEEK (LEGC-Ecology Center, 40 hours. For Interns). - Monday: What is a cetacean? The cetaceans and the human in history. Origin, evolution and diversity. Adaptations for aquatic life: Anatomy and Physiology. Life histories. Biogeography Distribution. Ecology Behavior. Conservation. - Tuesday: Identification of species reported for Venezuela. Basic logistics for the study of cetaceans on the mainland, sea and air. Basic equipment to collect information. - Wednesday: How to detect cetaceans and record an effective sighting? Basic data to collect during a sighting, calibration and use of GPS. Configuration and use of the SLR cameras. Download of sightings (GIS). Download pictures and selection (software). - Thursday: Daily encounter ratio. Photo-identification as a tool for ecological and behavioral studies. Estimates of abundance. Local distribution and areas of action. - Friday: Residential patterns. Behavior (deployments, states, daily budget). Habitat use. Social structure and social networks. Bioacoustics. Saturday: Break. Sunday: Transfer to the Cata Bay. 2nd WEEK (Cata Bay-Provita, 42 hours. For Interns and Volunteers). The field surveys will be carried out in a fishing vessel of 9 m in length by 2 of beam, no roof. The field work will depend on the climatic conditions, however, the Aragua coast offers few climatic inconveniences throughout the year. There will be 7 mornings of field surveys in the week, after each survey is lunch, rest and then proceed to download the data of sightings and then interpret them preliminarily and discuss them. We recommend wearing a long-sleeved shirt, cool pants, hat and sunscreen (30-50 PF). In the field surveys, it will be implemented: - The identification and recognition of the elements of the marine landscape and the method of tracking and detection of cetaceans. - Ethical navigation mode to study cetaceans. - The basic data collection / sighting. - Use of GPS. - Use of SRL digital camera. - Counting of individuals and composition of a group. - Identification of the behavioral states that configure group behavior and its recording. - Use of hydrophone. - Identification and counting of birds. -Identification and counting of vessels and other antropic objects. In the afternoon the information of the sightings will be downloaded: - Sighting forms. - Latitude and longitude. - Photographs and their selection. - Voice recordings (behavior). - Recordings of vocalizations. - Shark whales sightings. - Birds sightings. - Vessels and anthropic objects sightings. 3rd WEEK (LEGC-Ecology Center, 40 hours. For Interns and
