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    Acycle Short Course at Lehigh University (Sept 6, 2019) : September 2019

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    Acycle Short Course at Lehigh University (Sept 6, 2019) : September 2019

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    Osman Serdar
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    2019_AcycleShortCourseLehigUniversity

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    Acycle Short Course at Lehigh University (Sept 6, 2019) : September 2019

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    Osman Serdar

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    © All Rights Reserved
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    See discussions, stats, and author profiles for this publication at: https://www.researchgate.

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    Acycle short course at Lehigh University (Sept 6, 2019)

    Presentation · September 2019

    CITATIONS READS

    0 871

    1 author:

    Mingsong Li
    Peking University
    69 PUBLICATIONS 1,164 CITATIONS

    SEE PROFILE

    Some of the authors of this publication are also working on these related projects:

    Determining the Duration of the Ediacaran Shuram C-isotope Excursion using Rock Magnetic Cyclostratigraphy View project

    Acycle: Time-series analysis software for paleoclimate research and education View project

    All content following this page was uploaded by Mingsong Li on 10 September 2019.

    The user has requested enhancement of the downloaded file.


    Acycle: Time-series analysis software
    for paleoclimate research and education

    Mingsong Li
    Linda Hinnov, Lee Kump
    Penn Sate
    Sept. 6, 2019
    OUTLINE
    1. Introduction

    2. Getting Started

    3. Acycle Graphic User Interface (GUI)

    4. Case study: Carnian cyclostratigraphy


    Time series analysis
    • a statistical technique that deals with time series data.
    • accounts for the fact that data points taken over time may
    have an internal structure (such as trend or periodicity)
    that should be accounted for.

    • Economic Forecasting • STEM (Science, technology,


    • Sales Forecasting engineering, and
    mathematics)
    • Population Forecasting • …
    • Stock Market Analysis
    • Yield Projections
    Climate Time Series

    Monthly average CO2 at Mauna Loa Observatory, Hawaii

    https://www.esrl.noaa.gov/gmd/ccgg/trends/

    Global benthic marine δ18O stack (global ice volume and temperature)

    (Lisiecki & Raymo, 2005) (Hinnov, 2013)


    Download this paper
    Logo designed by Hewei Duan
    Total: 1782 unique visitors
    (Sept 2018 – Sept 2019)
    http://mingsongli.com/acycle
    Data source: https://analytics.google.com
    What they say

    “It is truly an amazing contribution to the geosciences


    community … It opens up much needed access to these
    powerful tools for a wide audience in the sedimentary geology
    and paleoclimate community. … A really marvellous job."
    —— Dr. J. Fred Read (Emeritus Professor, Virginia Tech)

    "His Acycle software will become the standard tool for


    time-scale applications by all international workers."

    —— Dr. James G. Ogg (Professor, Purdue University)

    “Not only is this software powerful and effective, it is also simple


    to use and therefore benefits researchers and at all levels within
    the paleoclimatology community, from novices to experts.”

    —— Dr. Paul E. Olsen (Professor, Columbia University)


    2. Getting Started
    * Stand-alone versions of Acycle only needs Runtime, not MatLab

    * MatLab Runtime is not MATLAB!

    * MatLab Runtime is free!

    Dropbox | OneDrive | BaiduCloud | GitHub

    Read more
    •Wiki: https://github.com/mingsongli/acycle/wiki
    •or: https://github.com/mingsongli/acycle/blob/master/doc/AC_Users_Guide.pdf
    •or: Acycle "Help" menu - "Manual",
    •or: /doc/AC_Users_Guide.pdf
    2. Getting Started

    Acycle for… MatLab Stand-alone **


    Platform Mac Windows
    Requirement MatLab Runtime 2019a (Free)
    MatLab
    download Runtime for Mac Runtime for Win

    Version Installer Green Installer Green

    Size 63.5 MB 97 MB 91 MB 122 MB 121 MB


    How to install Acycle2.0_Users_Guide.pdf (Chapter 3)

    ** Need to install the MatLab Runtime 2019a (!!!)


    Fast installation:

    1. Install MatLab Runtime 2019a (free)


    You don’t need to install MatLab (heavy and expensive)!
    After the installation, you don’t need to run runtime yourself
    If you have installed MatLab 2019a, this step can be skipped

    2. Download Acycle2.0 GREEN version


    No installation is needed.

    3. Follow the next slide to start up Acycle 2.0.

    ** Need to install the MatLab Runtime 2019a (!!!)


    Startup
    double-click

    1. Go to the installation folder

    2. Right click “Acycle” file, choose “Show Package Content”

    3. Drag the applauncher file to the dock


    Acycle Graphic User Interface (GUI)

    Don’t close this window!

    Press CTRL + C keys to kill Acycle


    Data Requirement

    comma-, table- or space-delimited text (.txt)


    comma-separated values files (.csv)

    No header is permitted.

    Most data files should contain two columns of series.

    depth
    or time value
    Plot Pro
    Insolation

    Based on the MatLab code inso.m by Jonathan Levine (2001), UC Berkeley.


    modified by Peter Huybers (Harvard)
    modified by Mingsong Li (Penn State, 2018)
    Astronomical Solution
    Signal/Noise Generator
    Math Time series

    Case studies:
    1. Insolation
    2. Laskar 2004 astronomical solution
    3. Carnian cyclostratigraphy (~235 Ma, Triassic)
    Carnian cyclostratigraphy (~235 Ma, Triassic)

    Proxy: gamma-ray with higher intensities


    indicating higher average clay contents

    Target: learn typical data process steps

    Wayao

    Zhang et al., 2015 Palaeo-3


    Flowchart of the cyclostratigraphic
    analysis in Acycle software (1)
    Flowchart of the cyclostratigraphic
    analysis in Acycle software (2)
    Step 1. Load Data

    The gamma ray data entitled


    “Example-WayaoCarnianGR0.txt”
    will be loaded and displayed in
    the Acycle main window.
    Step 2. Data Preparation (optional)

    Users can sort data in ascending


    order. Two or more values for the
    same time (or depth) may be
    averaged with the "Unique"
    function.
    Step 3. Interpolation

    Stratigraphic depth or time series are typically irregularly spaced due to


    uncertain timescales or difficulty in data collection. This necessitates
    interpolation to generate uniformly spaced time (or depth) series.

    “Example-WayaoCarnianGR0-rsp0.33.txt”.
    Step 4. Detrending
    Detrending is a critical step for power spectral analysis to ensure that data
    variability oscillates about a zero mean, and to avoid power leakage from very
    low-frequency components into higher frequencies of the spectrum.

    Read More: Detrending


    Step 5. Power spectral analysis

    Power spectral analysis evaluates the distribution of time series variance


    (power) as a function of frequency. The primary use of power spectral analysis
    is for the recognition of periodic or quasi-periodic components in a data series

    Read More: Spectral Analysis


    Step 6. Evolutionary power spectral analysis

    Read More
    Step 7. Correlation coefficient

    To estimate the optimal sedimentation rate.

    Read More: COCO/eCOCO

    Similar tool: TimeOpt / eTimeOpt


    You will have the following figure and a log file saving all settings.

    It tells the most likely sedimentation rate is ~9 cm/kyr,


    with a null hypothesis (no orbital forcing) significance level of <1%
    All seven orbital parameters are used in the estimation.
    eCOCO analysis to track variable sedimentation rate

    Similar tool: eTimeOpt


    eCOCO analysis to track variable sedimentation rate
    Step 8. Filtering
    Filters are also essential tools to aid in the isolation of specific frequency
    components in the paleoclimate data series.

    Read More
    Step 9. Age model and tuning
    transform original data (usually in the depth domain) to tuned data
    (usually in the time domain) when an age model file is available
    Select “Example-WayaoCarnianGR0-rsp0.33-80-LOWESS-gaus-0.028+-0.006.txt”

    a, Build age model

    Example-WayaoCarnianGR0-rsp0.33-80-LOWESS-gaus-0.028+-0.006-agemod-405-max.txt

    b, Age Scale
    Tuned data:
    “Example-WayaoCarnianGR0-TD-Example-WayaoCarnianGR0-rsp0.33-80-
    LOWESS-gaus-0.028+-0.006-agemod-405-max.txt”
    Mini robot
    Other useful tools
    Sedimentary noise model
    Lag-1 autocorrelation coefficient (ρ1)
    dynamic noise after orbital tuning (DYNOT) model

    Li, et al., 2018 Ancient ocean Credit: Hewei Duan


    Nature Communications
    Smoothing
    ‘Image’ Tool
    1. Select an image file
    2. Select “Show Image”
    3. (Optional) Transfer an RGB
    image to Grayscale image:
    Select “RGB to Grayscale”
    ‘Image’ Tool

    4: Image Profile
    5: Press ALT key, select 2 cursors
    6. Press “Enter” in the terminal window
    Step 6
    Plot Digitizer

    Example-PlotDigitizer.jpg
    Acknowledgement

    Astronomical solution: Jacques Laskar,


    Richard Zeebe
    Changepoint: Eric Ruggieri
    Insolation: Jonathan Levine, Peter Huybers
    Padding: Nicolas R. Thibault
    Spectral Moments: Matthias Sinnesael
    TimeOpt/eTimeOpt: Steve Meyers
    Linda Hinnov Lee Kump
    Wavelet: Christopher Torrence, Gilbert Compo

    Feng Cheng, Anne-Christine Da Silva, Hewei Duan,


    Yanan Fang, Marco Franceschi, Daniel R. Franco,
    Xiaoni Hu, Dorothée Husson, Arsenio Muñoz Jiménez,
    Dongyang Liu, James Ogg, Paul Olsen, J. Fred Read,
    Chen Shen, Chuanyue Wang, Mathieu Martinez, Meng
    Wang, Xu Yao, Qiyan Zhang, Yang (Wendy) Zhang,
    Christian Zeeden
    Make it a better software for your own research.
    ANY feedback is highly appreciated!!!

    Email: [email protected]; [email protected]


    https://github.com/mingsongli/acycle/issues

    Please cite:

    Li, M., Hinnov, L., Kump, L. (2019) Acycle: Time-series analysis software for
    paleoclimate research and education. Computers & Geosciences 127, 12-22.

    and other relevant publications.

    Thank you!
    View publication stats

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