SubjectsSubjects(version: 945)
Course, academic year 2023/2024
   Login via CAS
Datahandling and numerical analyses in biostratigraphy - MB120P132
Title: Datahandling and numerical analyses in biostratigraphy
Czech title: Zpracování dat a numerické analýzy v biostratigrafii a paleoekologii
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2021
Semester: winter
E-Credits: 4
Examination process: winter s.:
Hours per week, examination: winter s.:2/2, C+Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Note: enabled for web enrollment
Guarantor: doc. RNDr. Petr Kuneš, Ph.D.
Teacher(s): doc. RNDr. Petr Kuneš, Ph.D.
Class: Stavební úpravy prostor pro umístění chladové míst
Annotation
Last update: doc. RNDr. Petr Kuneš, Ph.D. (27.09.2021)
The participant will be introduced to the main format of palaeoecological data, will be able to recognize them, process them into the form of graphical output, and interpret it. The participant will list the main numerical analyses applicable to palaeoecological data, will be able to choose the best technique for statistical analysis and apply it to the data. The student will also examine particular scientific questions by proper numerical analysis. Finally, the student will be able to interpret the results, compare and evaluate different outcomes. The participant will learn to work with main open-access databases and design analyses for broader data syntheses.
Literature -
Last update: doc. RNDr. Petr Kuneš, Ph.D. (27.09.2021)

BIRKS, H. John B., LOTTER, André F., JUGGINS, Steve and SMOL, John P. (eds.), 2012, Tracking Environmental Change Using Lake Sediments [online]. Dordrecht : Springer Netherlands. Developments in Paleoenvironmental Research. ISBN 978-94-007-2744-1, 978-94-007-2745-8.

Requirements to the exam
Last update: doc. RNDr. Petr Kuneš, Ph.D. (27.09.2021)
  • home assignments

  • test - multi-choice questions

  • small project - present the solution for given scientific questions and training data in the form of a short scientific essay

Syllabus
Last update: doc. RNDr. Petr Kuneš, Ph.D. (27.09.2021)

The course will be divided into sessions in the class, mostly covering theoretical background, which will lay the ground for exercise at home. All topics, data, tasks for their analyses and results will be managed and collected within Moodle.

https://dl2.cuni.cz/course/view.php?id=2321

Block 1

Introduction to data formats

Data formats in paleoecology and biostratigraphy, data collection, file formats. Entering data into spreadsheet, calculations of percentages, import, export, data presentation (optional use of Tilia and/or C2 programs/or Rioja package in R).

Databases

Data bases and their use in biostratigraphy and palaeoecology. Data structure, relational tables. PostgreSQL. Import, export for numerical analyses. Examples of global data bases. Use of data from the databases.

 

Block 2

General information on dating and age-depth modelling

Calibration of single radiocarbon date. Various calibration curves. Classical and Bayesian age-depth modelling (CLAM, BACON, OXCAL). Adding different age controls to a sequence.

Quantification of numerical differences between fossil/modern assemblages

Introduction to dissimilarity indices. Calculation of dissimilarity indices for stratigraphic, determining the rate-of-change. Use of dissimilarity indices in further analyses.

Rate of change.

Classification and stratigraphically constrained classification, zonation, cluster analysis

How many zones are there in my stratigraphy? Divisive and agglomerative techniques (CONISS, CONSLINK, splitting, broken stick model), determining the change using a threshold.


Block 3

The dissimilarity between multivariate time-series

Comparison of two sequences assuming stratigraphic order of their samples

Introduction to multivariate data analysis

Data reduction by reducing number of dimensions. Use of dissimilarity indices. Introduction to ordination for use in palaeoecology. Indirect (PCA, CA, DCA) and direct (RDA, CCA) techniques. DCCA in paleoecology. NMDS.


Block 4

Reconstruction in paleoecology – modern analog technique and transfer functions

Modern training datasets. Classical and inverse methods. Weighted averaging, partial least squares regressions, modern analog technique, and analog matching.

Diversity in fossil assemblages

Why be concerned with diversity in the past? Two aspects of diversity: species richness and evenness. Introduction to diversity indices. Rarefaction, evenness.


Block 5

Introduction to quantitative palynology

POLLSCAPE, simulation of vegetation and pollen spectra. Pollen productivity estimates.

 

Block 6

Landscape Reconstruction Algorithm

Theory of pollen analysis with the use of landscape reconstruction algorithm. Past vegetation reconstruction.

Software for biostratigraphy: Tilia database and graphical program, C2 program

Collection of primary stratigraphical data, taxonomy, collection of various metadata

Neotoma Palaeoecology Database – use of Tilia with the database

 
Charles University | Information system of Charles University | http://www.cuni.cz/UKEN-329.html