Dendro-ecology and Eco-physiology


Bringing together expert knowledge to build the DEEP toolbox.

Our goal is to make methods more accessible, save time and standardize workflows to make them comparable.


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Materials

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Data Handling

Methods for wrangling and cleaning DEEP and environmental data

General Statistics

Spatial and temporal analyses, hierarchical modelling

Measurements

Techniques for typical DEEP data,
like tree rings, sap flow and dendrometer measurements

Software & Code Snippets

Solutions to frequent problems in DEEP

Workshops

Teaching sessions and talks

Advanced Tree Physiological Data Processing in R

We show how to facilitate the work with raw time series data and make methods for their processing accessible and reproducible.
Aug 19, 2022 10:00 — 11:30 Montreal, Canada (Room 514C)
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Advanced Tree Physiological Data Processing in R

Time series processing in R: from raw measurements to their analysis and interpretation

We show how to facilitate the work with raw time series data and make methods for their processing accessible and reproducible.
Jun 23, 2022 10:00 — 12:00 Rapide-Danseur, Quebec, Canada
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Time series processing in R: from raw measurements to their analysis and interpretation

A Comprehensive Toolbox for Tree Physiological Data Processing in R

Reproducible cleaning, processing and assessment of high-frequency time series data sets.
Aug 6, 2021 13:00 — 14:30 Virtual Meeting
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A Comprehensive Toolbox for Tree Physiological Data Processing in R

Time series data processing course

Introduction to methods for processing time series in ecological research
Feb 9, 2021 08:00 — 12:00 Virtual Meeting - University of Helsinki
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Time series data processing course

Advanced Analyses of Tree Physiological Time Series in R and PhytoSim

Introducing (R) software for processing high-frequency dendrometer and sapflow data.
Aug 3, 2020 — Aug 6, 2020 Virtual Meeting
Christoforos Pappas, Richard L. Peters, Roman Zweifel, Kathy Steppe, Alexander Hurley
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Advanced Analyses of Tree Physiological Time Series in R and PhytoSim

Recent News

The DEEP toolbox is updated for Q-NET

We are honoured to support the Q-NET topical groups “Online toolbox for data analysis” and “Analysing wood anatomical time series”, for which we updated the DEEP toolbox with new materials addressing quantitative wood anatomy.
Nov 27, 2020 1 min read News
The DEEP toolbox is updated for Q-NET

Climate correlations with tree rings

In this tutorial we show how to systematically screen different season lengths when performing climate-growth correlations. We also discuss the small difference between purely noise-related correlation coefficients and climate sensitivtiy derived from unstandardized regression slopes.
Last updated on Nov 23, 2020 8 min read Statistics
Climate correlations with tree rings

Reproducible and interactive processing with datacleanr

Ever more data is available to Earth System scientists - exploring, cleaning and curating it in a reproducible manner can be done efficiently and conveniently with interactive tools such as datacleanr. Learn how to use it for quantitative wood anatomy, as well as for environmental data in a guided tutorial.
Last updated on Nov 25, 2020 8 min read Data Handling
Reproducible and interactive processing with datacleanr

Sectoral analyses of radial growth profiles (SECTOR)

We introduce SECTOR, an R script capable of applying a sectoral approach, where wood anatomical measurements obtained from ROXAS are automatically assigned to a specified sector (or bin), accounting for the ring shape and rotation. SECTOR also allows for automatically providing intra-annual data on key wood anatomical parameters, while correcting for gaps in the area of interest (i.e., caused by cracks due to cutting).
Last updated on Nov 24, 2020 18 min read Measurements
Sectoral analyses of radial growth profiles (SECTOR)

Using RAPTOR (Row and Position Tracheid Organizer in R)

RAPTOR analyses wood cell anatomical data on spatially-explicit xylem (tracheids) datasets derived from thin sections of woody tissue. The package includes functions for visualisation, detection and alignment of continuous tracheid radial file (defined as rows) and individual tracheid position within an annual ring of coniferous species. This package is designed to be used with elaborate cell output.
Last updated on Nov 23, 2020 16 min read Measurements
Using RAPTOR (Row and Position Tracheid Organizer in R)

Using TREX for reproducible and multi-method sap flow quantification

TREX assimilate, process and analyse sap flow data from the thermal dissipation method (TDM). We showcase its features and introduce how to generate method comparisons and uncertainty assessments.
Last updated on Nov 23, 2020 17 min read Measurements
Using TREX for reproducible and multi-method sap flow quantification

Using treenetproc to assimilate continuous dendrometer data

treenetproc cleans, processes and visualises highly resolved time series of dendrometer data by aligning data to regular time intervals and removing conspicious measurements. Growth characteristics are also easily calculated.
Last updated on Nov 21, 2020 17 min read Measurements
Using treenetproc to assimilate continuous dendrometer data
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Popular Topics

angiosperm correction crown conductance data processing DEEP dendrometer diffuse-porous environmental data granier growth interactivity outliers R reproducibility sap flow tree water deficit treenetproc tutorial uncertainty wood anatomy

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