R-packages for dendrochronology

Author
Affiliation

Ronald Visser

Saxion University of Applied Sciences

Published

May 2, 2024

Dendrochronology and R

This site lists R-packages used in dendrochronology or tree-ring research. For more general information on dendrochronology: DendroHub is an excellent website (maintained by Joe Buck). This overview of R-packages might not be complete, and if you miss anything, please add these using a pull request in Github or contact me.

If you want to start with R, there are several options:

  • OpenDendro is a great resource for those who want to learn about dplR (or dplPy). There are some wonderful tutorials.
  • Software Carpentry is for teaching basic lab skills for research computing and is good for beginners.
  • Data carpentry helps you to gain foundational skills needed to work effectively and reproducibly with data and code.
  • R for Data Science (2e) is an extensive and accessible book on general R and doing data science using R.
  • CTV-Archaeology is a more general list maintained by Ben Marwick on possibilities and libraries in R, mostly aimed at Archaeology.

I would recommend working with an IDE such as RStudio and always use projects in your workflow!

List of R-packages for dendrochronology

Package name

Description1

Github
BIOdry Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity (Lara, Bogino and Bravo 2018). CRAN

GitHub

(read only)
burnr Basic tools to analyze forest fire history data (e.g. FHX) in R. This is designed for power users and projects with special needs (Malevich, Guiterman and Margolis 2018).

CRAN

Website

 GitHub
dfoliatR Tools to identify, quantify, analyze, and visualize growth suppression events in tree rings that are often produced by insect defoliation (Guiterman, Lynch and Axelson 2020).

CRAN

Website

 Github
dendRoAnalyst A package to analyse (daily) statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water (Aryal et al. 2020). CRAN

GitHub

(read only)
dendroNetwork dendroNetwork is a package to create dendrochronological networks for gaining insight into provenance or other patterns based on the statistical relations between tree ring curves. The networks can be used to visualise and understand the relations between tree-ring curves (Visser 2024).

CRAN

Website

 GitHub
dendroSync Provides functions for the calculation and plotting of synchrony in tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which the TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of ecological variables that have temporal autocorrelation corrected (Alday et al. 2018). CRAN GitHub
dendroTools Provides novel dendroclimatological methods, primarily used by the Tree-ring research community. There are four core functions. The first one is daily_response(), which finds the optimal sequence of days that are related to one or more tree-ring proxy records. Similar function is daily_response_seascorr(), which implements partial correlations in the analysis of daily response functions. For the enthusiast of monthly data, there is monthly_response() function. The last core function is compare_methods(), which effectively compares several linear and nonlinear regression algorithms on the task of climate reconstruction (Jevšenak and Levanič 2018). CRAN GitHub
detrendeR A Graphical User Interface (GUI) to import, save, detrend and perform standard tree-ring analyses. The interactive detrending allows the user to check how well the detrending curve fits each time-series and change it when needed (Campelo, García-González and Nabais 2012). CRAN

GitHub

(read only)
dplR General package for tree-ring analyses. It is possible to perform tree-ring analyses such as detrending, chronology building, and cross dating. The sotware reads and writes standard file formats used in dendrochronology (Bunn 2008; Bunn 2010). CRAN GItHub
fellingdater This R-package offers a set of functions that can assist you to infer felling date estimates from dated tree-ring series. The presence of (partially) preserved sapwood or waney edge allows to estimate a range for the actual felling date, for individual series as well as for a group of timbers. Furthermore, an additional function provides a tool to sum sapwood probability distributions, comparable to ‘summed probability densities’ commonly applied to sets of radiocarbon (14C) dates (Haneca 2024; Haneca, Debonne and Hoffsummer 2020). Website GitHub
measuRing Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical devices, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values. Most of the in-package routines can be recursively implemented using the multiDetect() function (Lara, Bravo and Sierra 2015). CRAN
MtreeRing2

A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images

Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats (Shi et al. 2019).

 CRAN GitHub
pointRes Functions to calculate and plot event and pointer years as well as resilience indices. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series (Maaten-Theunissen, Maaten and Bouriaud 2015). CRAN

GitHub

(read only)
RAPTOR Performs wood cell anatomical data analyses 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 (Peters et al. 2018). CRAN GitHub
RingdateR RingdateR is a graphical and statistical tool for crossdating annually resolved time series such as tree rings or mollusc, coral and otolith growth increments (Reynolds, Edge and Black 2021). Website GitHub
SapwoodModel This software package fits a model to sapwood data from scots pine (Pinus sylvestris L.) using heartwood data and tree ring width using a nonlinear model. Three models are implemented (Edvardsson et al. 2022). Shiny GitHub
tracheideR Contains functions to standardize tracheid profiles using the traditional method (Vaganov) and a new method to standardize tracheidograms based on the relative position of tracheids within tree rings (Campelo et al. 2016). CRAN

GitHub

(read only)
TRADER Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data (Altman et al. 2014). CRAN GitHub
treeclim Bootstrapped response and correlation functions, seasonal correlations and evaluation of reconstruction skills for use in dendroclimatology and dendroecology (Zang and Biondi 2015). CRAN GitHub
ttprocessing For processing the Tree Talker data. It implements the procedures described in the TT+ manual. It allows for converting the raw data into physical quantities and calculating the sap flow from raw temperatures recorded by the probes. It provides some plotting functions and a graphical user interface (Kabala, Niccoli and Battipaglia 2022; Kabala, Niccoli and Battipaglia 2024). GitHub
WIAD wiad: Wood Image Analysis and Dataset provides a user-friendly interface to digitize wood imagery such as tree ring scans. The package offers a web-based application that the user can run locally from their computers to analyze wood characteristics (Rademacher et al. n.d.). CRAN GitHub
xRing Identify and Measure Tree Rings on X-Ray Micro-Density Profiles. This package contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface (GUI) to visualize density profiles and correct tree-ring borders (Campelo, Mayer and Grabner 2019). CRAN

GitHub

(read only)

References

Alday, JG, Shestakova, TA, Resco de Dios, V and Voltas, J. 2018 DendroSync: An r package to unravel synchrony patterns in tree-ring networks. Dendrochronologia 47: 17–22. DOI: https://doi.org/10.1016/j.dendro.2017.12.003.
Altman, J, Fibich, P, Dolezal, J and Aakala, T. 2014 TRADER: A package for tree ring analysis of disturbance events in r. Dendrochronologia 32(2): 107–112. DOI: https://doi.org/10.1016/j.dendro.2014.01.004.
Aryal, S, Häusser, M, Grießinger, J, Fan, Z and Bräuning, A. 2020 “dendRoAnalyst”: A tool for processing and analysing dendrometer data. Dendrochronologia 64: 125772. DOI: https://doi.org/10.1016/j.dendro.2020.125772.
Bunn, AG. 2008 A dendrochronology program library in r (dplR). Dendrochronologia 26(2): 115124. DOI: https://doi.org/https://doi.org/10.1016/j.dendro.2008.01.002.
Bunn, AG. 2010 Statistical and visual crossdating in r using the dplR library. Dendrochronologia 28(4): 251–258. DOI: https://doi.org/10.1016/j.dendro.2009.12.001.
Campelo, F, García-González, I and Nabais, C. 2012 detrendeR - a graphical user interface to process and visualize tree-ring data using r. Dendrochronologia 30: 57–60. DOI: https://doi.org/16/j.dendro.2011.01.010.
Campelo, F, Mayer, K and Grabner, M. 2019 xRingAn R package to identify and measure tree-ring features using X-ray microdensity profiles. Dendrochronologia 53: 17–21. DOI: https://doi.org/10.1016/j.dendro.2018.11.002.
Campelo, F, Nabais, C, Carvalho, A and Vieira, J. 2016 tracheideRan r package to standardize tracheidograms. Dendrochronologia 37: 64–68. DOI: https://doi.org/10.1016/j.dendro.2015.12.006.
Edvardsson, J, Rögnvaldsson, K, Helgadóttir, EÞ, Linderson, H and Hrafnkelsson, B. 2022 A statistical model for the prediction of the number of sapwood rings in Scots pine (Pinus sylvestris L.). Dendrochronologia 74: 125963. DOI: https://doi.org/10.1016/j.dendro.2022.125963.
García-Hidalgo, M, García-Pedrero, ÁM, Caetano-Sánchez, C, Gómez-España, M, Lillo-Saavedra, M and Olano, JM. 2021 ρ-MtreeRing: A Graphical User Interface for X-ray Microdensity Analysis. Forests 12(10): 1405. DOI: https://doi.org/10.3390/f12101405.
Guiterman, CH, Lynch, AM and Axelson, JN. 2020 dfoliatR: An R package for detection and analysis of insect defoliation signals in tree rings. Dendrochronologia 63: 125750. DOI: https://doi.org/10.1016/j.dendro.2020.125750.
Haneca, K. 2024 Fellingdater: An r package to facilitate the organisation, analysis and interpretation of tree-ring data from wooden heritage objects and structures.
Haneca, K, Debonne, V and Hoffsummer, P. 2020 The ups and downs of the building trade in a medieval city: Tree-ring data as proxies for economic, social and demographic dynamics in Bruges (c. 12001500). Dendrochronologia 64: 125773. DOI: https://doi.org/10.1016/j.dendro.2020.125773.
Jevšenak, J and Levanič, T. 2018 dendroTools: R package for studying linear and nonlinear responses between tree-rings and daily environmental data. Dendrochronologia 48: 32–39. DOI: https://doi.org/10.1016/j.dendro.2018.01.005.
Kabala, JP, Niccoli, F and Battipaglia, G. 2022 2022 IEEE workshop on metrology for agriculture and forestry (MetroAgriFor). In: November 2022. pp. 70–74. DOI: https://doi.org/10.1109/MetroAgriFor55389.2022.9964512.
Kabala, JP, Niccoli, F and Battipaglia, G. 2024 Update to ttprocessing: The r-package to handle the TreeTalker monitoring data. Dendrochronologia 84: 126167. DOI: https://doi.org/10.1016/j.dendro.2024.126167.
Lara, W, Bogino, S and Bravo, F. 2018 Multilevel analysis of dendroclimatic series with the R-package BIOdry. PLOS ONE 13(5): e0196923. DOI: https://doi.org/10.1371/journal.pone.0196923.
Lara, W, Bravo, F and Sierra, CA. 2015 measuRing: An r package to measure tree-ring widths from scanned images. Dendrochronologia 34: 43–50. DOI: https://doi.org/10.1016/j.dendro.2015.04.002.
Maaten-Theunissen, M van der, Maaten, E van der and Bouriaud, O. 2015 pointRes: An r package to analyze pointer years and components of resilience. Dendrochronologia 35: 34–38. DOI: https://doi.org/10.1016/j.dendro.2015.05.006.
Malevich, SB, Guiterman, CH and Margolis, EQ. 2018 Burnr: Fire history analysis and graphics in r. Dendrochronologia 49: 9–15. DOI: https://doi.org/10.1016/j.dendro.2018.02.005.
Peters, RL, Balanzategui, D, Hurley, AG, Arx, G von, Prendin, AL, Cuny, HE, Björklund, J, Frank, DC and Fonti, P. 2018 RAPTOR: Row and position tracheid organizer in r. Dendrochronologia 47: 10–16. DOI: https://doi.org/10.1016/j.dendro.2017.10.003.
Rademacher, T, Seyednasrollah, B, Basler, D, Cheng, J, Mandra, T, Miller, E, Lin, Z, Orwig, DA, Pederson, N, Pfister, H, Wei, D, Yao, L and Richardson, AD. n.d. The Wood Image Analysis and Dataset (WIAD): Open-access visual analysis tools to advance the ecological data revolution. Methods in Ecology and Evolution n/a(n/a): DOI: https://doi.org/10.1111/2041-210X.13717.
Reynolds, DJ, Edge, DC and Black, BA. 2021 RingdateR: A statistical and graphical tool for crossdating. Dendrochronologia 65: 125797. DOI: https://doi.org/10.1016/j.dendro.2020.125797.
Shi, J, Xiang, W, Liu, Q and Shah, S. 2019 MtreeRing: An R package with graphical user interface for automatic measurement of tree ring widths using image processing techniques. Dendrochronologia 58: 125644. DOI: https://doi.org/10.1016/j.dendro.2019.125644.
Visser, R. 2024. dendroNetwork: A r-package to create dendrochronological networks. Zenodo. DOI: https://doi.org/10.5281/zenodo.10636310.
Zang, C and Biondi, F. 2015 treeclim: an R package for the numerical calibration of proxy-climate relationships. Ecography 38(4): 431–436. DOI: https://doi.org/10.1111/ecog.01335.

Footnotes

  1. All descriptions were copied from the website or CRAN archive and edited where needed.↩︎

  2. There is also ρ-MtreeRing (GitHub). This is not a R-package, but user-friendly FOSS that streamlines the entire microdensitometry analysis process through a graphical user interface based on Shiny R Software without any programming knowledge. 𝜌-MtreeRing can be personalized and developed by the microdensitometry research community(García-Hidalgo et al. 2021).↩︎