dplpy 0.1.5

Dendrochronology Program Library for Python

dplPy -the Dendrochronology Program Library in Python

The Dendrochronology Program Library (DPL) in Python has its roots in both the original FORTRAN program created by the legendary Richard Holmes and the subsequent R Project package by Andy Bunn, dplR. Our aim is to provide researchers working with tree-ring data the necessary tools in open-source environments, promoting open science practices, enhancing rigor and transparency in dendrochronology, and eventually allowing reproducible research entirely in a single programming language.

The development of dplPy is supported by a grant from the Paleoclimate program of the US National Science Foundation (AGS-2054516) to Andy Bunn, Kevin Anchukaitis, Ed Cook, and Tyson Swetnam.

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Index

• dplPy - the Dendrochronology Program Library in Python
  • Index
  • Requirements
  • Current Version and Changelog
  • Installation
  • Building directly from Github
  • Using VSCode in your operating system
    • Linux or MacOS
    • Windows
  • Functionalities and Usage
    • Loading data using readers
    • Data Summary from summary
    • Data Stastics from stats
    • Data Report from report
    • Plotting
    • Detrending using detrend
    • Autoregressive (AR) modeling
    • Build a chronology with chron
    • Crossdate with xdate

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Requirements

• Python (>=3.10)
• Conda (Anaconda or Miniconda)
• (Suggested) Mamba
• (Suggested) VSCode

Under the hood, dplPy uses numpy, pandas, matplotlib, statsmodels, scipy, and csaps.

:warning: dplPy has been successfully tested thus far on Ubuntu 20, Ubuntu 22, macOS (Intel and M2). Other operating systems may experience unexpected errors or conflicts. Please let the developers know.

Current Version and Changelog

dplPy is currently at version v0.1.2 - The project is changing to a new development structure where all development will be on main and releases and updates to Pypi will be branched and tagged from main.

Installation

dplPy is now available to install via pip:

pip install dplpy

To ensure you have the latest version of dplPy installed, you can run:

pip install dplpy --upgrade

You can install a conda virtual environment using the environment.yml for the project:

$ conda env create -f environment.yml     

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Building directly from Github

You can still still install dplPy firectly from Github if you wish:

1. Clone and change directory to this repository

$ git clone https://github.com/OpenDendro/dplPy.git
$ cd dplPy

2. Create a conda environment through the environment.yml file. This will ensure all packages required are installed.

$ conda env create -f environment.yml     

# if you have mamba installed you could instead do

$ mamba env create -f environment.yml

When prompted for permission to install required packages (with y/n), select y.

3. Activate your environment:

$ conda activate dplpy

Your environment should be successfully built.

4. Your python environment should be able to import numpy, pandas, matplotlib, statsmodels and csaps.

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Using VSCode in your operating system

Linux or MacOS

1. In your VSCode terminal, activate the conda environment with conda activate dplpy3.

2. Open a Jupyer Notebook (<file>.ipynb) and select the dplpy3 Kernel when prompted (or from the top right of your screen). This will automatically load the environment we created.

Windows

In VSCode:

1. In your VSCode terminal window, activate the conda environment with conda activate dplpy3.

2. In the same terminal window, start a Jupyter Notebook with jupyter notebook. Jupyter will then return URLs that you can copy; Copy one of these URLs.

3. Open a Jupyter Notebook (<file>.ipynb) and from the bottom right of the VSCode screen, click Jupyter Server;

A dropdown menu will open from the top of the screen: select Existing and paste the URL you copied.

4. Jupyter Notebook will now be able to access the environment created.

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Functionalities and Usage

Import the dplPy tool with

import dplpy as dpl

or alternatively:

import dplpy 

This will load the package and its functions.

Loading data using readers

• Description: reads data from supported file types (csv and rwl) and stores them in a dataframe.
• Options:
  • header: input files often have a header present; Default is False, use True if input has a header.
• Usage example:

  >>> data = dpl.readers("/path/to/file.rwl", header=True)
  

Data Summary from summary

• Description: generates a summary of each series recorded in rwl and csv format files
• Usage Example:

  >>> dpl.summary("/path/to/file.rwl")
  # or
  >>> dpl.summary(data)
  

Data Stastics from stats

• Description: generates summary statistics for rwl and csv format files
• Usage Example:

  >>> dpl.stats("/path/to/file.rwl")
  # or
  >>> dpl.stats(data)
  

Data Report from report

• Description: generates a report about absent rings in the data set
• Usage Example:

  >>> dpl.report("/path/to/file.rwl")
  # or
  >>> dpl.report(data)
  

Plotting

• Description: generates plots of tree ring with data from dataframes. Currently capable of generating line (default), spag (spaghetti) and seg (segment) plots.
• Options:
  • type="line": creates a line plot (default)
  • type="spag": creates a spaghetti plot
  • type="seg": creates a segment plot
• Usage Example:

  >>> dpl.report("/path/to/file.rwl")
  # or 
  >>> dpl.plot(data)
  
  # User is able to select specific series of interests.
  # In the example below, the user selects SERIES_1, SERIES_2, SERIES_3 
  # from the "data" dataset and generates a spaghetti plot
  >>> dpl.plot(data[[SERIES_1, SERIES_2, SERIES_3]], type="spag")
  

Detrending using detrend

• Description: Detrends a given series or data frame, first by fitting data to curve(s), and then by calculating residuals or differences compared to the original data.
• Options:
  • fit="spline": default detrending method.
  • fit="ModNegEx": detrending using negative exponent method.
  • fit="Hugershoff": detrending using the Hugenshoff method.
  • fit="linear": detrending using the linear method.
  • fit="horizontal": detrending using the horizontal method.
  • method="residual": calculates residuals vs original data (default).
  • method="difference": calculates differences vs original data.
  • Plot: plotting results default is True, accepts False.
• Usage Example:

  >>> dpl.detrend(data)
  # or
  >>> dpl.detrend(data, fit="Hugershoff", method="difference")
  
  # User is able to select specific series of interests.
  >>> dpl.detrend(data[[SERIES_1, SERIES_2, SERIES_3]], fit="Hugershoff", method="difference")
  

Autoregressive (AR) modeling

• Description: ontains methods that fit series to autoregressive models and perform functions related to AR modeling.
• Functions:
  • autoreg(data['Name of series'], max_lag): returns parameters of best fit AR model with maxlag of 5 (default) or other specified number
  • ar_func(data['Name of series'], max_lag): returns residuals plus mean of best fit from AR models with max lag of either 5 (default) or specified number
• Options:
  • max_lag: default 5, can be specified to user's needs.
• Usage Example:

  >>> dpl.autoreg(data[SERIES_1])
  # or
  >>> dpl.ar_func(data[SERIES_2], max_lag=7)
  

Build a chronology with chron

• Description: creates a mean value chronology for a dataset, typically the ring width indices of a detrended series. Note: input data has to be detrended first.
• Options:
  • biweight: find means using Tukey's biweight robust mean; default True.
  • prewhiten: prewhitens data by fitting to an AR model; default False.
  • plot: plots results; default True.
• Usage Example:

  # Detrend data first!
  >>> rwi_data = dpl.detrend(data)
  
  # Perform chronology
  >>> dpl.chron(rwi_data, biweight=False, plot=False)
  

Crossdate with xdate

• Description: evaluate the dating accuracy of a set of tree-ring measurements
• Options: