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chillR (version 0.62)

Statistical Methods for Phenology Analysis in Temperate Fruit Trees

Description

The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat. 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records.

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Version

Install

install.packages('chillR')

Monthly Downloads

1,162

Version

0.62

License

GPL-3

Maintainer

Eike Luedeling

Last Published

March 12th, 2016

Functions in chillR (0.62)

GDH

Calculation of cumulative heat according to the Growing Degree Hours Model
KA_weather

Weather data for Klein-Altendorf, Germany
handle_chile_agromet

List, download or convert to chillR format data from the Chilean Agromet database
chile_agromet2chillR

Convert a weather file downloaded from the Chilean Agromet website to chillR format
make_multi_pheno_trend_plot

Combine multiple phenology contour plots in one figure
stack_hourly_temps

Stacking of hourly temperatures
tempResponse

Calculation of climatic metrics from hourly temperature records
daily_chill

Calculation of daily chill and heat accumulation
fix_weather

Weather data fixer and quality checker
Dynamic_Model

Calculation of cumulative chill according to the Dynamic Model
KA_bloom

Cherry bloom data for Klein-Altendorf, Germany
runn_mean

Running mean of a vector
step_model

Calculation of cumulative temperature metric according to a user-defined stepwise weight function
Utah_Model

Calculation of cumulative chill according to the Utah Model
YEARMODA2Date

YEARMODA to Date conversion
california_stations

Weather stations in California
Chilling_Hours

Calculation of cumulative chill according to the Chilling Hours Model
bloom_prediction

Bloom prediction from chilling and forcing requirements, assumed to be fulfilled strictly in sequence
make_california_UCIPM_station_list

Makes a list of the UC IPM weather stations
make_chill_plot

Plot climate metrics over time
chilling_hourtable

Add chilling and heat accumulation to table of hourly temperatures
PLS_pheno

Partial Least Squares analysis of phenology vs. daily mean temperatures
color_bar_maker

Make color scheme for bar plots in outputs of the chillR package
make_daily_chill_plot

Plot daily climate metric accumulation throughout the year
weather2chillR

Convert downloaded weather to chillR format
make_pheno_trend_plot

Make image showing phenology response to temperatures during two phases
chilling

Calculation of chilling and heat from hourly temperature records
handle_gsod

List, download or convert to chillR format data from the Global Summary of the Day database
make_daily_chill_figures

Produce image of daily chill and heat accumulation
get_last_date

Get the last date from a phenology record
interpolate_gaps

Linear gap interpolation
leap_year

Leap year finder
get_weather

Download weather data from online database
plot_PLS

Output of Partial Least Squares analysis results of phenology vs. daily mean temperatures
make_hourly_temps

Make hourly temperature record from daily data
VIP

Calculate VIP scores for PLS regression
PLS_chill_force

Partial Least Squares analysis of phenology vs. accumulated daily chill and heat
chillR-package

Statistical methods for phenology analysis in temperate fruit trees
handle_ucipm

List, download or convert to chillR format data from the UCIPM database
handle_cimis

List, download or convert to chillR format data from the CIMIS database
handle_wunderground

List, download or convert to chillR format data from the Weather Underground airport database
make_all_day_table

Fill in missing days in incomplete time series