chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

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.

AuthorEike Luedeling
Date of publication2016-03-12 09:36:15
MaintainerEike Luedeling <eike@eikeluedeling.com>
LicenseGPL-3
Version0.62

View on CRAN

Man pages

bloom_prediction: Bloom prediction from chilling and forcing requirements,...

california_stations: Weather stations in California

chile_agromet2chillR: Convert a weather file downloaded from the Chilean Agromet...

chilling: Calculation of chilling and heat from hourly temperature...

Chilling_Hours: Calculation of cumulative chill according to the Chilling...

chilling_hourtable: Add chilling and heat accumulation to table of hourly...

chillR-package: Statistical methods for phenology analysis in temperate fruit...

color_bar_maker: Make color scheme for bar plots in outputs of the chillR...

daily_chill: Calculation of daily chill and heat accumulation

Dynamic_Model: Calculation of cumulative chill according to the Dynamic...

fix_weather: Weather data fixer and quality checker

GDH: Calculation of cumulative heat according to the Growing...

get_last_date: Get the last date from a phenology record

get_weather: Download weather data from online database

handle_chile_agromet: List, download or convert to chillR format data from the...

handle_cimis: List, download or convert to chillR format data from the...

handle_gsod: List, download or convert to chillR format data from the...

handle_ucipm: List, download or convert to chillR format data from the...

handle_wunderground: List, download or convert to chillR format data from the...

interpolate_gaps: Linear gap interpolation

KA_bloom: Cherry bloom data for Klein-Altendorf, Germany

KA_weather: Weather data for Klein-Altendorf, Germany

leap_year: Leap year finder

make_all_day_table: Fill in missing days in incomplete time series

make_california_UCIPM_station_list: Makes a list of the UC IPM weather stations

make_chill_plot: Plot climate metrics over time

make_daily_chill_figures: Produce image of daily chill and heat accumulation

make_daily_chill_plot: Plot daily climate metric accumulation throughout the year

make_hourly_temps: Make hourly temperature record from daily data

make_multi_pheno_trend_plot: Combine multiple phenology contour plots in one figure

make_pheno_trend_plot: Make image showing phenology response to temperatures during...

plot_PLS: Output of Partial Least Squares analysis results of phenology...

PLS_chill_force: Partial Least Squares analysis of phenology vs. accumulated...

PLS_pheno: Partial Least Squares analysis of phenology vs. daily mean...

runn_mean: Running mean of a vector

stack_hourly_temps: Stacking of hourly temperatures

step_model: Calculation of cumulative temperature metric according to a...

tempResponse: Calculation of climatic metrics from hourly temperature...

Utah_Model: Calculation of cumulative chill according to the Utah Model

VIP: Calculate VIP scores for PLS regression

weather2chillR: Convert downloaded weather to chillR format

YEARMODA2Date: YEARMODA to Date conversion

Files in this package

chillR
chillR/NAMESPACE
chillR/data
chillR/data/KA_weather.rda
chillR/data/california_stations.rda
chillR/data/KA_bloom.rda
chillR/R
chillR/R/daily_chill.R chillR/R/PLS_pheno.R chillR/R/fix_weather.R chillR/R/PLS_chill_force.R chillR/R/temp_models.R chillR/R/VIP.R chillR/R/get_last_date.R chillR/R/interpolate_gaps.R chillR/R/weather2chillR.R chillR/R/chilling_hourtable.R chillR/R/make_daily_chill_plot.R chillR/R/make_pheno_trend_plot.R chillR/R/make_daily_chill_figures.R chillR/R/make_all_day_table.R chillR/R/stack_hourly_temps.R chillR/R/bloom_prediction.R chillR/R/leap_year.R chillR/R/make_multi_pheno_trend_plot.R chillR/R/handle_wunderground.R chillR/R/get_weather.R chillR/R/chile_agromet2chillR.R chillR/R/plot_pheno_results.R chillR/R/tempResponse.R chillR/R/chillR.R chillR/R/handle_cimis.R chillR/R/make_hourly_temps.R chillR/R/make_california_UCIPM_station_list.R chillR/R/color_bar_maker.R chillR/R/chilling.R chillR/R/YEARMODA2Date.R chillR/R/handle_gsod.R chillR/R/handle_ucipm.R chillR/R/chillR-package.R chillR/R/make_chill_plot.R chillR/R/runn_mean.R chillR/R/handle_chile_agromet.R
chillR/MD5
chillR/DESCRIPTION
chillR/man
chillR/man/make_pheno_trend_plot.Rd chillR/man/chillR-package.Rd chillR/man/daily_chill.Rd chillR/man/Dynamic_Model.Rd chillR/man/make_daily_chill_plot.Rd chillR/man/bloom_prediction.Rd chillR/man/PLS_pheno.Rd chillR/man/make_all_day_table.Rd chillR/man/make_daily_chill_figures.Rd chillR/man/KA_weather.Rd chillR/man/GDH.Rd chillR/man/handle_gsod.Rd chillR/man/get_weather.Rd chillR/man/handle_ucipm.Rd chillR/man/interpolate_gaps.Rd chillR/man/weather2chillR.Rd chillR/man/VIP.Rd chillR/man/handle_wunderground.Rd chillR/man/make_hourly_temps.Rd chillR/man/make_california_UCIPM_station_list.Rd chillR/man/color_bar_maker.Rd chillR/man/make_multi_pheno_trend_plot.Rd chillR/man/runn_mean.Rd chillR/man/Utah_Model.Rd chillR/man/PLS_chill_force.Rd chillR/man/get_last_date.Rd chillR/man/fix_weather.Rd chillR/man/stack_hourly_temps.Rd chillR/man/chilling.Rd chillR/man/tempResponse.Rd chillR/man/handle_chile_agromet.Rd chillR/man/leap_year.Rd chillR/man/Chilling_Hours.Rd chillR/man/california_stations.Rd chillR/man/plot_PLS.Rd chillR/man/chile_agromet2chillR.Rd chillR/man/step_model.Rd chillR/man/chilling_hourtable.Rd chillR/man/make_chill_plot.Rd chillR/man/KA_bloom.Rd chillR/man/handle_cimis.Rd chillR/man/YEARMODA2Date.Rd

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