chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

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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.

Author
Eike Luedeling
Date of publication
2016-03-12 09:36:15
Maintainer
Eike Luedeling <eike@eikeluedeling.com>
License
GPL-3
Version
0.62

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