chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Version 0.66

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. As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses.

AuthorEike Luedeling
Date of publication2017-03-24 13:28:48 UTC
MaintainerEike Luedeling <eike@eikeluedeling.com>
LicenseGPL-3
Version0.66
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("chillR")

Getting started

Package overview

Popular man pages

check_temperature_scenario: Check temperature scenario for consistency
chillR-package: Statistical methods for phenology analysis in temperate fruit...
extract_differences_between_characters: Identify shared leading or trailing character strings
get_last_date: Get the last date from a phenology record
make_hourly_temps: Make hourly temperature record from daily data
make_multi_pheno_trend_plot: Combine multiple phenology contour plots in one figure
VIP: Calculate VIP scores for PLS regression
See all...

All man pages Function index File listing

Man pages

bloom_prediction: Bloom prediction from chilling and forcing requirements,...
california_stations: Weather stations in California
check_temperature_scenario: Check temperature scenario for consistency
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...
extract_differences_between_characters: Identify shared leading or trailing character strings
extract_temperatures_from_grids: Extract temperature information from gridded dataset
fix_weather: Weather data fixer and quality checker
GDD: Calculation of cumulative heat according to the Growing...
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...
identify_common_string: Identify shared leading or trailing character strings
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_climate_scenario_from_files: Make climate scenario from multiple saved csv files
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_JDay: Make Julian Day in dataframe
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...
ordered_climate_list: Sort files in a folder, so that numbers are in ascending...
plot_climate_scenarios: Plot multiple chilling scenario groups (or for other metrics)
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...
read_tab: Read csv table regardless of whether it is a true csv or the...
runn_mean: Running mean of a vector
select_by_file_extension: Select string that end in a particular way (e.g. a certain...
stack_hourly_temps: Stacking of hourly temperatures
step_model: Calculation of cumulative temperature metric according to a...
temperature_generation: Generation of synthetic temperature records
temperature_scenario_baseline_adjustment: Make temperature scenario relative to a particular baseline
temperature_scenario_from_records: Make monthly temperature scenario from historic records
tempResponse: Calculation of climatic metrics from hourly temperature...
test_if_equal: Test if all character vectors in a string are equal
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

Functions

Chilling_Hours Man page Source code
Dynamic_Model Man page Source code
GDD Man page Source code
GDH Man page Source code
KA_bloom Man page
KA_weather Man page
PLS_chill_force Man page Source code
PLS_pheno Man page Source code
Utah_Model Man page Source code
VIP Man page Source code
YEARMODA2Date Man page Source code
bloom_prediction Man page Source code
california_stations Man page
check_temperature_scenario Man page Source code
chile_agromet2chillR Man page Source code
chillR Man page
chillR-package Man page
chilling Man page Source code
chilling_hourtable Man page Source code
color_bar_maker Man page Source code
daily_chill Man page Source code
extract_differences_between_characters Man page Source code
extract_temperatures_from_grids Man page Source code
fix_weather Man page Source code
get_last_date Man page Source code
get_weather Man page Source code
handle_chile_agromet Man page Source code
handle_cimis Man page Source code
handle_gsod Man page Source code
handle_ucipm Man page Source code
handle_wunderground Man page Source code
identify_common_string Man page Source code
interpolate_gaps Man page Source code
leap_year Man page Source code
make_JDay Man page Source code
make_all_day_table Man page Source code
make_california_UCIPM_station_list Man page Source code
make_chill_plot Man page Source code
make_climate_scenario_from_files Man page Source code
make_daily_chill_figures Man page Source code
make_daily_chill_plot Man page Source code
make_hourly_temps Man page Source code
make_multi_pheno_trend_plot Man page Source code
make_pheno_trend_plot Man page Source code
ordered_climate_list Man page Source code
plot_PLS Man page Source code
plot_climate_scenarios Man page Source code
read_tab Man page Source code
runn_mean Man page Source code
select_by_file_extension Man page Source code
stack_hourly_temps Man page Source code
step_model Man page Source code
tempResponse Man page Source code
temperature_generation Man page Source code
temperature_scenario_baseline_adjustment Man page Source code
temperature_scenario_from_records Man page Source code
test_if_equal Man page Source code
weather2chillR Man page Source code

Files

NAMESPACE
data
data/KA_weather.rda
data/california_stations.rda
data/KA_bloom.rda
R
R/plot_climate_scenarios.R
R/daily_chill.R
R/PLS_pheno.R
R/fix_weather.R
R/PLS_chill_force.R
R/temp_models.R
R/select_by_file_extension.R
R/VIP.R
R/read_tab.R
R/get_last_date.R
R/temperature_scenario_from_records.R
R/interpolate_gaps.R
R/weather2chillR.R
R/chilling_hourtable.R
R/make_JDay.R
R/identify_common_string.R
R/check_temperature_scenario.R
R/make_daily_chill_plot.R
R/test_if_equal.R
R/make_pheno_trend_plot.R
R/make_daily_chill_figures.R
R/make_all_day_table.R
R/stack_hourly_temps.R
R/bloom_prediction.R
R/leap_year.R
R/make_multi_pheno_trend_plot.R
R/handle_wunderground.R
R/get_weather.R
R/chile_agromet2chillR.R
R/plot_pheno_results.R
R/tempResponse.R
R/chillR.R
R/handle_cimis.R
R/temperature_generation.R
R/make_hourly_temps.R
R/make_california_UCIPM_station_list.R
R/ordered_climate_list.R
R/color_bar_maker.R
R/make_climate_scenario_from_files.R
R/chilling.R
R/YEARMODA2Date.R
R/handle_gsod.R
R/handle_ucipm.R
R/extract_differences_between_characters.R
R/temperature_scenario_baseline_adjustment.R
R/chillR-package.R
R/make_chill_plot.R
R/extract_temperatures_from_grids.R
R/runn_mean.R
R/handle_chile_agromet.R
MD5
DESCRIPTION
man
man/make_pheno_trend_plot.Rd
man/chillR-package.Rd
man/temperature_generation.Rd
man/daily_chill.Rd
man/read_tab.Rd
man/Dynamic_Model.Rd
man/test_if_equal.Rd
man/make_daily_chill_plot.Rd
man/bloom_prediction.Rd
man/PLS_pheno.Rd
man/temperature_scenario_baseline_adjustment.Rd
man/extract_differences_between_characters.Rd
man/make_all_day_table.Rd
man/make_daily_chill_figures.Rd
man/KA_weather.Rd
man/GDH.Rd
man/handle_gsod.Rd
man/make_climate_scenario_from_files.Rd
man/get_weather.Rd
man/handle_ucipm.Rd
man/interpolate_gaps.Rd
man/GDD.Rd
man/weather2chillR.Rd
man/VIP.Rd
man/select_by_file_extension.Rd
man/handle_wunderground.Rd
man/make_JDay.Rd
man/make_hourly_temps.Rd
man/make_california_UCIPM_station_list.Rd
man/color_bar_maker.Rd
man/make_multi_pheno_trend_plot.Rd
man/runn_mean.Rd
man/Utah_Model.Rd
man/PLS_chill_force.Rd
man/get_last_date.Rd
man/temperature_scenario_from_records.Rd
man/fix_weather.Rd
man/stack_hourly_temps.Rd
man/chilling.Rd
man/identify_common_string.Rd
man/tempResponse.Rd
man/handle_chile_agromet.Rd
man/leap_year.Rd
man/Chilling_Hours.Rd
man/check_temperature_scenario.Rd
man/california_stations.Rd
man/plot_PLS.Rd
man/ordered_climate_list.Rd
man/extract_temperatures_from_grids.Rd
man/chile_agromet2chillR.Rd
man/step_model.Rd
man/chilling_hourtable.Rd
man/make_chill_plot.Rd
man/KA_bloom.Rd
man/handle_cimis.Rd
man/plot_climate_scenarios.Rd
man/YEARMODA2Date.Rd
chillR documentation built on May 20, 2017, 4:40 a.m.

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