Statistical Methods for Phenology Analysis in Temperate Fruit Trees


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Documentation for package ‘chillR’ version 0.70.24

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chillR-package Statistical methods for phenology analysis in temperate fruit trees
bloom_prediction Bloom prediction from chilling and forcing requirements, assumed to be fulfilled strictly in sequence
bloom_prediction2 Bloom prediction from chilling and forcing requirements, assumed to be fulfilled strictly in sequence - version 2
bloom_prediction3 Bloom prediction from chilling and forcing requirements, assumed to be fulfilled strictly in sequence - version 3
california_stations Weather stations in California
check_temperature_record Check a daily or hourly temperature record for compliance with chillR's standards
check_temperature_scenario Check temperature scenario for consistency
chile_agromet2chillR Convert a weather file downloaded from the Chilean Agromet website to chillR format
chilling Calculation of chilling and heat from hourly temperature records
Chilling_Hours Calculation of cumulative chill according to the Chilling Hours Model
chilling_hourtable Add chilling and heat accumulation to table of hourly temperatures
chillR Statistical methods for phenology analysis in temperate fruit trees
color_bar_maker Make color scheme for bar plots in outputs of the chillR package
daily_chill Calculation of daily chill and heat accumulation
Date2YEARMODA Date to YEARMODA conversion
daylength Compute sunrise and sunset times, and daylength
Dynamic_Model Calculation of cumulative chill according to the Dynamic Model
Empirical_daily_temperature_curve Empirical daily temperature curve
Empirical_hourly_temperatures Empirical daily temperature prediction
extract_differences_between_characters Identify shared leading or trailing character strings
extract_temperatures_from_grids Extract temperature information from gridded dataset
filter_temperatures Quality filter for temperature records
fix_weather Weather data fixer and quality checker
GDD Calculation of cumulative heat according to the Growing Degree Day Model
GDH Calculation of cumulative heat according to the Growing Degree Hours Model
GDH_model Calculation of cumulative heat according to the Growing Degree Hours Model (alternative function name)
getClimateWizardData Extract climate data from the ClimateWizard database
getClimateWizard_scenarios Extract mutltiple scenarios from the ClimateWizard database
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 Chilean Agromet database
handle_cimis List, download or convert to chillR format data from the CIMIS database
handle_gsod List, download or convert to chillR format data from the Global Summary of the Day database
handle_ucipm List, download or convert to chillR format data from the UCIPM database
handle_wunderground List, download or convert to chillR format data from the Weather Underground airport database
identify_common_string Identify shared leading or trailing character strings
interpolate_gaps Linear gap interpolation
interpolate_gaps_hourly Interpolate gaps in hourly temperature records
JDay_count Count days between two Julian dates
JDay_earlier Check whether a Julian date is before or after another one
JDay_later Check whether a Julian date is after another one
KA_bloom Cherry bloom data for Klein-Altendorf, Germany
KA_weather Weather data for Klein-Altendorf, Germany
leap_year Leap year finder
load_ClimateWizard_scenarios Load climate wizard scenarios
load_temperature_scenarios Load temperature scenarios
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 Make climate scenario
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_daily_chill_plot2 Plot daily climate metric accumulation throughout the year (2)
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 two phases
ordered_climate_list Sort files in a folder, so that numbers are in ascending sequence
patch_daily_temperatures Patch gaps in daily weather records
plot_climateWizard_scenarios Plot mutltiple ClimateWizard scenarios obtained with getClimateWizard_scenarios
plot_climate_scenarios Plot multiple chilling scenario groups (or for other metrics)
plot_PLS Output of Partial Least Squares analysis results of phenology vs. daily mean temperatures
PLS_chill_force Partial Least Squares analysis of phenology vs. accumulated daily chill and heat
PLS_pheno Partial Least Squares analysis of phenology vs. daily mean temperatures
read_tab Read csv table regardless of whether it is a true csv or the French type
RMSEP Root Mean Square Error of Prediction (RMSEP)
RPD Residual Prediction Deviation (RPD)
RPIQ Ratio of Performance to InterQuartile distance (RPIQ)
runn_mean Running mean of a vector
runn_mean_pred Prediction based on a running mean
save_temperature_scenarios Save temperature scenarios generated with temperature_generation
select_by_file_extension Select string that end in a particular way (e.g. a certain file extension)
stack_hourly_temps Stacking of hourly temperatures
stage_transitions Compute what it takes to advance through development stages
step_model Calculation of cumulative temperature metric according to a user-defined stepwise weight function
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 records
tempResponse_daily_list Calculation of climatic metrics from lists of daily temperature records
tempResponse_hourtable Add metric accumulation to table of hourly temperatures
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
Winters_hours_gaps Hourly temperature data sample
YEARMODA2Date YEARMODA to Date conversion