Statistical Methods for Phenology Analysis in Temperate Fruit Trees


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Documentation for package ‘chillR’ version 0.72.2

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A B C D E F G H I J K L M O P R S T U V W Y

chillR-package chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

-- A --

add_date Add date/time column to data.frame

-- B --

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
bootstrap.phenologyFit bootstrap.phenologyFit

-- C --

c.bootstrap_phenologyFit Concatenate bootstrap_phenologyfit objects
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
chifull chifull
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 chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
ChuineCF ChuineCF
ChuineFstar ChuineFstar
color_bar_maker Make color scheme for bar plots in outputs of the chillR package

-- D --

daily_chill Calculation of daily chill and heat accumulation
Date2YEARMODA Date to YEARMODA conversion
daylength Compute sunrise and sunset times, and daylength
Dynamic_Model Dynamic_Model
DynModel_driver DynModel_driver

-- E --

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

-- F --

filter_temperatures Quality filter for temperature records
fix_weather Weather data fixer and quality checker

-- G --

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)
genSeason Generate Seasons
genSeasonList genSeasonList
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

-- H --

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

-- I --

identify_common_string Identify shared leading or trailing character strings
interpolate_gaps Linear gap interpolation
interpolate_gaps_hourly Interpolate gaps in hourly temperature records

-- J --

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

-- K --

KA_bloom Cherry bloom data for Klein-Altendorf, Germany
KA_weather Weather data for Klein-Altendorf, Germany

-- L --

leap_year Leap year finder
load_ClimateWizard_scenarios Load climate wizard scenarios
load_temperature_scenarios Load temperature scenarios

-- M --

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

-- O --

ordered_climate_list Sort files in a folder, so that numbers are in ascending sequence

-- P --

patch_daily_temperatures Patch gaps in daily weather records
PhenoFlex PhenoFlex
PhenoFlex_fixedDynModelGAUSSwrapper PhenoFlex_fixedDynModelGAUSSwrapper
PhenoFlex_fixedDynModelwrapper PhenoFlex_fixedDynModelwrapper
PhenoFlex_GAUSSwrapper PhenoFlex_GAUSSwrapper
PhenoFlex_GDHwrapper PhenoFlex_GDHwrapper
phenologyFit phenologyFit
phenologyFitter phenologyFitter
plot.bootstrap_phenologyFit plot bootstrap_phenologyFit
plot.phenologyFit plot phenologyFit
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
predict.bootstrap_phenologyFit predict bootstrap_phenologyFit
predict.phenologyFit predict phenologyFit
print.phenologyFit print phenologyFit

-- R --

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

-- S --

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
StepChill_Wrapper StepChill_Wrapper
step_model Calculation of cumulative temperature metric according to a user-defined stepwise weight function
summary.bootstrap_phenologyFit summary.bootstrap_phenologyFit
summary.phenologyFit summary phenologyFit

-- T --

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

-- U --

UniChill_Wrapper UniChill_Wrapper
UnifiedModel_Wrapper UnifiedModel_Wrapper
UniForce_Wrapper UniForce_Wrapper
Utah_Model Calculation of cumulative chill according to the Utah Model

-- V --

VIP Calculate VIP scores for PLS regression

-- W --

weather2chillR Convert downloaded weather to chillR format
Winters_hours_gaps Hourly temperature data sample

-- Y --

YEARMODA2Date YEARMODA to Date conversion