R: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

# Statistical Methods for Phenology Analysis in Temperate Fruit Trees

## Documentation for package ‘chillR’ version 0.77

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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

## -- 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
ChuineCF | ChuineCF
ChuineFstar | ChuineFstar
color_bar_maker | Make color scheme for bar plots in outputs of the chillR package
convert_scen_information | Converts list of change scenarios to data.frame or vice versa

## -- D --

daily_chill | Calculation of daily chill and heat accumulation
Date2YEARMODA | Date to YEARMODA conversion
daylength | Compute sunrise and sunset times, and daylength
download_baseline_cmip6_ecmwfr | Download historical CMIP6 Data via the ecwfr package
download_cmip6_ecmwfr | Download CMIP6 Data via the ecwfr package
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_cmip6_data | Unpacks and formats downloaded CMIP6 data
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
gen_rel_change_scenario | Generates relative climate change scenarios based on extracted CMIP6 data
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_cimis | List, download or convert to chillR format data from the CIMIS database
handle_dwd | List, download or convert to chillR format data from the Deutscher Wetterdienst database
handle_dwd_old | List, download or convert to chillR format data from the Deutscher Wetterdienst database
handle_gsod | List, download or convert to chillR format data from the Global Summary of the Day database
handle_gsod_old | Deprecated version of 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

## -- 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
patch_daily_temps | Patch gaps in daily weather records - updated
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_phenology_trends | Visualizing phenology responses to temperatures during two phases
plot_PLS | Output of Partial Least Squares analysis results of phenology vs. daily mean temperatures
plot_scenarios | Plot historic and future scenarios for climate-related metrics ('ggplot2' version)
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