Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
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Documentation for package ‘chillR’ version 0.75
Help Pages
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 |
| 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 |