Microclimatic Data Processing
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Documentation for package ‘myClim’ version 1.4.0
Help Pages
-- L --
| length.myClimList | Length function for myClim object |
-- M --
| mc_agg | Aggregate data by function |
| mc_calc_cumsum | Cumulative sum |
| mc_calc_fdd | Freezing Degree Days |
| mc_calc_gdd | Growing Degree Days |
| mc_calc_snow | Snow detection from temperature |
| mc_calc_snow_agg | Summary of TRUE/FALSE snow sensor |
| mc_calc_tomst_dendro | Converting Tomst dendrometer values to micrometers |
| mc_calc_vpd | Calculate vapor pressure deficit (in kPa) |
| mc_calc_vwc | Conversion of raw TMS soil moisture values to volumetric water content (VWC) |
| mc_calib_moisture | Calculates coefficients for TMS moisture conversion to VWC |
| mc_const_CALIB_MOIST_ACOR_T | Default temperature drift for TMS moisture in the air. |
| mc_const_CALIB_MOIST_REF_T | Default ref. temperate for TMS moisture calibration |
| mc_const_CALIB_MOIST_WCOR_T | Default temperature drift for TMS moisture in the water |
| mc_const_SENSOR_count | Count sensor id see 'mc_agg()' |
| mc_const_SENSOR_coverage | Coverage sensor id see 'mc_agg()' |
| mc_const_SENSOR_dendro_l_um | Radius difference sensor id |
| mc_const_SENSOR_Dendro_raw | Default sensor for TOMST Dendrometer radius difference |
| mc_const_SENSOR_Dendro_T | Default sensor for TOMST Dendrometer temperature |
| mc_const_SENSOR_FDD | Freezing Degree Days sensor id see 'mc_calc_fdd()' |
| mc_const_SENSOR_GDD | Growing Degree Days sensor id see 'mc_calc_gdd()' |
| mc_const_SENSOR_HOBO_EXTT | Onset HOBO external temperature sensor id |
| mc_const_SENSOR_HOBO_RH | Onset HOBO humidity sensor id |
| mc_const_SENSOR_HOBO_T | Onset HOBO temperature sensor id |
| mc_const_SENSOR_integer | General integer sensor id |
| mc_const_SENSOR_logical | General logical sensor id |
| mc_const_SENSOR_precipitation | Precipitation sensor id |
| mc_const_SENSOR_real | General real sensor id |
| mc_const_SENSOR_RH | Relative humidity sensor id |
| mc_const_SENSOR_snow_bool | Snow existence sensor id see 'mc_calc_snow()' |
| mc_const_SENSOR_snow_fresh | Height of newly fallen snow sensor id |
| mc_const_SENSOR_snow_total | Height snow sensor id |
| mc_const_SENSOR_sun_shine | Time of sun shine sensor id |
| mc_const_SENSOR_Thermo_T | Default sensor for TOMST Thermologger temperature |
| mc_const_SENSOR_TMS_moist | Default sensor for TOMST TMS raw soil moisture |
| mc_const_SENSOR_TMS_T1 | Default sensor for TOMST TMS soil temperature |
| mc_const_SENSOR_TMS_T2 | Default sensor for TOMST TMS temperature of soil surface |
| mc_const_SENSOR_TMS_T3 | Default sensor for TOMST TMS air temperature |
| mc_const_SENSOR_T_C | Temperature sensor id |
| mc_const_SENSOR_VPD | Vapor Pressure Deficit sensor id see 'mc_calc_vpd()' |
| mc_const_SENSOR_VWC | Volumetric soil moisture sensor id see 'mc_calc_vwc()' |
| mc_const_SENSOR_wind_speed | Speed of wind sensor id |
| mc_DataFormat | Class for Logger File Data Format |
| mc_DataFormat-class | Class for Logger File Data Format |
| mc_data_example_agg | Example data in Agg-format. |
| mc_data_example_clean | Example cleaned data in Raw-format. |
| mc_data_example_raw | Example data in Raw-format |
| mc_data_formats | Formats of source data files |
| mc_data_heights | Default heights of sensors |
| mc_data_physical | Physical quantities definition |
| mc_data_sensors | Sensors definition. |
| mc_data_vwc_parameters | Volumetric water content parameters |
| mc_env_moist | Standardised myClim soil moisture variables |
| mc_env_temp | Standardised myClim temperature variables |
| mc_env_vpd | Standardised myClim vapor pressure deficit variables |
| mc_filter | Filter data from myClim object |
| mc_HOBODataFormat | Class for reading HOBO logger files |
| mc_HOBODataFormat-class | Class for reading HOBO logger files |
| mc_info | Get sensors info table |
| mc_info_clean | Call cleaning log |
| mc_info_count | Count data |
| mc_info_logger | Get loggers info table |
| mc_info_meta | Get localities metadata table |
| mc_info_range | Get table of sensors range |
| mc_info_states | Get states (tags) info table |
| mc_join | Joining time-series from repeated downloads |
| mc_load | Load myClim object |
| mc_LocalityMetadata | Class for locality metadata |
| mc_LocalityMetadata-class | Class for locality metadata |
| mc_LoggerCleanInfo | Class for logger clean info |
| mc_LoggerCleanInfo-class | Class for logger clean info |
| mc_LoggerMetadata | Class for logger metadata |
| mc_LoggerMetadata-class | Class for logger metadata |
| mc_MainMetadata | Class for myClim object metadata |
| mc_MainMetadata-class | Class for myClim object metadata |
| mc_MainMetadataAgg | Class for myClim object metadata in Agg-format |
| mc_MainMetadataAgg-class | Class for myClim object metadata in Agg-format |
| mc_Physical | Class for physical |
| mc_Physical-class | Class for physical |
| mc_plot_image | Plot data - image |
| mc_plot_line | Plot data - ggplot2 geom_line |
| mc_plot_loggers | Plot data from loggers |
| mc_plot_raster | Plot data - ggplot2 geom_raster |
| mc_prep_calib | Sensors calibration |
| mc_prep_calib_load | Load sensor calibration parameters to correct microclimatic records |
| mc_prep_clean | Cleaning datetime series |
| mc_prep_crop | Crop datetime |
| mc_prep_fillNA | Fill NA |
| mc_prep_merge | Merge myClim objects |
| mc_prep_meta_locality | Set metadata of localities |
| mc_prep_meta_sensor | Set metadata of sensors |
| mc_prep_solar_tz | Set solar time offset against UTC time |
| mc_prep_TMSoffsoil | Detection of out-of-soil measurements from TMS logger |
| mc_read_data | Reading files with locality metadata |
| mc_read_files | Reading files or directories |
| mc_read_long | Reading data from long data.frame |
| mc_read_problems | Environment for reading problems |
| mc_read_tubedb | Reading data from TubeDB |
| mc_read_wide | Reading data from wide data.frame |
| mc_reshape_long | Export values to long table |
| mc_reshape_wide | Export values to wide table |
| mc_save | Save myClim object |
| mc_save_localities | Save myClim object separated by localities |
| mc_Sensor | Class for sensor definition |
| mc_Sensor-class | Class for sensor definition |
| mc_SensorMetadata | Class for sensor metadata |
| mc_SensorMetadata-class | Class for sensor metadata |
| mc_states_delete | Delete sensor states (tags) |
| mc_states_from_sensor | Convert a sensor to a state |
| mc_states_insert | Insert new sensor states (tags) |
| mc_states_join | Create states for join conflicts |
| mc_states_outlier | Create states for outlying values |
| mc_states_replace | Replace values by states with tag |
| mc_states_to_sensor | Convert states to logical (TRUE/FALSE) sensor |
| mc_states_update | Update sensor states (tags) |
| mc_TOMSTDataFormat | Class for reading TOMST logger files |
| mc_TOMSTDataFormat-class | Class for reading TOMST logger files |
| mc_TOMSTJoinDataFormat | Class for reading TMS join files |
| mc_TOMSTJoinDataFormat-class | Class for reading TMS join files |
| myClimList | Custom list for myClim object |
-- P --
| print.myClimList | Print function for myClim object |
-- misc --
| [.myClimList | Extract localities with [] |