# Microclimatic Data Processing

## Documentation for package ‘myClim’ version 1.4.0

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

## Help Pages

L M P misc

## -- 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 []