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myClim

Install

Install from CRAN:

install.packages("myClim")

Or install the latest development version from GitHUB:

remotes::install_github("https://github.com/ibot-geoecology/myClim")

# optional package rTubeDB
remotes::install_github('environmentalinformatics-marburg/tubedb/rTubeDB')

Documentation & user manual

Source code of package

Related

  • myClimGui - package for visualisation data and editing states

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Version

Install

install.packages('myClim')

Monthly Downloads

368

Version

1.4.0

License

GPL (>= 2)

Issues

5

Pull Requests

0

Stars

7

Forks

4

Maintainer

Vojtěch Kalčík

Last Published

February 21st, 2025

Functions in myClim (1.4.0)

mc_calc_tomst_dendro

Converting Tomst dendrometer values to micrometers
mc_calc_snow_agg

Summary of TRUE/FALSE snow sensor
mc_calc_gdd

Growing Degree Days
mc_TOMSTJoinDataFormat-class

Class for reading TMS join files
mc_calc_fdd

Freezing Degree Days
mc_const_SENSOR_FDD

Freezing Degree Days sensor id see mc_calc_fdd()
mc_agg

Aggregate data by function
mc_const_SENSOR_RH

Relative humidity sensor id
mc_calib_moisture

Calculates coefficients for TMS moisture conversion to VWC
mc_const_SENSOR_Dendro_raw

Default sensor for TOMST Dendrometer radius difference
mc_const_SENSOR_HOBO_T

Onset HOBO temperature sensor id
mc_const_SENSOR_T_C

Temperature sensor id
mc_const_CALIB_MOIST_ACOR_T

Default temperature drift for TMS moisture in the air.
mc_const_SENSOR_Dendro_T

Default sensor for TOMST Dendrometer temperature
mc_const_SENSOR_VPD

Vapor Pressure Deficit sensor id see mc_calc_vpd()
mc_const_SENSOR_TMS_T3

Default sensor for TOMST TMS air temperature
mc_calc_vpd

Calculate vapor pressure deficit (in kPa)
mc_const_SENSOR_Thermo_T

Default sensor for TOMST Thermologger temperature
mc_const_SENSOR_real

General real sensor id
mc_const_SENSOR_TMS_moist

Default sensor for TOMST TMS raw soil moisture
mc_const_SENSOR_snow_bool

Snow existence sensor id see mc_calc_snow()
mc_const_SENSOR_GDD

Growing Degree Days sensor id see mc_calc_gdd()
mc_const_SENSOR_dendro_l_um

Radius difference sensor id
mc_const_SENSOR_integer

General integer sensor id
mc_data_example_raw

Example data in Raw-format
mc_const_SENSOR_count

Count sensor id see mc_agg()
mc_data_formats

Formats of source data files
mc_calc_vwc

Conversion of raw TMS soil moisture values to volumetric water content (VWC)
mc_data_physical

Physical quantities definition
mc_const_SENSOR_VWC

Volumetric soil moisture sensor id see mc_calc_vwc()
mc_const_SENSOR_coverage

Coverage sensor id see mc_agg()
mc_const_SENSOR_HOBO_RH

Onset HOBO humidity sensor id
mc_const_SENSOR_precipitation

Precipitation sensor id
mc_const_SENSOR_sun_shine

Time of sun shine sensor id
mc_data_heights

Default heights of sensors
mc_const_SENSOR_logical

General logical sensor id
mc_const_SENSOR_HOBO_EXTT

Onset HOBO external temperature sensor id
mc_info_count

Count data
mc_filter

Filter data from myClim object
mc_env_vpd

Standardised myClim vapor pressure deficit variables
mc_const_SENSOR_snow_fresh

Height of newly fallen snow sensor id
mc_const_SENSOR_wind_speed

Speed of wind sensor id
mc_const_SENSOR_snow_total

Height snow sensor id
mc_data_sensors

Sensors definition.
mc_prep_meta_sensor

Set metadata of sensors
mc_env_moist

Standardised myClim soil moisture variables
mc_info_logger

Get loggers info table
mc_prep_meta_locality

Set metadata of localities
mc_calc_snow

Snow detection from temperature
mc_const_CALIB_MOIST_WCOR_T

Default temperature drift for TMS moisture in the water
mc_const_CALIB_MOIST_REF_T

Default ref. temperate for TMS moisture calibration
mc_plot_loggers

Plot data from loggers
mc_plot_line

Plot data - ggplot2 geom_line
mc_reshape_wide

Export values to wide table
mc_prep_TMSoffsoil

Detection of out-of-soil measurements from TMS logger
mc_data_vwc_parameters

Volumetric water content parameters
mc_plot_raster

Plot data - ggplot2 geom_raster
mc_prep_clean

Cleaning datetime series
mc_read_wide

Reading data from wide data.frame
mc_env_temp

Standardised myClim temperature variables
mc_prep_crop

Crop datetime
mc_info_meta

Get localities metadata table
mc_info_range

Get table of sensors range
mc_read_tubedb

Reading data from TubeDB
mc_prep_calib

Sensors calibration
mc_prep_calib_load

Load sensor calibration parameters to correct microclimatic records
mc_read_problems

Environment for reading problems
mc_save

Save myClim object
mc_reshape_long

Export values to long table
mc_prep_merge

Merge myClim objects
mc_prep_fillNA

Fill NA
mc_read_files

Reading files or directories
mc_const_SENSOR_TMS_T1

Default sensor for TOMST TMS soil temperature
print.myClimList

Print function for myClim object
myClimList

Custom list for myClim object
mc_states_join

Create states for join conflicts
mc_info_states

Get states (tags) info table
mc_states_outlier

Create states for outlying values
mc_states_from_sensor

Convert a sensor to a state
mc_prep_solar_tz

Set solar time offset against UTC time
mc_join

Joining time-series from repeated downloads
mc_read_data

Reading files with locality metadata
mc_states_update

Update sensor states (tags)
myClim-package

myClim: Microclimatic Data Processing
mc_const_SENSOR_TMS_T2

Default sensor for TOMST TMS temperature of soil surface
mc_states_insert

Insert new sensor states (tags)
mc_states_to_sensor

Convert states to logical (TRUE/FALSE) sensor
mc_states_replace

Replace values by states with tag
mc_read_long

Reading data from long data.frame
mc_data_example_agg

Example data in Agg-format.
mc_load

Load myClim object
mc_info

Get sensors info table
mc_info_clean

Call cleaning log
mc_plot_image

Plot data - image
mc_data_example_clean

Example cleaned data in Raw-format.
mc_save_localities

Save myClim object separated by localities
[.myClimList

Extract localities with []
mc_states_delete

Delete sensor states (tags)
mc_Physical-class

Class for physical
mc_HOBODataFormat-class

Class for reading HOBO logger files
mc_Sensor-class

Class for sensor definition
mc_LoggerCleanInfo-class

Class for logger clean info
length.myClimList

Length function for myClim object
mc_LoggerMetadata-class

Class for logger metadata
mc_LocalityMetadata-class

Class for locality metadata
mc_DataFormat-class

Class for Logger File Data Format
mc_MainMetadata-class

Class for myClim object metadata
mc_MainMetadataAgg-class

Class for myClim object metadata in Agg-format
mc_calc_cumsum

Cumulative sum
mc_SensorMetadata-class

Class for sensor metadata
mc_TOMSTDataFormat-class

Class for reading TOMST logger files