myClim-package: myClim: Microclimatic Data Processing
In myClim: Microclimatic Data Processing
myClim-package R Documentation
myClim: Microclimatic Data Processing
Description
Package myClim was designed for microclimate data processing, storing, and analyzing.
The myClim wofrkflow consists of reading logger files, pre-processing the time-series,
time-series aggregation, and microclimatic variables calculation. The microclimatic
data are stored in size-efficient hierarchical structure which respects the
hierarchy of field microclimate measurement (locality>loggers>sensors).
After data import, myClim can summarize the data and automatically correct
for the most common problems. The myClim package provides functions to
calculate aggregated microclimate statistics as well as methods for data
calibration, conversion and calculation of derived microclimatic variables
like growing degree days, freezing degree days, snow cover duration,
volumetric water content and vapor pressure deficit.
Standardized microclimatic variables can be stored efficiently in myClim
data format or easily exported to standard R long or wide tables for further
analyses and visualization.
myClim object
We implemented two slightly different data formats of myClim objects calling them:
Raw-format and Agg-format.
Raw-format is designed for data preparation. Mainly data cleaning,
metadata gathering, time zones handling and multiple downloads joining.
Outputs of functions mc_read_files() and mc_read_data() are a Raw-format.
Raw-format has the levels of: localities, loggers and sensors.
Function mc_agg() converts data from Raw-format to Agg-format.
Agg-format is designed mainly for calculations,analysis and microclimatic variables
derivations on the basis of cleaned microclimatic data.
Agg-format is missing the level of loggers. In Agg-format sensors are organized
directly in localities, without loggers.
The highest hierarchical level of myClim structure is the locality. It has own metadata e.g.
coordinates and elevation. For detail description of locality metadata see mc_LocalityMetadata.
On the locality in Raw-format there are loggers; in Agg-format the sensors.
See below. Loggers represents the files imported with myClim reading functions.
Both loggesr and sensors have own metadata. One logger could host more sensors e.g.
Tomst TMS logger hosing TMS_T1 soil temperature, TMS_T2 surface temperature,
TMS_T3 air temperature , TMS_moist soil moisture.
For detailed description of logger and sensor metadata
see mc_LoggerMetadata, mc_SensorMetadata, mc_data_sensors
In Raw-format Within the logger all sensors share time series. In Agg-format where level of
logger is missing, all sensors within the locality share time series. In Raw-format
the time series between the loggers or between the localities can be of different time
step. E.g. on the locality there can be one logger measuring in time step
15 minutes and another one measuring once a day. In Agg-format this is not allowed.
Therefore it is necessary to use mc_agg() to switch from Raw-format to the Agg-format.
myClim time step is defined in seconds (data$metadata@step).
But some steps (especially irregular ones) may not be represented by seconds.
For example step month has variable number of seconds within the year. Therefore, metadata contains also text
representation of the step (data$metadata@period).
Schema of myClim Raw-format
+-------------------------+
$metadata | mc_MainMetadata - class |
+-------------------------+
| @version |
| @format_type |
+-------------------------+
+-------------------------------------------------------------------------------+
$localities | locality[1] |
+-------------------------------------------------------------------------------+
| +-----------------------------+ |
| $metadata | mc_LocalityMetadata - class | |
| +-----------------------------+ |
| | @locality_id | |
| | @elevation | |
| | @lat_wgs84 | |
| | @lon_wgs84 | |
| | @tz_offset | |
| | @tz_type | |
| | @user_data | |
| +-----------------------------+ |
| +------------------------------------------------------------------+|
| $loggers | logger[1] ||
| +------------------------------------------------------------------+|
| | +---------------------------+ ||
| | $metadata | mc_LoggerMetadata - class | ||
| | +---------------------------+ ||
| | | @type | ||
| | | @serial_number | ||
| | | @step | ||
| | +---------------------------+ ||
| | +----------------------------+ ||
| | $clean_info | mc_LoggerCleanInfo - class | ||
| | +----------------------------+ ||
| | | @step | ||
| | | @count_duplicities | ||
| | | @count_missing | ||
| | | @count_disordered | ||
| | | @rounded | ||
| | +----------------------------+ ||
| | $datetime POSIXct vector ||
| | +---------------------------------------------------+||
| | $sensors | sensor[1] |||
| | +---------------------------------------------------+||
| | | +---------------------------+ |||
| | | $metadata | mc_SensorMetadata - class | |||
| | | +---------------------------+ |||
| | | | @sensor_id | |||
| | | | @name | |||
| | | | @height | |||
| | | | @calibrated | |||
| | | +---------------------------+ |||
| | | $values numeric/logical vector |||
| | | +----------+------------+-----------+|||
| | | $calibration | datetime | cor_factor | cor_slope ||||
| | | | ... | ... | ... ||||
| | | +----------+------------+-----------+|||
| | | +-----+-------+-----+-------+ |||
| | | $states | tag | start | end | value | |||
| | | | ... | ... | ... | ... | |||
| | | +-----+-------+-----+-------+ |||
| | +---------------------------------------------------+||
| | +---------------------------------------------------+||
| | | sensor[2] |||
| | +---------------------------------------------------+||
| | ... ||
| | +---------------------------------------------------+||
| | | sensor[n] |||
| | +---------------------------------------------------+||
| +------------------------------------------------------------------+|
| +------------------------------------------------------------------+|
| | logger[2] ||
| +------------------------------------------------------------------+|
| ... |
| +------------------------------------------------------------------+|
| | logger[n] ||
| +------------------------------------------------------------------+|
+-------------------------------------------------------------------------------+
+-------------------------------------------------------------------------------+
| locality[2] |
+-------------------------------------------------------------------------------+
...
+-------------------------------------------------------------------------------+
| locality[n] |
+-------------------------------------------------------------------------------+
Agg-format is the output of mc_agg() function.
Agg-format is mainly designed for calculations which are faster in Agg and slower in Raw.
Schema of myClim Agg-format
+----------------------------+
$metadata | mc_MainMetadataAgg - class |
+----------------------------+
| @version |
| @format_type |
| @step |
| @period |
| @intervals_start |
| @intervals_end |
+----------------------------+
+-----------------------------------------------------------------+
$localities | locality[1] |
+-----------------------------------------------------------------+
| +-----------------------------+ |
| $metadata | mc_LocalityMetadata - class | |
| +-----------------------------+ |
| | @locality_id | |
| | @elevation | |
| | @lat_wgs84 | |
| | @lon_wgs84 | |
| | @tz_offset | |
| | @tz_type | |
| | @user_data | |
| +-----------------------------+ |
| $datetime POSIXct vector |
| +---------------------------------------------------+|
| $sensors | sensor[1] ||
| +---------------------------------------------------+|
| | +---------------------------+ ||
| | $metadata | mc_SensorMetadata - class | ||
| | +---------------------------+ ||
| | | @sensor_id | ||
| | | @name | ||
| | | @height | ||
| | | @calibrated | ||
| | +---------------------------+ ||
| | $values numeric/logical vector ||
| | +----------+------------+-----------+||
| | $calibration | datetime | cor_factor | cor_slope |||
| | | ... | ... | ... |||
| | +----------+------------+-----------+||
| | +-----+-------+-----+-------+ ||
| | $states | tag | start | end | value | ||
| | | ... | ... | ... | ... | ||
| | +-----+-------+-----+-------+ ||
| +---------------------------------------------------+|
| +---------------------------------------------------+|
| | sensor[2] ||
| +---------------------------------------------------+|
| ... |
| +---------------------------------------------------+|
| | sensor[n] ||
| +---------------------------------------------------+|
+-----------------------------------------------------------------+
+-----------------------------------------------------------------+
| locality[2] |
+-----------------------------------------------------------------+
...
+-----------------------------------------------------------------+
| locality[n] |
+-----------------------------------------------------------------+
Author(s)
Maintainer: Vojtěch Kalčík Vojtech.Kalcik@ibot.cas.cz
Authors:
Matěj Man Matej.Man@ibot.cas.cz
Martin Macek Martin.Macek@ibot.cas.cz
Josef Brůna Josef.Bruna@ibot.cas.cz
Lucia Hederová Lucia.Hederova@ibot.cas.cz
Jan Wild Jan.Wild@ibot.cas.cz
Martin Kopecký Martin.Kopecky@ibot.cas.cz
Other contributors:
Institute of Botany of the Czech Academy of Sciences [copyright holder]
See Also
Useful links:
myClim documentation built on Oct. 21, 2024, 5:07 p.m.
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| myClim-package | R Documentation |
myClim: Microclimatic Data Processing
Description
Package myClim was designed for microclimate data processing, storing, and analyzing. The myClim wofrkflow consists of reading logger files, pre-processing the time-series, time-series aggregation, and microclimatic variables calculation. The microclimatic data are stored in size-efficient hierarchical structure which respects the hierarchy of field microclimate measurement (locality>loggers>sensors).
After data import, myClim can summarize the data and automatically correct for the most common problems. The myClim package provides functions to calculate aggregated microclimate statistics as well as methods for data calibration, conversion and calculation of derived microclimatic variables like growing degree days, freezing degree days, snow cover duration, volumetric water content and vapor pressure deficit.
Standardized microclimatic variables can be stored efficiently in myClim data format or easily exported to standard R long or wide tables for further analyses and visualization.
myClim object
We implemented two slightly different data formats of myClim objects calling them:
Raw-format and Agg-format.
Raw-format is designed for data preparation. Mainly data cleaning,
metadata gathering, time zones handling and multiple downloads joining.
Outputs of functions mc_read_files() and mc_read_data() are a Raw-format.
Raw-format has the levels of: localities, loggers and sensors.
Function mc_agg() converts data from Raw-format to Agg-format.
Agg-format is designed mainly for calculations,analysis and microclimatic variables
derivations on the basis of cleaned microclimatic data.
Agg-format is missing the level of loggers. In Agg-format sensors are organized
directly in localities, without loggers.
The highest hierarchical level of myClim structure is the locality. It has own metadata e.g.
coordinates and elevation. For detail description of locality metadata see mc_LocalityMetadata.
On the locality in Raw-format there are loggers; in Agg-format the sensors.
See below. Loggers represents the files imported with myClim reading functions.
Both loggesr and sensors have own metadata. One logger could host more sensors e.g.
Tomst TMS logger hosing TMS_T1 soil temperature, TMS_T2 surface temperature,
TMS_T3 air temperature , TMS_moist soil moisture.
For detailed description of logger and sensor metadata
see mc_LoggerMetadata, mc_SensorMetadata, mc_data_sensors
In Raw-format Within the logger all sensors share time series. In Agg-format where level of
logger is missing, all sensors within the locality share time series. In Raw-format
the time series between the loggers or between the localities can be of different time
step. E.g. on the locality there can be one logger measuring in time step
15 minutes and another one measuring once a day. In Agg-format this is not allowed.
Therefore it is necessary to use mc_agg() to switch from Raw-format to the Agg-format.
myClim time step is defined in seconds (data$metadata@step).
But some steps (especially irregular ones) may not be represented by seconds.
For example step month has variable number of seconds within the year. Therefore, metadata contains also text
representation of the step (data$metadata@period).
Schema of myClim Raw-format
+-------------------------+
$metadata | mc_MainMetadata - class |
+-------------------------+
| @version |
| @format_type |
+-------------------------+
+-------------------------------------------------------------------------------+
$localities | locality[1] |
+-------------------------------------------------------------------------------+
| +-----------------------------+ |
| $metadata | mc_LocalityMetadata - class | |
| +-----------------------------+ |
| | @locality_id | |
| | @elevation | |
| | @lat_wgs84 | |
| | @lon_wgs84 | |
| | @tz_offset | |
| | @tz_type | |
| | @user_data | |
| +-----------------------------+ |
| +------------------------------------------------------------------+|
| $loggers | logger[1] ||
| +------------------------------------------------------------------+|
| | +---------------------------+ ||
| | $metadata | mc_LoggerMetadata - class | ||
| | +---------------------------+ ||
| | | @type | ||
| | | @serial_number | ||
| | | @step | ||
| | +---------------------------+ ||
| | +----------------------------+ ||
| | $clean_info | mc_LoggerCleanInfo - class | ||
| | +----------------------------+ ||
| | | @step | ||
| | | @count_duplicities | ||
| | | @count_missing | ||
| | | @count_disordered | ||
| | | @rounded | ||
| | +----------------------------+ ||
| | $datetime POSIXct vector ||
| | +---------------------------------------------------+||
| | $sensors | sensor[1] |||
| | +---------------------------------------------------+||
| | | +---------------------------+ |||
| | | $metadata | mc_SensorMetadata - class | |||
| | | +---------------------------+ |||
| | | | @sensor_id | |||
| | | | @name | |||
| | | | @height | |||
| | | | @calibrated | |||
| | | +---------------------------+ |||
| | | $values numeric/logical vector |||
| | | +----------+------------+-----------+|||
| | | $calibration | datetime | cor_factor | cor_slope ||||
| | | | ... | ... | ... ||||
| | | +----------+------------+-----------+|||
| | | +-----+-------+-----+-------+ |||
| | | $states | tag | start | end | value | |||
| | | | ... | ... | ... | ... | |||
| | | +-----+-------+-----+-------+ |||
| | +---------------------------------------------------+||
| | +---------------------------------------------------+||
| | | sensor[2] |||
| | +---------------------------------------------------+||
| | ... ||
| | +---------------------------------------------------+||
| | | sensor[n] |||
| | +---------------------------------------------------+||
| +------------------------------------------------------------------+|
| +------------------------------------------------------------------+|
| | logger[2] ||
| +------------------------------------------------------------------+|
| ... |
| +------------------------------------------------------------------+|
| | logger[n] ||
| +------------------------------------------------------------------+|
+-------------------------------------------------------------------------------+
+-------------------------------------------------------------------------------+
| locality[2] |
+-------------------------------------------------------------------------------+
...
+-------------------------------------------------------------------------------+
| locality[n] |
+-------------------------------------------------------------------------------+
Agg-format is the output of mc_agg() function.
Agg-format is mainly designed for calculations which are faster in Agg and slower in Raw.
Schema of myClim Agg-format
+----------------------------+
$metadata | mc_MainMetadataAgg - class |
+----------------------------+
| @version |
| @format_type |
| @step |
| @period |
| @intervals_start |
| @intervals_end |
+----------------------------+
+-----------------------------------------------------------------+
$localities | locality[1] |
+-----------------------------------------------------------------+
| +-----------------------------+ |
| $metadata | mc_LocalityMetadata - class | |
| +-----------------------------+ |
| | @locality_id | |
| | @elevation | |
| | @lat_wgs84 | |
| | @lon_wgs84 | |
| | @tz_offset | |
| | @tz_type | |
| | @user_data | |
| +-----------------------------+ |
| $datetime POSIXct vector |
| +---------------------------------------------------+|
| $sensors | sensor[1] ||
| +---------------------------------------------------+|
| | +---------------------------+ ||
| | $metadata | mc_SensorMetadata - class | ||
| | +---------------------------+ ||
| | | @sensor_id | ||
| | | @name | ||
| | | @height | ||
| | | @calibrated | ||
| | +---------------------------+ ||
| | $values numeric/logical vector ||
| | +----------+------------+-----------+||
| | $calibration | datetime | cor_factor | cor_slope |||
| | | ... | ... | ... |||
| | +----------+------------+-----------+||
| | +-----+-------+-----+-------+ ||
| | $states | tag | start | end | value | ||
| | | ... | ... | ... | ... | ||
| | +-----+-------+-----+-------+ ||
| +---------------------------------------------------+|
| +---------------------------------------------------+|
| | sensor[2] ||
| +---------------------------------------------------+|
| ... |
| +---------------------------------------------------+|
| | sensor[n] ||
| +---------------------------------------------------+|
+-----------------------------------------------------------------+
+-----------------------------------------------------------------+
| locality[2] |
+-----------------------------------------------------------------+
...
+-----------------------------------------------------------------+
| locality[n] |
+-----------------------------------------------------------------+
Author(s)
Maintainer: Vojtěch Kalčík Vojtech.Kalcik@ibot.cas.cz
Authors:
Matěj Man Matej.Man@ibot.cas.cz
Martin Macek Martin.Macek@ibot.cas.cz
Josef Brůna Josef.Bruna@ibot.cas.cz
Lucia Hederová Lucia.Hederova@ibot.cas.cz
Jan Wild Jan.Wild@ibot.cas.cz
Martin Kopecký Martin.Kopecky@ibot.cas.cz
Other contributors:
Institute of Botany of the Czech Academy of Sciences [copyright holder]
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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