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Commit 91aec409 authored by Peter Lünenschloß's avatar Peter Lünenschloß
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changed function description according to naming contributions

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docs/FunctionDescriptions.md
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......@@ -17,11 +17,11 @@ Main documentation of the implemented functions, their purpose and parameters an
- [constant](#constant)
- [constants_varianceBased](#constants_variancebased)
- [soilMoisture_plateaus](#soilmoisture_plateaus)
- [SoilMoistureSpikes](#soilmoisturespikes)
- [SoilMoistureBreaks](#soilmoisturebreaks)
- [SoilMoistureByFrost](#soilmoisturebyfrost)
- [SoilMoistureByPrecipitation](#soilmoisturebyprecipitation)
- [Breaks_SpektrumBased](#breaks_spektrumbased)
- [soilMoisture_spikes](#soilmoisture_spikes)
- [soilMoisture_breaks](#soilmoisture_breaks)
- [soilMoisture_byFrost](#soilmoisture_byfrost)
- [soilMoisture_byPrecipitation](#soilmoisture_byprecipitation)
- [breaks_spektrumBased](#breaks_spektrumbased)
- [machinelearning](#machinelearning)
- [harmonize](#harmonize)
- [deharmonize](#deharmonize)
......@@ -56,7 +56,7 @@ isolated(isolation_range, max_isolated_group_size=1, continuation_range='1min',
| isolation_range | string | | Offset string. The range, within there are no valid values allowed for a valuegroup to get flagged isolated. See condition (1) and (2).|
| max_isolated_group_size | integer | `1` | The upper bound for the size of a value group to be considered an isolated group. See condition (3).|
| continuation_range | string | `"1min"` | Offset string. The upper bound for the temporal extension of a value group to be considered an isolated group. See condition (4). Only relevant if `max_islated_group_size` > 1.|
| drop_flags | list or Nonetype| `None` | A list of flags, that are to be considered, signifying invalid values. See condition (1) and (2).|
| drop_flags | list or Nonetype| `None` | A list of flags, that are to be regarded as signifying invalid values. See condition (1) and (2).|
The function flags isolated values / value groups.
......@@ -92,7 +92,7 @@ missing(nodata=NaN)
| parameter | data type | default value | description |
| --------- | ---------- | -------------- | ----------- |
| nodata | any | `NaN` | Value indicating missing values in the passed data |
| nodata | any | `NaN` | Value indicating missing values in the passed data. |
The function flags those values in the the passed data series, that are
......@@ -150,8 +150,8 @@ spikes_basic(thresh, tolerance, window_size)
| parameter | data type | default value | description |
| ------ | ------ | ------ | ---- |
| thresh | float | | Minimum jump margin for spikes. See condition (1). |
| tolerance | float | | Range of area, containing al "valid return values". See condition (2). |
| window_size | ftring | | An offset string, denoting the maximal length of "spikish" value courses. See condition (3). |
| tolerance | float | | Range of area, containing all "valid return values". See condition (2). |
| window_size | string | | An offset string, denoting the maximum length of "spikish" value courses. See condition (3). |
A basic outlier test, that is designed to work for harmonized, as well as raw
(not-harmonized) data.
......@@ -258,12 +258,12 @@ spikes_spektrumBased(raise_factor=0.15, dev_cont_factor=0.2,
| parameter | data type | default value | description |
| ------ | ------ | ------ | ---- |
| raise_factor | float | `0.15` | Minimum change margin for a datapoint to become a candidate for a spike. See condition (1). |
| raise_factor | float | `0.15` | Minimum margin of value change, a datapoint has to represent, to become a candidate for a spike. See condition (1). |
| dev_cont_factor | float | `0.2` | See condition (2). |
| noise_barrier | float | `1` | Upper bound for noisyness of data surrounding potential spikes. See condition (3). |
| noise_window_range | string | `"12h"` | Any offset string. Determines the range of the timewindow of the "surrounding" data of a potential spike. See condition (3). |
| noise_statistic | string | `"CoVar"` | Operator to calculate noisyness of data, surrounding potential spike. Either `"Covar"` (=Coefficient od Variation) or `"rvar"` (=relative Variance). |
| smooth_poly_order | integer | `2` | Order of the polynomial fit, applied for smoothing |
| noise_window_range | string | `"12h"` | Any offset string. Determines the range of the time window of the "surrounding" data of a potential spike. See condition (3). |
| noise_statistic | string | `"CoVar"` | Operator to calculate noisyness of data, surrounding potential spikes. Either `"Covar"` (=Coefficient od Variation) or `"rvar"` (=relative Variance). |
| smooth_poly_order | integer | `2` | Order of the polynomial fit, applied with savitsky-Golay-filter. |
| filter_window_size | Nonetype or string | `None` | Options: <br/> - `None` <br/> - any offset string <br/><br/> Controlls the range of the smoothing window applied with the Savitsky-Golay filter. If None is passed (default), the window size will be two times the sampling rate. (Thus, covering 3 values.) If you are not very well knowing what you are doing - do not change that value. Broader window sizes caused unexpected results during testing phase. |
......@@ -347,7 +347,7 @@ soilMoisture_plateaus(plateau_window_min="12h", plateau_var_limit=0.0005,
rainfall_window_range="12h", var_total_nans=np.inf,
var_consec_nans=np.inf, derivative_max_lb=0.0025,
derivative_min_ub=0, data_max_tolerance=0.95,
filter_window_size=None, smooth_poly_order=2, **kwargs)
filter_window_size=None, smooth_poly_order=2)
```
| parameter | data type | default value | description |
......@@ -393,10 +393,10 @@ doi:10.2136/vzj2012.0097.
All parameters default to the values, suggested in this publication.
## SoilMoistureSpikes
## SoilMoisture_spikes
```
SoilMoistureSpikes(filter_window_size="3h", raise_factor=0.15, dev_cont_factor=0.2,
SoilMoisture_spikes(filter_window_size="3h", raise_factor=0.15, dev_cont_factor=0.2,
noise_barrier=1, noise_window_size="12h", noise_statistic="CoVar")
```
......@@ -422,7 +422,7 @@ Vadoze Zone J. doi:10.2136/vzj2012.0097.
## SoilMoistureBreaks
```
SoilMoistureBreaks(diff_method="raw", filter_window_size="3h",
SoilMoisture_breaks(diff_method="raw", filter_window_size="3h",
rel_change_rate_min=0.1, abs_change_min=0.01, first_der_factor=10,
first_der_window_size="12h", scnd_der_ratio_margin_1=0.05,
scnd_der_ratio_margin_2=10, smooth_poly_order=2)
......@@ -453,7 +453,7 @@ Vadoze Zone J. doi:10.2136/vzj2012.0097.
## SoilMoistureByFrost
```
SoilMoistureByFrost(soil_temp_reference, tolerated_deviation="1h", frost_level=0)
SoilMoisture_byFrost(soil_temp_reference, tolerated_deviation="1h", frost_level=0)
```
| parameter | data type | default value | description |
......@@ -479,10 +479,10 @@ All parameters default to the values, suggested in this publication.
## SoilMoistureByPrecipitation
## SoilMoisture_byPrecipitation
```
SoilMoistureByPrecipitation(prec_reference, sensor_meas_depth=0,
SoilMoisture_byPrecipitation(prec_reference, sensor_meas_depth=0,
sensor_accuracy=0, soil_porosity=0,
std_factor=2, std_factor_range="24h"
ignore_missing=False)
......@@ -537,7 +537,7 @@ All parameters default to the values, suggested in this publication.
## Breaks_SpektrumBased
```
Breaks_SpektrumBased(rel_change_min=0.1, abs_change_min=0.01, first_der_factor=10,
Breaks_spektrumBased(rel_change_min=0.1, abs_change_min=0.01, first_der_factor=10,
first_der_window_size="12h", scnd_der_ratio_margin_1=0.05,
scnd_der_ratio_margin_2=10, smooth_poly_order=2,
diff_method="raw", filter_window_size="3h")
......@@ -552,7 +552,7 @@ Breaks_SpektrumBased(rel_change_min=0.1, abs_change_min=0.01, first_der_factor=1
| scnd_der_ratio_margin_1 | float | `0.05` | Range of the area, covering all the values of the second derivatives quotient, that are regarded "sufficiently close to 1" for signifying a break. See condition (5).|
| scnd_der_ratio_margin_2 | float | `10.0` | Lower bound for the break succeeding second derivatives quotients. See condition (5). |
| smooth_poly_order | integer | `2` | When calculating derivatives from smoothed timeseries (diff_method="savgol"), this value gives the order of the fitting polynomial calculated in the smoothing process.|
| diff_method | string | `"savgol" | Options: <br/> - `"savgol"` <br/> - `"raw"` <br/><br/> Select "raw", to skip smoothing before differenciation. |
| diff_method | string | `"savgol"` | Options: <br/> - `"savgol"` <br/> - `"raw"` <br/><br/> Select "raw", to skip smoothing before differenciation. |
| filter_window_size | Nonetype or string | `None` | Options: <br/> - `None` <br/> - any offset string <br/><br/> Controlls the range of the smoothing window applied with the Savitsky-Golay filter. If None is passed (default), the window size will be two times the sampling rate. (Thus, covering 3 values.) If you are not very well knowing what you are doing - do not change that value. Broader window sizes caused unexpected results during testing phase.|
......@@ -778,7 +778,7 @@ harmonize_shift2Grid(freq, shift_method='nearest_shift', drop_flags=None)
| --------- | --------- | ------------- | ----------- |
| freq | string | | Offset string. Detemining the frequency grid, the data shall be shifted to. |
| shift_method | string | `nearest_shift` | Method, used for shifting of data and flags. See a list of methods below. |
| drop_flags | list or Nonetype | None | Flags to be excluded from harmonization. See description of step 3 below. |
| drop_flags | list or Nonetype | `None` | Flags to be excluded from harmonization. See description of step 3 below. |
The function "harmonizes" the data-to-be-flagged, to match an equidistant
......@@ -824,8 +824,8 @@ harmonize_aggregate2Grid(freq, agg_func, agg_method='nearest_agg', flag_agg_func
| freq | string | | Offset string. Determining the sampling rate of the frequency grid, the data shall be aggregated to. |
| agg_func | func | | Function. Function used for data aggregation.|
| agg_method | string | `nearest_agg` | Method, determining the range of data and flags aggregation. See a list of methods below. |
| flag_agg_func | func | max | Function used for flags aggregation.|
| drop_flags | list or Nonetype | None | Flags to be excluded from harmonization. See description of step 2 below. |
| flag_agg_func | func | `max` | Function used for flags aggregation.|
| drop_flags | list or Nonetype | `None` | Flags to be excluded from harmonization. See description of step 2 below. |
The function aggregates the data-to-be-flagged, to match an equidistant
......@@ -880,8 +880,8 @@ harmonize_linear2Grid(freq, flag_assignment_method='nearest_agg', flag_agg_func=
| --------- | --------- | ------------- | ----------- |
| freq | string | | Offset string. Determining the sampling rate of the frequency grid, the data shall be interpolated at.|
| flag_assignment_method| string | "nearest_agg" | Method keyword, signifying method used for flags aggregation. See step 4 and table below|
| flag_agg_func | func | max | Function used for flags aggregation.|
| drop_flags | list or Nonetype | None | Flags to be excluded from harmonization. See description of step 2 below. |
| flag_agg_func | func | `max` | Function used for flags aggregation.|
| drop_flags | list or Nonetype | `None` | Flags to be excluded from harmonization. See description of step 2 below. |
Linear interpolation of an inserted equidistant frequency grid of sampling rate `freq`.
......@@ -934,10 +934,10 @@ harmonize_interpolate2Grid(freq, interpolation_method, interpolation_order=1, fl
| --------- | --------- | ------------- | ----------- |
| freq | string | | Offset string. Determining the sampling rate of the frequency grid, the data shall be interpolated at.|
| interpolation_method | string | | Method keyword, signifying method used for grid interpolation. See step 3 and table below|
| interpolation_order | func | 1 | If needed - order of the interpolation, carried out.|
| flag_assignment_method| string | "nearest_agg" | Method keyword, signifying method used for flags aggregation. See step 4 and table below|
| flag_agg_func | func | max | Function used for flags aggregation.|
| drop_flags | list or Nonetype | None | Flags to be excluded from harmonization. See description of step 2 below. |
| interpolation_order | func | `1` | If needed - order of the interpolation, carried out.|
| flag_assignment_method| string | `"nearest_agg"` | Method keyword, signifying method used for flags aggregation. See step 4 and table below|
| flag_agg_func | func | `max` | Function used for flags aggregation.|
| drop_flags | list or Nonetype | `None` | Flags to be excluded from harmonization. See description of step 2 below. |
Interpolation of an inserted equidistant frequency grid of sampling rate `freq`.
......@@ -1001,9 +1001,9 @@ harmonize_downsample(sample_freq, agg_freq, sample_func=np.mean, agg_func=np.mea
| --------- | --------- | ------------- | ----------- |
| sample_freq | string | | Offset String. Determining the intended sampling rate of the data-to-be aggregated |
| agg_freq | string | | Offset String. Determining the frequency to aggregate to. |
| sample_func | func or Nonetype | np.mean | Function to gather/aggregate data within every sampling interval. If `None` is passed, data is expected to already match a sampling grid of `sample_freq` |
| agg_func | func | np.mean | Aggregation function, used to downsample data from `sample_freq` to `agg_freq`. |
| invalid_flags | list or Nonetype | None | List of flags, to be regarded as signifying invalid values. By default (=`None`), `NaN` data and `BAD`-flagged data is considered invalid. See description below.|
| sample_func | func or Nonetype | `mean` | Function to gather/aggregate data within every sampling interval. If `None` is passed, data is expected to already match a sampling grid of `sample_freq` |
| agg_func | func | `mean` | Aggregation function, used to downsample data from `sample_freq` to `agg_freq`. |
| invalid_flags | list or Nonetype | `None` | List of flags, to be regarded as signifying invalid values. By default (=`None`), `NaN` data and `BAD`-flagged data is considered invalid. See description below.|
| max_invalid | integer | `Inf` | Maximum number of invalid data points allowed for an aggregation interval to not get assigned `NaN` |
The function downsamples the data-to-be flagged from its intended sampling rate, assumed to be `sample_freq`, to a lower
......
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