From 8efbb27fe80e5c126167397fd8aeda1fcb08eb71 Mon Sep 17 00:00:00 2001
From: David Schaefer <david.schaefer@ufz.de>
Date: Wed, 27 Nov 2019 22:16:31 +0100
Subject: [PATCH] Update FunctionDescriptions.md
---
docs/FunctionDescriptions.md | 154 +++++++++++++++++++++++++++--------
1 file changed, 119 insertions(+), 35 deletions(-)
diff --git a/docs/FunctionDescriptions.md b/docs/FunctionDescriptions.md
index a07000185..08a9543a0 100644
--- a/docs/FunctionDescriptions.md
+++ b/docs/FunctionDescriptions.md
@@ -66,35 +66,70 @@ clear()
### Description
Remove all previously set flags.
-## force
+## `force`
+
### Signature
```
force()
```
+
+### Parameters
+| parameter | data type | default value | description |
+| --------- | ----------- | ---- | ----------- |
+
### Description
-## sliding_outlier
+## `sliding_outlier`
+
### Signature
```
sliding_outlier(winsz="1h", dx="1h", count=1, deg=1, z=3.5, method="modZ")
```
+
+### Parameters
+| parameter | data type | default value | description |
+| --------- | ----------- | ---- | ----------- |
+| winsz | string | `"1h"` | |
+| dx | string | `"1h"` | |
+| count | integer | `1` | |
+| deg | integer | `1"` | |
+| z | float | `3.5` | |
+| method | string | `"modZ"` | |
+
### Description
-## mad
+## `mad`
+
### Signature
```
mad(length, z=3.5, freq=None)
```
+
+### Parameters
+| parameter | data type | default value | description |
+| --------- | ----------- | ---- | ----------- |
+| length | | | |
+| z | float | `3.5` | |
+| freq | | `None` | |
+
+
### Description
-## Spikes_Basic
+## `Spikes_Basic`
### Signature
```
Spikes_Basic(thresh, tolerance, window_size)
```
+### Parameters
+| 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). |
+
### Description
A basic outlier test, that is designed to work for harmonized, as well as raw
(not-harmonized) data.
@@ -120,19 +155,27 @@ outliers, but also plateau-ish value courses.
The implementation is a time-window based version of an outlier test from the
UFZ Python library, that can be found [here](https://git.ufz.de/chs/python/blob/master/ufz/level1/spike.py).
-| parameter | data format | 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 | Offset String. | An offset string, denoting the maximal length of "spikish" value courses. See condition (3). |
-## Spikes_SpektrumBased
+## `Spikes_SpektrumBased`
### Signature
```
Spikes_SpektrumBased(raise_factor=0.15, dev_cont_factor=0.2,
noise_barrier=1, noise_window_size="12h", noise_statistic="CoVar",
smooth_poly_order=2, filter_window_size=None)
```
+
+### Parameters
+| 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). |
+| 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"` | 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|
+| filter_window_size | string | `None` | Range of the smoothing window. The default value (='None') results in a window range, equalling 3 times the sampling rate and thus including always 3 values in a smoothing window. |
+
+
### Description
The function detects and flags spikes in input data series by evaluating the
@@ -166,32 +209,41 @@ Dorigo,W,.... Global Automated Quality Control of In Situ Soil Moisture
Data from the international Soil Moisture Network. 2013. Vadoze Zone J.
doi:10.2136/vzj2012.0097.
-All parameters default to the values given there.
-| parameter | data format | description |
-| ------ | ------ | ------ |
-| raise_factor | Float. (0.15). | Minimum change margin for a datapoint 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| Offset String. ("12h"). | 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. | Order of the polynomial fit, applied for smoothing|
-| filter_window_size | Offset String. (None) | Range of the smoothing window. The default value (='None') results in a window range, equalling 3 times the sampling rate and thus including always 3 values in a smoothing window. |
-
-## constant
+## `constant`
### Signature
```
constant(eps, length, thmin=None)
```
+
+### Parameters
+| parameter | data type | default value | description |
+| ------ | ------ | ------ | ---- |
+| eps | | | |
+| length | | | |
+| thmin | | `None` | |
+
### Description
-## constants_varianceBased
+## `constants_varianceBased`
+
### Signature
```
constants_varianceBased(plateau_window_min="12h", plateau_var_limit=0.0005,
var_total_nans=Inf, var_consec_nans=Inf)
```
+
+### Parameters
+
+| parameter | data type | default value | description |
+| ------ | ------ | ------ | ---- |
+| plateau_window_min | string | | Minimum barrier for the duration, values have to be continouos to be plateau canditaes. See condition (1). |
+| plateau_var_limit | float | `0.0005` | Barrier, the variance of a group of values must not exceed to be flagged a plateau .See condition (2). |
+| var_total_nans | integer | `Inf` | Maximum number of nan values allowed, for a calculated variance to be valid. |
+| var_consec_nans | integer | `Inf` | Maximum number of consecutive nan values allowed, for a calculated variance to be valid. |
+
+
### Description
Function flags plateaus/series of constant values. Any set of consecutive values
$`x_k,..., x_{k+n}`$ of a timeseries $`x`$ is flagged, if:
@@ -200,23 +252,29 @@ $`x_k,..., x_{k+n}`$ of a timeseries $`x`$ is flagged, if:
2. $`\sigma(x_k,..., x_{k+n})`$ < `plateau_var_limit`
NOTE, that the dataseries-to-be flagged is supposed to be harmonized to an
-equadistant frequencie grid.
-
-| parameter | data format (default) | description |
-| ------ | ------ | ------ |
-| plateau_window_min | Offset String. | Minimum barrier for the duration, values have to be continouos to be plateau canditaes. See condition (1). |
-| plateau_var_limit | Float. (0.0005). | Barrier, the variance of a group of values must not exceed to be flagged a plateau .See condition (2). |
-| var_total_nans | Integer (np.inf) | Maximum number of nan values allowed, for a calculated variance to be valid. |
-| var_consec_nans | Integer (np.inf) | Maximum number of consecutive nan values allowed, for a calculated variance to be valid. |
+equadistant frequency grid.
+## `SoilMoistureSpikes`
-## SoilMoistureSpikes
### Signature
```
SoilMoistureSpikes(filter_window_size="3h", raise_factor=0.15, dev_cont_factor=0.2,
noise_barrier=1, noise_window_size="12h", noise_statistic="CoVar")
```
+
+### Parameters
+
+| parameter | data type | default value | description |
+| ------ | ------ | ------ | ---- |
+| filter_window_size | string | `"3h"` | |
+| raise_factor | float | `0.15` | |
+| dev_cont_factor | float | `0.2` | |
+| noise_barrier | integer | `1` | |
+| noise_window_size | string | `"12h"` | |
+| noise_statistic | string | `"CoVar"` | |
+
+
### Description
The Function is just a wrapper around `flagSpikes_spektrumBased`, from the
@@ -228,7 +286,8 @@ Data from the international Soil Moisture Network. 2013.
Vadoze Zone J. doi:10.2136/vzj2012.0097.
-## SoilMoistureBreaks
+## `SoilMoistureBreaks`
+
### Signature
```
SoilMoistureBreaks(diff_method="raw", filter_window_size="3h",
@@ -236,6 +295,22 @@ SoilMoistureBreaks(diff_method="raw", filter_window_size="3h",
first_der_window_size="12h", scnd_der_ratio_margin_1=0.05,
scnd_der_ratio_margin_2=10, smooth_poly_order=2)
```
+
+### Parameters
+
+| parameter | data type | default value | description |
+| ------ | ------ | ------ | ---- |
+| diff_method | string | `"raw"` | |
+| filter_window_size | string | `"3h"` | |
+| rel_change_rate_min | float | `0.1` | |
+| abs_change_min | float | `0.01` | |
+| first_der_factor | integer | `10` | |
+| first_der_window_size | string | `"12h"` | |
+| scnd_der_ratio_margin_1 | float | `0.05` | |
+| scnd_der_ratio_margin_2 | float | `10.0` | |
+| smooth_poly_order | integer | `2` | |
+
+
### Description
The Function is just a wrapper around `flagBreaks_spektrumBased`, from the
@@ -247,16 +322,25 @@ Data from the international Soil Moisture Network. 2013.
Vadoze Zone J. doi:10.2136/vzj2012.0097.
-## SoilMoistureByFrost
+## `SoilMoistureByFrost`
### Signature
```
SoilMoistureByFrost(soil_temp_reference, tolerated_deviation="1h", frost_level=0)
```
+
+### Parameters
+
+| parameter | data type | default value | description |
+| ------ | ------ | ------ | ---- |
+| soil_temp_reference | | | |
+| tolerated_deviation | string | `"1h"` | |
+| frost_level | integer | `0` | |
+
### Description
-## SoilMoistureByPrecipitation
+## `SoilMoistureByPrecipitation`
### Signature
```
SoilMoistureByPrecipitation(prec_reference, sensor_meas_depth=0,
--
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