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Refs #12651 add latex formulas
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VickieLynch committed May 13, 2016
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41 changes: 32 additions & 9 deletions docs/source/algorithms/StatisticsOfPeaksWorkspace-v1.rst
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Expand Up @@ -10,17 +10,40 @@ Description
-----------

Statistics of the Peaks Workspaces are calculated for all peaks and by
default for resolution shell. There is a SortBy option to change this
default for resolution shell(d-Spacing). There is a SortBy option to change this
to by orientation (RunNumber) or by Anger camera (bank) or only do all peaks.
This algorithm call SortHKL, so more details are in the documentation for that algorithm.

Statistics include:
No of Unique Reflections
Resolution range
Multiplicity
Mean ((I)/sd(I))
Rmerge
Rplm
Data Completeness
After removing invalid peaks with :math:`I \leq 0`, :math:`\sigma \leq 0` and :math:`h=k=l=0`,
the peaks are assigned to their respective unique reflection so that each theoretically present
reflection may have :math:`n` observations (:math:`n` can be zero). The number of unique reflections
which have at least one observation can be labeled :math:`N_{unique}`.

The intensities of peaks in each reflection are checked for outliers, which are removed. Outliers
in this context are peaks with an intensity that deviates more than :math:`3\sigma_{hkl}` from the
mean of the reflection, where :math:`\sigma_{hkl}` is the standard deviation of the peak intensities.

Formulas for the statistics columns are:

:math:`N_{unique}`

:math:`dSpacing_{min}`

:math:`dSpacing_{max}`

:math:`Multiplicity = \frac{N_{observed}}{N_{unique}}`

:math:`\langle \frac{I}{\sigma_I} \rangle`

In the following, all sums over hkl extend only over unique reflections with more than one observation! Output is percentages.

:math:`R_{merge} = 100 * \frac{\sum_{hkl} \sum_{j} \vert I_{hkl,j}-\langle I_{hkl}\rangle\vert}{\sum_{hkl} \sum_{j}I_{hkl,j}}`
where :math:`\langle I_{hkl}\rangle` is the average of j multiple measurements of the n equivalent reflections.


:math:`R_{pim} = 100 * \frac{\sum_{hkl} \sqrt \frac{1}{n-1} \sum_{j=1}^{n} \vert I_{hkl,j}-\langle I_{hkl}\rangle\vert}{\sum_{hkl} \sum_{j}I_{hkl,j}}`

:math:`Completeness = 100 * \frac{N_{unique}}{N_{theoretical}}`


Usage
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