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Update text descriptions and reference
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jbeilstenedmands committed Nov 18, 2024
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2 changes: 1 addition & 1 deletion src/dials/algorithms/symmetry/cosym/__init__.py
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Expand Up @@ -93,7 +93,7 @@
.help = "If not None, a weights matrix is used in the cosym procedure."
"weights=count uses the number of reflections used to calculate a pairwise correlation coefficient as its weight"
"weights=standard_error uses the reciprocal of the standard error as the weight. The standard error is given by"
"(1-CC*2)/sqrt(n-2), where (n-2) are the degrees of freedom in a pairwise CC calculation."
"(1-CC*2)/sqrt(N), where N=(n-2) or N=(neff-1) depending on the cc_weights option."
cc_weights = None sigma
.type = choice
.help = "If not None, a weighted cc-half formula is used for calculating pairwise correlation coefficients and degrees of"
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5 changes: 3 additions & 2 deletions src/dials/algorithms/symmetry/cosym/target.py
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Expand Up @@ -179,8 +179,9 @@ def __init__(
is to use no weights. If "count" is set, then weights are equal to the
number of pairs of reflections used in calculating each value of the
rij matrix. If "standard_error" is used, then weights are defined as
:math:`w_{ij} = 1/s`, where :math:`s = \sqrt{(1-r_{ij}^2)/(n-2)}`.
See also http://www.sjsu.edu/faculty/gerstman/StatPrimer/correlation.pdf.
:math:`w_{ij} = 1/s`, where :math:`s = (1-r_{ij}^2)/sqrt(N)`.
Where N=(n-2) or N=(neff-1) depending on the cc_weights option.
See also https://doi.org/10.1525/collabra.87615.
min_pairs (int): Only calculate the correlation coefficient between two
datasets if they have more than `min_pairs` of common reflections.
lattice_group (cctbx.sgtbx.space_group): Optionally set the lattice
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