validate_gmean_byelt_LOO_xpr: Geometric mean by elements occurring within assembly motif...
In functClust: Functional Clustering of Redundant Components of a System
Description
Usage
Arguments
Details
Value
See Also
View source: R/validating_loo.R
Description
Take a vector fobs
of performances of assemblages
over several experiments
that share a same assembly motif,
and return a vector of performances
predicted as the geometric mean
of performances of assemblages
that contain the same elements as the assemblage to predict.
All assemblages share the same assembly motif.
Usage
1
validate_gmean_byelt_LOO_xpr(fobs, assMotif, mOccur, xpr)
Arguments
fobs
a numeric vector. The vector fobs contains the
quantitative performances of assemblages.
assMotif
a vector of labels of length(fobs).
The vector assMotif contains the assembly motifs of assemblages.
mOccur
a matrix of occurrence (occurrence of elements).
Its first dimension equals to length(fobs). Its second dimension
equals to the number of elements.
xpr
a vector of numerics of length(fobs).
The vector xpr contains the weight of each experiment,
and the labels (in names(xpr)) of different experiments.
The weigth of each experiment is used
in the computation of the Residual Sum of Squares
in the function rss_clustering.
The used formula is rss
if each experiment has the same weight.
The used formula is wrss
(barycenter of RSS for each experiment)
if each experiment has different weights.
All assemblages that belong to a given experiment
should then have a same weigth.
Each experiment is identified by its names (names(xpr))
and the RSS of each experiment is weighted by values of xpr.
The vector is generated
by the function stats::setNames.
Details
Predicted performances are computed
using geometric mean (opt.mean = "gmean")
of performances.
Assemblages share a same assembly motif (opt.model = "bymot").
Predicted performances are the average,
experiment by experiment,
of mean performances of assemblages
that contain the same elements
as the assemblage to predict,
except the assemblage to predict.
This procedure corresponds to a linear model with each assembly motif
based on the element occurrence in each assemblage.
Value
Return a vector of length(fobs).
Its values are computed as the average
of mean performances of all assemblages,
experiment by experiment,
that contain the same elements
as the assemblage to predict (opt.model = "byelt") .
See Also
validate_amean_bymot_LOO_xpr arithmetic mean
byassembly motif
validate_amean_byelt_LOO_xpr arithmetic mean
by elements occurring within assembly motif
validate_gmean_bymot_LOO_xpr geometric mean
by assembly motif
functClust documentation built on Dec. 2, 2020, 5:06 p.m.
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Description Usage Arguments Details Value See Also
View source: R/validating_loo.R
Description
Take a vector fobs
of performances of assemblages
over several experiments
that share a same assembly motif,
and return a vector of performances
predicted as the geometric mean
of performances of assemblages
that contain the same elements as the assemblage to predict.
All assemblages share the same assembly motif.
Usage
1 | validate_gmean_byelt_LOO_xpr(fobs, assMotif, mOccur, xpr)
|
Arguments
fobs |
a numeric vector. The vector |
assMotif |
a vector of labels of |
mOccur |
a matrix of occurrence (occurrence of elements).
Its first dimension equals to |
xpr |
a vector of numerics of |
Details
Predicted performances are computed
using geometric mean (opt.mean = "gmean")
of performances.
Assemblages share a same assembly motif (opt.model = "bymot").
Predicted performances are the average,
experiment by experiment,
of mean performances of assemblages
that contain the same elements
as the assemblage to predict,
except the assemblage to predict.
This procedure corresponds to a linear model with each assembly motif
based on the element occurrence in each assemblage.
Value
Return a vector of length(fobs).
Its values are computed as the average
of mean performances of all assemblages,
experiment by experiment,
that contain the same elements
as the assemblage to predict (opt.model = "byelt") .
See Also
validate_amean_bymot_LOO_xpr arithmetic mean
byassembly motif
validate_amean_byelt_LOO_xpr arithmetic mean
by elements occurring within assembly motif
validate_gmean_bymot_LOO_xpr geometric mean
by assembly motif
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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