cocoreg: Extracts Shared Variation in Collections of Datasets Using Regression Models
Version 0.1.0

The cocoreg algorithm extracts shared variation from a collection of datasets using regression models.

AuthorJussi Korpela [aut, cre], Andreas Henelius [aut], Finnish Institute of Occupational Health [cph]
Date of publication2016-05-03 18:35:21
MaintainerJussi Korpela <jussi.korpela@iki.fi>
LicenseMIT + file LICENSE
Version0.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cocoreg")

Getting started

README.md
COCOREG basics

Popular man pages

df_scale: Apply scale on a numeric data.frame
generate_mapping_function: Generate a mapping function between two datasets
generate_paths_noncyclic: Generate non-cyclic paths
ggplot_dflst: Plot a list of data.frames using ggplot2
matrix_variability: Compute "variance" of the matrices using Frobenius norm....
rename_variables: Rename variables of a data collection
se: Standard error of mean
See all...

All man pages Function index File listing

Man pages

add_notches: Add notch-like gaussian snippets to an existing signal x
apply_dc_meta: Apply extracted properties of a data collection to a data...
average_R2_dflst: Computes the R^2 (variance explained) between two lists of...
BGFA_cocoreg_interface: Apply GFA using the same interface as cocoreg()
BGFA_joint_info: Project BGFA components common to all datasets back to the...
cocoreg: The Common Components by Regression (CoCoReg) algorith.
cocoreg_by_path: Compute D_joint for dataset i separately for all paths Can be...
compose: Calculate the composition formed by applying all functions in...
compose_all: Calculate the average of the composition formed by applying...
create_mappings: Generate all possible pairwise mappings between the given...
create_syndata_mv: Create multivariate synthetic data
create_syn_data_puvar: A data collection with variables that "become unrelated...
create_syndata_pwl: A non-linear data collection using piecewise linearity
create_syn_data_toy: An illustrative synthetic datacollection
create_syn_data_uds: A data collection with one unrelated dataset
create_syn_data_uvar: A dollection with unrelated variables
create_Z_linear: Contains functions to create synthetic datasets with...
cshift: Circularly shift vector elements
data_collections2ggdf: Catenate a set of data collections (lists of data.frames)...
data_matrix_rmse: Compute RMSE between data.matrices dm1 and dm2
dc_variability: Compute ds_variability for all datasets in a data collection
df_ggplot_melt: Melt data.frame into ggplottable format
dflst2array: Catenate a list of data.frames to a matrix along dim
dflst2df: Catenate a list of data.frames vertically to a single...
dflst2dfmelt: Combine a list of data.frames to a single molten data.frame
dflst_add_ds: Add a data.frame (dataset) to a list of data.frames...
dflst_dsnames2varnames: Append dataset names to variable names of the respective...
dflst_pca: Apply PCA to the data after catenating data.frames...
df_scale: Apply scale on a numeric data.frame
df_scale_ols: Scales variables in data.frame dfx using ordinary least...
dl_remove_NA: Remove rows with NA values from a list of data.frames
dl_scale: Run scale() on a list of data.frames
ds_variability: Compute variability_components for a dataset
generate_mapping_function: Generate a mapping function between two datasets
generate_paths: Generate all/some paths between points
generate_paths_cyclic: Generate cyclic paths
generate_paths_noncyclic: Generate non-cyclic paths
get_dc_meta: Extract important properties of data collection
get_range_datalist: Get [min, max] of a list of numeric objects
get_starting_dataset: Helper function to get the starting dataset based on a path.
ggcompare_dclst: Compare data collections variable by variable
ggplot_dclst: Plotting data collections using ggplot
ggplot_df: Plotting data.frame using ggplot
ggplot_dflst: Plot a list of data.frames using ggplot2
make_data_gauss_2d: Make 2D gauss data (maybe obsolete)
mapping_glmnet: Define a mapping function using glmnet::glmnet
mapping_lm: Mapping stats::lm
mapping_lmridge: Define a mapping function using MASS::lm.ridge
mapping_pcr: Define a mapping function using pls::pcr
mapping_rf: Mapping randomForest
mapping_rlm: Mapping MASS::rlm
mappings_R2_matrix: Extract R2 values from a list of mappings using summary()
mapping_svm: Mapping svm
mapping_svm_sigmoid: Mapping svm using sigmoid
matrix_variability: Compute "variance" of the matrices using Frobenius norm....
nplst_reorder_grid: Reorders a nested list of ggplots
pathify: Create a path
PCA_cocoreg_interface: PCA projection using cocoreg interface
rename_variables: Rename variables of a data collection
repmat: Replicate matrix to create a larger one
RGCCA_cocoreg_interface: COCOREG style analysis using RGCCA projection
rmse: Compute RMSE between vectors v1 and v2
rotation_matrix: A rotation matrix
row_suffle_variability: Determine the variability of matrices under row suffling
SCA_cocoreg_interface: SCA projection using cocoreg interface
se: Standard error of mean
ss: Sum of squares
svm_sigmoid: SVM using sigmoid kernel
to_unit_vec: Make vector of unit norm
traverse_nested_list: Apply fun to the bottom level of a nested list structure
validate_data: Validate a data collection for use with cocoreg
var_explained: Sum-of-squares values showing what portion of variance in...
variability_components: Compute total, within group and between group variability...
variation_shared_by: Return a specific variation component
vecnorm: Compute Euclidean norm of vector
vector_variability: Compute "variance" of the vectors var()
wrapper_BGFA: Run BGFA by Klami et al using data format conventions of this...

Functions

Files

inst
inst/doc
inst/doc/cocoreg-basics.html
inst/doc/cocoreg-basics.R
inst/doc/cocoreg-basics.Rmd
NAMESPACE
R
R/common_tools.R
R/cocoreg.R
R/common_plots.R
R/synthetic_datasets.R
vignettes
vignettes/cocoreg-basics.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/mapping_rf.Rd
man/apply_dc_meta.Rd
man/BGFA_cocoreg_interface.Rd
man/generate_paths_cyclic.Rd
man/compose.Rd
man/mapping_rlm.Rd
man/cocoreg.Rd
man/ggplot_dclst.Rd
man/make_data_gauss_2d.Rd
man/rmse.Rd
man/compose_all.Rd
man/variability_components.Rd
man/repmat.Rd
man/create_syn_data_toy.Rd
man/traverse_nested_list.Rd
man/mapping_pcr.Rd
man/dl_scale.Rd
man/mapping_lmridge.Rd
man/ss.Rd
man/vecnorm.Rd
man/get_dc_meta.Rd
man/dflst2array.Rd
man/to_unit_vec.Rd
man/create_syn_data_uds.Rd
man/dflst2df.Rd
man/dc_variability.Rd
man/dflst_add_ds.Rd
man/df_scale.Rd
man/add_notches.Rd
man/create_syndata_pwl.Rd
man/ggplot_dflst.Rd
man/SCA_cocoreg_interface.Rd
man/create_syn_data_uvar.Rd
man/ds_variability.Rd
man/generate_mapping_function.Rd
man/df_scale_ols.Rd
man/get_range_datalist.Rd
man/variation_shared_by.Rd
man/get_starting_dataset.Rd
man/mappings_R2_matrix.Rd
man/pathify.Rd
man/average_R2_dflst.Rd
man/vector_variability.Rd
man/validate_data.Rd
man/RGCCA_cocoreg_interface.Rd
man/mapping_glmnet.Rd
man/se.Rd
man/row_suffle_variability.Rd
man/dflst2dfmelt.Rd
man/cshift.Rd
man/generate_paths.Rd
man/PCA_cocoreg_interface.Rd
man/mapping_svm.Rd
man/wrapper_BGFA.Rd
man/rotation_matrix.Rd
man/dl_remove_NA.Rd
man/df_ggplot_melt.Rd
man/generate_paths_noncyclic.Rd
man/ggplot_df.Rd
man/nplst_reorder_grid.Rd
man/mapping_svm_sigmoid.Rd
man/rename_variables.Rd
man/data_collections2ggdf.Rd
man/dflst_dsnames2varnames.Rd
man/dflst_pca.Rd
man/matrix_variability.Rd
man/create_syn_data_puvar.Rd
man/create_mappings.Rd
man/ggcompare_dclst.Rd
man/create_Z_linear.Rd
man/svm_sigmoid.Rd
man/create_syndata_mv.Rd
man/BGFA_joint_info.Rd
man/cocoreg_by_path.Rd
man/var_explained.Rd
man/data_matrix_rmse.Rd
man/mapping_lm.Rd
LICENSE
cocoreg documentation built on May 19, 2017, 1:47 p.m.

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