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

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

Install the latest version of this package by entering the following in R:
install.packages("cocoreg")
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

View on CRAN

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

add_notches Man page
apply_dc_meta Man page
average_R2_dflst Man page
BGFA_cocoreg_interface Man page
BGFA_joint_info Man page
cocoreg Man page
cocoreg_by_path Man page
compose Man page
compose_all Man page
create_mappings Man page
create_syndata_mv Man page
create_syn_data_puvar Man page
create_syndata_pwl Man page
create_syn_data_toy Man page
create_syn_data_uds Man page
create_syn_data_uvar Man page
create_Z_linear Man page
cshift Man page
data_collections2ggdf Man page
data_matrix_rmse Man page
dc_variability Man page
df_ggplot_melt Man page
dflst2array Man page
dflst2df Man page
dflst2dfmelt Man page
dflst_add_ds Man page
dflst_dsnames2varnames Man page
dflst_pca Man page
df_scale Man page
df_scale_ols Man page
dl_remove_NA Man page
dl_scale Man page
ds_variability Man page
generate_mapping_function Man page
generate_paths Man page
generate_paths_cyclic Man page
generate_paths_noncyclic Man page
get_dc_meta Man page
get_range_datalist Man page
get_starting_dataset Man page
ggcompare_dclst Man page
ggplot_dclst Man page
ggplot_df Man page
ggplot_dflst Man page
make_data_gauss_2d Man page
mapping_glmnet Man page
mapping_lm Man page
mapping_lmridge Man page
mapping_pcr Man page
mapping_rf Man page
mapping_rlm Man page
mappings_R2_matrix Man page
mapping_svm Man page
mapping_svm_sigmoid Man page
matrix_variability Man page
nplst_reorder_grid Man page
pathify Man page
PCA_cocoreg_interface Man page
rename_variables Man page
repmat Man page
RGCCA_cocoreg_interface Man page
rmse Man page
rotation_matrix Man page
row_suffle_variability Man page
SCA_cocoreg_interface Man page
se Man page
ss Man page
svm_sigmoid Man page
to_unit_vec Man page
traverse_nested_list Man page
validate_data Man page
var_explained Man page
variability_components Man page
variation_shared_by Man page
vecnorm Man page
vector_variability Man page
wrapper_BGFA Man page

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

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