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.

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...

Files in this package

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

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