Man pages for plmmr
Penalized Linear Mixed Models for Correlated Data
| add_predictors | A helper function to add predictors to a filebacked matrix of... |
| admix | Admix: Semi-simulated SNP data |
| align_ids | A helper function to support 'process_plink()' |
| big_cbind | a version of cbind() for file-backed matrices |
| check_for_file_extension | check_for_file_extension: a function to make our package... |
| coef.cv_plmm | Coef method for "cv_plmm" class |
| coef.plmm | Coef method for "plmm" class |
| construct_variance | a function to create the estimated variance matrix from a... |
| count_constant_features | A helper function to count constant features |
| count_cores | A helper function to count the number of cores available on... |
| create_design | a function to create a design for PLMM modeling |
| create_design_filebacked | A function to create a design matrix, outcome, and penalty... |
| create_design_in_memory | A function to create a design with an in-memory X matrix |
| create_log | create_log_file |
| cvf | Cross-validation internal function for cv_plmm |
| cv_plmm | Cross-validation for plmm |
| eigen_K | A function to take the eigendecomposition of K Note: This is... |
| estimate_eta | Estimate eta (to be used in rotating the data) This function... |
| fbm2bm | Functions to convert between FBM and big.matrix type objects |
| find_example_data | A function to help with accessing example PLINK files |
| get_data | Read in processed data This function is intended to be called... |
| get_hostname | a function to return the computer's host name |
| impute_snp_data | A function to impute SNP data |
| index_samples | A function to align genotype and phenotype data |
| lam_names | Generate nicely formatted lambda vec |
| lasso | helper function to implement lasso penalty |
| log_lik | Evaluate the negative log-likelihood of an intercept-only... |
| MCP | helper function to implement MCP penalty The helper functions... |
| name_and_count_bigsnp | A helper function to label and summarize the contents of a... |
| plmm | Fit a linear mixed model via penalized maximum likelihood. |
| plmm_checks | plmm_checks |
| plmm_fit | PLMM fit: a function that fits a PLMM using the values... |
| plmm_format | PLMM format: a function to format the output of a model... |
| plmm_loss | Loss method for "plmm" class |
| plmm_prep | PLMM prep: a function to run checks, SVD, and rotation prior... |
| plmmr-package | plmmr: Penalized Linear Mixed Models for Correlated Data |
| plot.cv_plmm | Plot method for cv_plmm class |
| plot.plmm | Plot method for plmm class |
| predict.plmm | Predict method for plmm class |
| predict_within_cv | Predict method to use in cross-validation (within 'cvf') |
| pretty_time | a function to format the time |
| print.summary.cv_plmm | Print method for summary.cv_plmm objects |
| print.summary.plmm | A function to print the summary of a 'plmm' model |
| process_delim | A function to read in large data files as an FBM |
| process_plink | Preprocess PLINK files using the 'bigsnpr' package |
| read_data_files | A function to read in a large file as a numeric file-backed... |
| read_plink_files | A function to read in PLINK files using 'bigsnpr' methods |
| relatedness_mat | Calculate a relatedness matrix |
| rotate_filebacked | A function to rotate filebacked data |
| SCAD | helper function to implement SCAD penalty |
| setup_lambda | Compute sequence of lambda values |
| standardize_filebacked | A helper function to standardize a filebacked matrix |
| standardize_in_memory | A helper function to standardize matrices |
| subset_filebacked | A helper function to subset 'big.matrix' objects |
| summary.cv_plmm | A summary function for cv_plmm objects |
| summary.plmm | A summary method for the plmm objects |
| untransform | Untransform coefficient values back to the original scale |
| untransform_delim | Untransform coefficient values back to the original scale for... |
| untransform_in_memory | Untransform coefficient values back to the original scale _In... |
| untransform_plink | Untransform coefficient values back to the original scale for... |
| unzip_example_data | For Linux/Unix and MacOS only, here is a companion function... |
