Package index
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SPAtest_analysis() - Helper: function to run a binary analysis using SPAtest
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brglm2_analysis() - Helper: function to run a binary analysis using brglm2
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chopr() - Helper for truncating probabilities
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`:=`() - Export data.table infix operator for use within package
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cooccurrence_analysis() - Perform rapid unweighted or weighted cooccurrence analysis
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create_formula() - Helper: create formula for analysis
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crossfit_lasso_weights() - estimate crossfit lasso-based weights
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data0() - Prep data for obtaining predictions
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.check_for_deps() - Helper: Check for packages needed to use libri()
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.check_library_loaded() - Helper: Check to see if packages are loaded
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.check_package_installed() - Helper: Check to see if packages are installed
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.correlation() - Helper: perform rapid unweighted and weighted correlation
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.onAttach() - Print data.table with nice features
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.partial_correlation() - Helper: perform rapid (parallel) partial correlation calculations on a matrix
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.quick_cooccur_mod() - Helper: perform rapid unweighted and weighted cooccurrence analysis
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.scale_manual() - Helper: mean standardize a vector
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.weighted_partial_correlation() - Helper: perform rapid (parallel) weighted partial correlation calculations on a matrix
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fcor() - Perform rapid (parallel) unweighted and weighted (partial) correlations on a matrix
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glm_analysis() - Helper: function to run a binary analysis using glm
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`%dopar%` - Export foreach infix operator for use within package
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icd10 - ICD10 code description
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icd10cm - ICD10CM code description
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icd9cm - ICD9CM code description
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icd_desc() - Quickly attach ICD-10 and ICD-9/ICD10-CM codes descriptions to a data.table
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ipw() - estimate inverse probability weights based on Beesley & Mukhherjee
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libri() - Check for, install, and load CRAN and GitHub R packages
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logistf_analysis() - Helper: function to run a binary analysis using logistf
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map_phewas() - function to map a binary analysis by vector of exposures using a method specified by the method argument
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merge_list() - Quickly merge across a list using dplyr-based merge functions
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pbfor() - For loop function with lapply syntax and pretty progress bar
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phe_desc() - Quickly attanch phecode descriptions to a data.table
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phecodex_icd_map - PhenomeX ICD10 (WHO) mapping
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phecodex_icdcm_map - PhenomeX ICD9/10CM mapping
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phecodex_labels - PhenomeX label information
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phecodex_rollup - PhenomeX phenome structure
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phecodex_sex - PhenomeX phecode-sex mappings
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pheinfo - PheWAS catalog information
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pheinfox - PheWAS catalog information
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phewas_analysis() - function to run a binary analysis using a method specified by the method argument
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plot_phewasx() - Plot PhecodeX PheWAS results
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psw() - estimate poststratification weights based on Beesley & Mukhherjee
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scale_color_ms() - Maxwell Salvatore's custom ggplot2 color palette
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scale_fill_ms() - Maxwell Salvatore's custom ggplot2 fill palette
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standardize_variables() - Rapidly standarize variables in a datasset
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svyglm_analysis() - Helper: function to run a binary analysis using survey::svyglm
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theme_ms() - Maxwell Salvatore's custom ggplot2 theme
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tidy_forest() - Conduct a tidy random forest analysis with hyperparameter tuning via tidymodels framework
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weighted_analysis() - Helper: function to run a weighted binary analysis using svyglm unless there's a separation concern, then run weighted logsitf