Package index • fxtas

All functions

add_default_labels(): Add default variable labels
add_labels(): Add labels to biomarkers
age_range_medians(): replace decade codes with medians of those decades
all_potential_biomarkers(): Get a list of all potential biomarkers available in dataset
autoplot(<PF>): Create positional variance diagram (PVD)
autoplot(<permutation_test>): Plot the distribution of a permuted test statistic
build_abbrevs_caption(): Build abbreviations caption
build_abstract_plot(): Build ggplot with abstract text for cowplot
build_rds_path(): Find path to RDS file with output
build_score_vals(): Construct the table indicating how many levels each biomarker has
clean_gender(): Clean the variable Gender
clean_mol_act_ratio(): Clean mol_act_ratio variable from gp4
clean_numeric(): Clean a Numeric Variable
collapse_mri_levels(): Collapse MRI levels
collapse_scid_levels(): Collapse SCID domain levels
collect_permutation_test_stats(): Collect permutation test statistics
combine_tremor(): Combine exam and history tremor vars
compact_pvd_est_data_prep(): plot_compact_pvd_est: data prep
compact_pvd_facet_labels(): Create facet labels
compile_biomarker_group_list(): Compile a list of biomarker groups
compile_biomarker_groups_table(): Compile biomarker groups table
compute_confus_matrix(): compute confus_matrix as in python version
compute_prob_correct(): Compute each biomarker's probability of being recorded at its baseline level
compute_prob_correct2(): Title
compute_prob_dist(): Computes p(true | obs)? for each biomarker
compute_prob_dist2(): Title
compute_prob_scores(): Compute probabilities of true biomarker levels
compute_score_levels(): Title
counts_and_pcts(): Compute and paste counts and proportions
create_scid_domains(): Create SCID domain variables
cvic_sim_data: CVIC results from simulated data
define_cases_and_controls(): Categorize `CGG“
.onLoad(): Actions taken when fxtas is loaded
event_order_heatmap(): Event order heatmap
example_likelihoods: example likelihoods matrix
extract_cvic(): Extract CVIC element from an object
extract_figs_from_pickle(): Extact PVDs from pickle file
extract_permuted_likelihoods(): Extract permuted log-likelihoods from pickle files
extract_results_from_pickle(): Extract results from pickle file
extract_results_from_pickles(): Extract results from multiple pickle files
flex_biomarkers_table(): Print method for biomarkers_table
format_likelihoods(): Title
format_results_list(): Format results list extracted from pickle file
get_biomarker_event_names(): Extract biomarker event names
get_biomarker_events_table(): Construct biomarker events table
get_levels(): Extract levels from a set of variable names
get_observed_permutation_test_stat(): Compute permutation test statistic
get_visit1(): Get each participant's first visit in dataset
graph_CGG_repeats(): Barplot of CGG repeats
graph_likelihoods_v2(): Title
graph_stage_by_age(): graph stage by age
graphical_abstract(): Graphical Abstract
group_colors(): Extract group colors
install_pySuStaIn(): Install the pySuStaIn python package from github
labels(<list>): Extract variable labels from list
make_biomarker_events_table(): Construct biomarker events table
make_biomarkers_table(): Make biomarkers table
make_demographics_table(): Make demographics table
missing_pattern_by_ID(): Title
missingness_reasons.factor(): Compute missingness reasons for a vector of factor variables
missingness_reasons.numeric(): Title
model_dists(): Title
pander(<prob_correct>): Print prob_correct objects as Pandoc markdown tables
permutation_test(): Compute permutation test p-value
plot_CVIC(): Plot a CVIC curve
plot_compact_pvd(): Plot compact PVD tmp function using list of extract_figs_from_pickle
plot_compact_pvd_est(): Plot compact PVD with point estimates only
plot_compact_pvd_est2(): Plot SuStaIn Sequential Estimate
plot_cv_loglik(): Plot cross-validated per-fold log-likelihood distributions
plot_heatmap(): Title
plot_permutation_results(): Plot permutation test results
plot_positional_var(): Plot positional variance diagram
print(<permutation_test>): print method for "permutation_test" objects
print_PVDs(): Print a list of PVDs
pvd_lineplot(): Plot change in Stage ranking
pvd_subtype_lineplot(): Display Sequential Order of Events by Subtype
remove_missingness_reason_vars(): Remove variable
replace_missing_codes(): Replace missing codes in a vector of factor variables
replace_missing_codes_with_NAs(): Replace missing codes with NAs
report_sex_differences(): Report sex differences
run_OSA(): Run the Ordinal SuStaIn Algorithm (OSA)
run_OSA_permuted(): Randomly permute some some variables and run the OSA model on the permuted data
run_and_save_OSA(): Run the Ordinal SuStaIn algorithm (OSA) or load results from presaved .rds file if available
run_app(): Run the Shiny Application
save_run_info(): Save run info to file
scid_vars_for_table1(): List SCID variables to display in data summary tables
search_articles(): Search PubMed for FXTAS-related articles
shared_flextable_settings(): Apply flextable settings to match Brain journal requirements
sim_data: Simulated data
sim_subtype_and_stage_table: Simulated subtype-and-stage table
stage_barplot(): Plot estimated stage counts
stage_barplot(<SuStaIn_model>): Plot estimated stage counts
stage_barplot(<default>): Plot estimated stage counts
stage_barplot(<list>): Plot estimated stage counts
stratified_formula(): Build a formula for table1::table1()
summary(<permutation_test>): Summary method for permutation_test objects
table1a(): table1::table1() with customized settings
table_subtype_by_demographics(): Create table of demographics statistics by most-likely latent subtype
test_data: Test Data
test_data_v1: Test Data - Visit 1
test_subtype_and_stage_table: Simulated subtype-and-stage table
var_label(<list>): Extract variable labels from a list object
write_permuted_test_stats(): Write permuted test stats as RDS