Releases: BRANCHlab/abcdutils
Releases · BRANCHlab/abcdutils
0.2.0
Final release supporting ABCD Releases 4.0 and earlier.
New functions
Extraction
cbcl_raw_to_thresh
converts raw cbcl depress, anxiety, attention, and aggressive scores to ordinal scale (normal, borderline clinical, and clinical) using the threshold cutoffs of 93rd - 97th percentile being borderline clinical and 97th percentile + being clinicalget_all_wmnd
extracts all non-summary white matter ROIs according to both the AtlasTrack major regions as well as the Desikan Cortical Parcellation peri-cortical/sub-adjacent regionsget_mtbi_age_l
determines age at latest mTBI for subjects at the 1yfu and 2yfu timepointget_mtbi_loc_l
,get_mtbi_mem_daze_l
, andget_mtbi_mechanism_l
functions added for 1yfu and 2yfu timepointsget_uninjured_subjects
returns those subjects who were never injured
QC
- qc functions added for neuroimaging:
qc_rsfmri
,qc_dmri
,qc_smri
Plotting
clean_plot
allows elements of a generated plot to easily be removed (currently only xlabel, ylabel, and legend)
General utility
generate_mock_data
safely scrambles a provided dataframe, generating practice/demo data for sharingpath_maker
,make_reader
, andmake_writer
functions to help organize file importing and exportingcommon_subjects
function returns subjects present in all dataframes stored in a provided list of dataframescol_to_num_all_possible
converts all pure number features into numeric typetrain_test_assign
consistently assigns subjects with a UID to train or test set using the one-at-a-time hash function- convenience filtering function for train/test data:
keep_split
merge_df_list
inner joins all dataframes in a listflex_cond
variation of the if function that returns FALSE when the conditional statement would originally have returned an error or 0-length vectorae
quickly check if two objects are equal, not considering their attributes (wrapper for all.equal)
Changes
get_exercise
now returns a single-feature scaled average of all physical activity scores (physical_activity1_y, physical_activity2_y, physical_activity5_y) rather than each score separatelyget_cbcl_depress_r
and similar functions (anxiety, aggressive, depress) now haveraw
parameter set asTRUE
by default to allow extraction of raw or thresholded scoresget_mtbi_mechanism
now returns undummied data instead of dummied data by default- bug fixes for tbi variable renaming
- restructuring of table in
original_tbi_names
- better handling of longitudinal data in various tbi extraction functions
0.1.0
abcdutils 0.1.0
First release of the abcdutils package to facilitate working with NDA's ABCD dataset.
-
Initial package release, including:
- utility functions:
dummy
: generate dummy variablescol_to_num
: convert specific factor columns to numericcol_to_fac
: convert specific character columns to numeric
- tbi functions:
rename_tbi
: provide meaningful column names to abcd_otbi01.txtoriginal_otbi_names
: view original abcd_otbi01.txt column namesidentify_all_tbi
: label mTBIs and moderate/severe TBIsidentify_mtbi
: identify which mechanism of injury counts as an mTBIidentify_mtbi_times
: identify time since most recent mTBIidentify_latest_mtbi_mechanism
: identify mechanism of injury for latest mTBIidentify_num_mtbi
: identify how many mTBIs a subject sustainedidentify_latest_mtbi_loc
: identify LOC time for latest mTBIidentify_latest_mtbi_mem_daze
: identify if memory loss / feeling dazed or confused occurred for latest mTBIdetail_mtbi
: apply all other TBI functions to a dataframe
- extraction functions:
get_mtbi_subjects
get_cbcl_aggressive_r
get_cbcl_anxiety_r
get_cbcl_attention_r
get_cbcl_depress_r
get_cbcl_dizzy
get_cbcl_headaches
get_cbcl_overtired
get_cbcl_sleeping_less
get_cbcl_sleeping_more
get_cbcl_vomiting
get_cort_sa
get_cort_t
get_exercise
get_family_function
get_full_sleep_df
get_gord_cor
get_gord_var
get_headaches
get_income
get_loneliness
get_mtbi_age
get_mtbi_count
get_mtbi_loc
get_mtbi_mechanism
get_mtbi_mem_daze
get_nihtbx_cardsort_fc
get_nihtbx_list_fc
get_nihtbx_pattern_fc
get_parent_psychopathology
get_prosocial_behaviour
get_pubertal_status
get_race
get_screen_time
get_sex
get_sports_and_activities
get_subc_cor
get_subc_v
get_subc_var
get_wmnd
- subsetting functions:
filter_timepoint
: (isolate to specific data collection year)filter_subjects
: (isolate to provided list of subjects)
- data dictionary functions:
remove_dd
: remove the data dictionary from a dataframesearch_dd
: open the data dictionary search results for a stringabcd_dd
: open the data dictionary page for a data item's short name
- plotting functions:
vis_missing_by_df
: visualize missing data across multiple dataframes
- utility functions:
-
Added a
NEWS.md
file to track changes to the package.