Man pages for PennStateDEPENdLab/dependlab
Useful functions for the Penn State DEPENd Lab (Director: Michael Hallquist)

apathy_adultScore the NIH Toolbox Emotion Measures (2019) This is for the...
build_design_matrixCreates an fmri design matrix, including timing files for for...
check_singularityProbe singular fits of random effects in mixed effects...
cleanup_regressorSmall utility function to handle any NAs in the regressor...
concat_design_runsConcatenate design matrices for each run to form a single...
convolve_cppInternal function to convolve two vectors using nested for...
convolve_dcv_hrfThis function takes in a matrix of generated neural events...
convolve_double_gammaThis function convolves a stimulus vector with the...
convolve_fft_cppInternal function to convolve two vectors using FFT
convolve_regressorThis function convolves a regressor with a normalized HRF...
cor_heatmapFunction to generate ggplot correlation heatmap
cor_with_targetThis function correlates a set of target variables (target)...
deconvolve_nlregC++ port of Bush and Cisler 2013, Magnetic Resonance Imaging...
deconvolve_nlreg_rR port of Bush and Cisler 2013, Magnetic Resonance Imaging...
deconvolve_nlreg_resampleThis function deconvolves the BOLD signal using Bush 2011...
dependlabUseful functions for the Penn State DEPENd Lab (Director:...
detrendtsDetrend a time series up to quadratic trend. Used by...
dsigmoidDsigmoid transform
example_eventsexample events structure for build_design_matrix
example_nuisrun1example nuisance regressors for run1 used in...
example_nuisrun2example nuisance regressors for run2 used in...
example_signalsexample signals structure for build_design_matrix
fir1BandpassApply a FIR-1 bandpass filter a signal. Can low- or high-pass...
flex_vifRender Variance Inflation Factor (VIF) in flextable
fmri.stimulusConvolve a regressor with a hemodynamic response function for...
generate_featureThis function creates K shifts of a neural events vector...
generate_feature_armadilloThis function creates K shifts of a neural events vector...
generate_fsf_contrast_syntaxThis function generates syntax for FSL Feat .fsf files for...
generate_fsf_ev_syntaxThis function generates syntax for FSL Feat .fsf files for...
generate_fsf_lvl1_ev_syntaxThis function generates syntax for FSL Feat .fsf files for...
generate_spm_contrastsThis function reads an SPM.mat file and generate contrasts...
generate_spm_matUses an object from build_design_matrix to generate a...
gmcmapplyexpand.grid-based multi-core multivariate apply (mcmapply)...
installMissingPkgsInstalls packages that are missing based off a list provided....
lmer_predictThis function predicts outcome variable from a (g)lmer object...
mean_impute_itemsFunction to impute the mean for missing items on a per-case...
place_dmat_on_time_gridFunction to convert dmat (runs x regressor list) to a...
qsub_fileThis function submits a single script using the qsub command....
rat.brainrat.brain data in Chapter 5 of West, Welch, and Galecki...
render_flex_aictabRender a pretty AIC comparison table in flextable for...
retrieve_onedriveretrieve .csv and excel (xls/xlsx) files from...
runAFNICommandWrapper for running an AFNI command safely within R
runFSLCommandWrapper for running an fsl command safely within R
runmeancompute a moving average smooth over a time series (here, a...
score_aswsScore the Adolescent Sleep Wake Scale (ASWS)
score_bfiScore The Big Five Inventory-2 - 60 items BFI-2 (Soto & John,...
score_bpqScore the Borderline Personality Questionnaire (BPQ)
score_ctqScore the Childhood Trauma Questionnaire - CTQ scale...
score_ctsScore the Conflict Tactics Scale (CTS)
score_dasScores the Dyadic Adjustment Scale (Spanier 1976) This is for...
score_dersScore the Difficulties in Emotion Regulation Scale (DERS)...
score_ecrScore the experiences in close relationships - revised...
score_fsScore the Flourishing Scale (Diener, Wirtz, Tov, Kim-Prieto,...
score_iip90Score the Inventory for Interpersonal Problems - 90 items PD...
score_iscScore the Interpersonal Stressors Circumplex (ISC)
score_neoScore the NEO Five-Factor Inventory (NEO-FFI) scale (Costa &...
score_panasScore the Positive and Negative Affect Schedule (PANAS) scale
score_pid5Score the Personality Inventory for DSM-5 Faceted Brief Form...
score_rseScore the Relationship and Sex Education (RSE) scale
score_rtScore the Risk Taking - 18 item scale (RT-18)
score_sbpniScore the 12-item Super-Brief Pathological Narcissism...
score_swlsScore the Satisfaction with Life Scale (Diener, Emmons,...
score_uppsScore the UPPS-P Impulsive Behavior scale - revised 59 item...
setup_studysetup a study-level directory structure
sigmoidSigmoid transform
spm_extract_anatomical_roisThis is a wrapper around the spm_extract_anatomical_rois.m...
spm_hrfR port of spm8 functions needed for deconvolution spm_hrf -...
visualize_design_matrixVisualize design matrix, including event onset times and run...
wait_for_jobThis function pauses execution of an R script while a...
wgr_deconv_canonhrf_parR port of Wu et al. 2013, Medical Image Analysis Adapted from...
PennStateDEPENdLab/dependlab documentation built on Oct. 1, 2022, 3:16 a.m.