Index

Symbols

--alpha moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --check-every moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --checkpoint-freq moseq2-model-learn-model command line option --cluster-type moseq2-model-kappa-scan command line option --default-group moseq2-model-learn-model command line option --e-step moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --gamma moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --get-cmd moseq2-model-kappa-scan command line option --hold-out moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --hold-out-seed moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --index moseq2-model-apply-model command line option moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --kappa moseq2-model-learn-model command line option --load-groups moseq2-model-apply-model command line option moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --max-kappa moseq2-model-kappa-scan command line option --max-states moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --memory moseq2-model-kappa-scan command line option --min-kappa moseq2-model-kappa-scan command line option --n-models moseq2-model-kappa-scan command line option --ncpus moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --nfolds moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --nlags moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --noise-level moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --npcs moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --num-iter moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --out-script moseq2-model-kappa-scan command line option --partition moseq2-model-kappa-scan command line option --percent-split moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option

--prefix moseq2-model-kappa-scan command line option --progressbar moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --robust moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --run-cmd moseq2-model-kappa-scan command line option --save-every moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --save-model moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --scan-scale moseq2-model-kappa-scan command line option --separate-trans moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --use-checkpoint moseq2-model-learn-model command line option --var-name moseq2-model-apply-model command line option moseq2-model-count-frames command line option moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option --verbose moseq2-model-learn-model command line option --version moseq2-model command line option --wall-time moseq2-model-kappa-scan command line option --whiten moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -a moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -c moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -g moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -h moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -i moseq2-model-apply-model command line option moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -k moseq2-model-learn-model command line option -m moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -n moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -p moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -s moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option -v moseq2-model-learn-model command line option -w moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option

A

apply_model() (in module moseq2_model.train.util) apply_model_command() (in module moseq2_model.gui)

apply_model_wrapper() (in module moseq2_model.helpers.wrappers) ARHMM() (in module moseq2_model.train.models)

C

copy_model() (in module moseq2_model.util)

count_frames() (in module moseq2_model.util) create_command_strings() (in module moseq2_model.util)

D

DEST_FILE moseq2-model-apply-model command line option moseq2-model-learn-model command line option

dict_to_h5() (in module moseq2_model.util)

G

get_crosslikes() (in module moseq2_model.train.util) get_current_model() (in module moseq2_model.util) get_heldout_data_splits() (in module moseq2_model.helpers.data) get_labels_from_model() (in module moseq2_model.train.util) get_loglikelihoods() (in module moseq2_model.util) get_model_summary() (in module moseq2_model.train.util)

get_parameter_strings() (in module moseq2_model.util) get_parameters_from_model() (in module moseq2_model.util) get_scan_range_kappas() (in module moseq2_model.util) get_session_groupings() (in module moseq2_model.util) get_training_data_splits() (in module moseq2_model.helpers.data) graph_modeling_loglikelihoods() (in module moseq2_model.helpers.data)

H

h5_to_dict() (in module moseq2_model.util)

I

INPUT_FILE moseq2-model-count-frames command line option moseq2-model-kappa-scan command line option moseq2-model-learn-model command line option

is_uuid() (in module moseq2_model.util)

K

kappa_scan_fit_models_wrapper() (in module moseq2_model.helpers.wrappers)

L

learn_model_command() (in module moseq2_model.gui) learn_model_wrapper() (in module moseq2_model.helpers.wrappers) load_arhmm_checkpoint() (in module moseq2_model.util)

load_cell_string_from_matlab() (in module moseq2_model.util) load_data_from_matlab() (in module moseq2_model.util) load_dict() (in module moseq2_model.util) load_pcs() (in module moseq2_model.util)

M

MODEL_FILE moseq2-model-apply-model command line option module moseq2_model.gui moseq2_model.helpers.data moseq2_model.helpers.wrappers moseq2_model.train.models moseq2_model.train.util moseq2_model.util moseq2-model command line option --version moseq2-model-apply-model command line option --index --load-groups --var-name -i DEST_FILE MODEL_FILE PC_FILE moseq2-model-count-frames command line option --var-name INPUT_FILE moseq2-model-kappa-scan command line option --alpha --check-every --cluster-type --e-step --gamma --get-cmd --hold-out --hold-out-seed --index --load-groups --max-kappa --max-states --memory --min-kappa --n-models --ncpus --nfolds --nlags --noise-level --npcs --num-iter --out-script --partition --percent-split --prefix --progressbar --robust --run-cmd --save-every --save-model --scan-scale --separate-trans --var-name --wall-time --whiten -a -c -g -h -i -m -n -p -s -w INPUT_FILE OUTPUT_DIR

moseq2-model-learn-model command line option --alpha --check-every --checkpoint-freq --default-group --e-step --gamma --hold-out --hold-out-seed --index --kappa --load-groups --max-states --ncpus --nfolds --nlags --noise-level --npcs --num-iter --percent-split --progressbar --robust --save-every --save-model --separate-trans --use-checkpoint --var-name --verbose --whiten -a -c -g -h -i -k -m -n -p -s -v -w DEST_FILE INPUT_FILE moseq2_model.gui module moseq2_model.helpers.data module moseq2_model.helpers.wrappers module moseq2_model.train.models module moseq2_model.train.util module moseq2_model.util module

O

OUTPUT_DIR moseq2-model-kappa-scan command line option

P

PC_FILE moseq2-model-apply-model command line option

prepare_model_metadata() (in module moseq2_model.helpers.data) process_indexfile() (in module moseq2_model.helpers.data)

R

rleslices() (in module moseq2_model.train.util)

run_e_step() (in module moseq2_model.train.util)

S

save_arhmm_checkpoint() (in module moseq2_model.util) save_dict() (in module moseq2_model.util)

select_data_to_model() (in module moseq2_model.helpers.data) slices_from_indicators() (in module moseq2_model.train.util)

T

train_model() (in module moseq2_model.train.util)

training_checkpoint() (in module moseq2_model.train.util)

W

whiten_all() (in module moseq2_model.train.util)

whiten_each() (in module moseq2_model.train.util)

Z

zscore_all() (in module moseq2_model.train.util)

zscore_each() (in module moseq2_model.train.util)