biopsykit.example_data module¶
Module providing functions to load different example data.
The data is either taken from the local file system in case biopsykit was installed manually or the example data is downloaded into the local user folder.
- biopsykit.example_data.get_condition_list_example()[source]¶
Return example data for subject condition assignment.
- Returns
dataframe with example subject condition assignment
- Return type
- biopsykit.example_data.get_saliva_example_plate_format(sample_id_col=None, data_col=None, id_col_names=None, regex_str=None, sample_times=None, condition_list=None)[source]¶
Return example saliva data from “plate” format.
- Parameters
sample_id_col (str, optional) – column name of the Excel sheet containing the sample ID. Default: “sample ID”
data_col (str, optional) – column name of the Excel sheet containing saliva data to be analyzed. Default: Select default column name based on
biomarker_type, e.g.cortisol=>cortisol (nmol/l)id_col_names (list of str, optional) – names of the extracted ID column names.
Noneto use the default column names ([‘subject’, ‘day’, ‘sample’])regex_str (str, optional) – regular expression to extract subject ID, day ID and sample ID from the sample identifier.
Noneto use default regex string (r"(Vp\d+) (S\d)")sample_times (list of int, optional) – times at which saliva samples were collected
condition_list (1d-array, optional) – list of conditions which subjects were assigned to
- Returns
data – saliva data in SalivaRawDataFrame format
- Return type
See also
load_saliva_plate()loader function for saliva data in plate format
- biopsykit.example_data.get_saliva_example(sample_times=None)[source]¶
Return saliva example data.
- Parameters
sample_times (list of int, optional) – sample times of saliva samples in minutes
- Returns
dataframe with example raw saliva data
- Return type
- biopsykit.example_data.get_saliva_mean_se_example()[source]¶
Return dictionary with mean and standard error from example data for different saliva types.
- Returns
dictionary with
SalivaMeanSeDataFramefrom different saliva types- Return type
- biopsykit.example_data.get_mist_hr_example()[source]¶
Return heart rate time-series example data collected during MIST from one subject.
- Returns
dictionary with heart rate time-series data from one subject during multiple phases
- Return type
- biopsykit.example_data.get_hr_result_sample()[source]¶
Return heart rate results example data.
The heart rate results example data consists of the mean normalized heart rate for different subjects, different study phases, and study subphases.
- Returns
dataframe with heart rate results example data
- Return type
- biopsykit.example_data.get_hr_ensemble_sample()[source]¶
Return heart rate ensemble example data.
The example data consists of time-series heart rate of multiple subjects for different study phases, each synchronized and resampled to 1 Hz, and normalized to baseline heart rate.
- Returns
dictionary with pandas dataframes containing heart rate ensemble data
- Return type
- biopsykit.example_data.get_hr_subject_data_dict_example()[source]¶
Return heart rate example data in the form of a
HeartRateSubjectDataDict.- Returns
dictionary with heart rate time-series data from multiple subjects, each containing data from different phases.
- Return type
- biopsykit.example_data.get_hr_subject_data_dict_tuple_example()[source]¶
Return HR example data as a
HeartRateSubjectDataDict, but with tuples as keys instead of strings.- Returns
dictionary with heart rate time-series, each containing data from different phases.
- Return type
- biopsykit.example_data.get_ecg_processing_results_path_example()[source]¶
Return folder path to ECG processing results.
- Returns
path to folder with ECG processing results
- Return type
Pathor str
- biopsykit.example_data.get_ecg_path_example()[source]¶
Return folder path to ECG example data.
- Returns
path to folder with ECG raw files
- Return type
Pathor str
- biopsykit.example_data.get_ecg_example()[source]¶
Return raw ECG example data from one subject.
- Returns
DataFrame– dataframe with raw ECG datasampling_rate (float) – sampling rate of recorded data
- Return type
- biopsykit.example_data.get_ecg_example_02()[source]¶
Return second raw ECG example data from another subject.
- Returns
DataFrame– dataframe with raw ECG datasampling_rate (float) – sampling rate of recorded data
- Return type
- biopsykit.example_data.get_eeg_example()[source]¶
Return raw EEG example data collected from a Muse EEG headband.
- Returns
data (
DataFrame) – dataframe with raw EEG datasampling_rate (float) – sampling rate of recorded data
- Return type
- biopsykit.example_data.get_sleep_analyzer_raw_file_unformatted(data_source)[source]¶
Return unformatted Withings Sleep Analyzer raw data example file.
- biopsykit.example_data.get_sleep_analyzer_raw_file(data_source, split_into_nights=True)[source]¶
Return Withings Sleep Analyzer raw data example file.
- Parameters
data_source (str) – Withings Sleep Analyzer data source name. Must be one of [‘heart_rate’, ‘respiration_rate’, ‘sleep_state’, ‘snoring’].
split_into_nights (bool, optional) – whether to split the dataframe into the different recording nights (and return a dictionary of dataframes) or not. Default:
True
- Returns
dataframe (or dict of dataframes, if
split_into_nightsisTrue) with Sleep Analyzer data- Return type
DataFrameor dict of such
- biopsykit.example_data.get_sleep_analyzer_raw_example(split_into_nights=True)[source]¶
Return Withings Sleep Analyzer example raw data.
- Parameters
split_into_nights (bool, optional) –
Trueto split data into single dataframes per recording night, and return a dict of dataframes,Falseto keep all data in one dataframe. Default:True- Returns
dataframe with raw sleep analyzer data or a dict of such if
split_into_nightsisTrue- Return type
DataFrameor dict
- biopsykit.example_data.get_sleep_analyzer_summary_example()[source]¶
Return Withings Sleep Analyzer example summary data.
- Returns
dataframe with example sleep endpoints computed from Withings Sleep Analyzer Summary data
- Return type
- biopsykit.example_data.get_sleep_imu_example()[source]¶
Return raw IMU example data collected from a wrist-worn IMU sensor during night.
- Returns
data (
DataFrame) – dataframe with raw IMU datasampling_rate (float) – sampling rate of recorded data
- Return type
- biopsykit.example_data.get_time_log_example()[source]¶
Return time log example data.
- Returns
data – dataframe with example time log information. The time log match the data from the two ECG data example functions
get_ecg_example()andget_ecg_example_02()- Return type
- biopsykit.example_data.get_questionnaire_example()[source]¶
Return questionnaire example data.
- Returns
data – dataframe with questionnaire example data
- Return type
- biopsykit.example_data.get_questionnaire_example_wrong_range()[source]¶
Return questionnaire example data with score in the wrong range.
In this example the items of the “PSS” questionnaire are coded in the wrong range ([1, 5] instead of [0, 4]) originally defined in the paper.
This example data is used to demonstrate BioPsyKit’s feature of asserting that questionnaire score items are provided in the correct score range according to the original definition of the questionnaire.
- Returns
data – dataframe with questionnaire example data where the items of the PSS questionnaire are coded in the wrong range
- Return type