17-cgm

17 - cgm

Continuous Glucose Monitoring (CGM) measures glucose levels in a continuous manner.
This measure provides information on blood glucose control and glucose variability and could be used to monitor patients with diabetes.

Each 14-day continuous measure is termed a single CGM-connection.

Using the glucose measured in the CGM connection we can calculate summary features (which was done using the iglu package) summarizing information on glucose control and variability.
These were calculated for the entire CGM connection as well as for daily segments of the data.

The actual glucose measures are stored in multiple parquet files, each file holds the glucose measures for a single CGM connection.
The metadata and summary features are stored in 2 main statistics parquet files: main.parquet, daily_iglu.parquet.

from pheno_utils import PhenoLoader

dl = PhenoLoader('cgm', age_sex_dataset=None)
dl

DataLoader for cgm with
94 fields
2 tables: ['main_cgm', 'daily_iglu']

dl.dict

	field_string	description_string	parent_dataframe	relative_location	value_type	units	sampling_rate	item_type	array	cohorts	data_type	debut	pandas_dtype
tabular_field_name
connection_id	ConnectionID	CGM device connection id	main	main_cgm.parquet	Text	Text	NaN	Data	Single	10K	tabular	2018-12-27	int
cgm_filename	CGM timeseries	Name of the file containing the participants' ...	main	main_cgm.parquet	Text	NaN	NaN	Bulk	Single	10K	text	2018-12-27	string
glucose	Glucose	cgm temporal glucose values	cgm_filename	NaN	Series data, continous	mg/dl	15min	Data	Single	10K	time series	2018-12-27	float
collection_timestamp	Collection timestamp	CGM connection first data point timestamp	main	main_cgm.parquet	Time	Time	NaN	Data	Single	10K	tabular	2018-12-27	datetime64[ns, Asia/Jerusalem]
cgm_first_date	CGM first date	CGM connection first date	main	main_cgm.parquet	Time	Time	NaN	Data	Single	10K	tabular	2018-12-27	datetime64[ns, Asia/Jerusalem]
cgm_last_date	CGM last date	CGM connection last date	main	main_cgm.parquet	Time	Time	NaN	Data	Single	10K	tabular	2018-12-27	datetime64[ns, Asia/Jerusalem]
cgm_device_type	CGM Device type	CGM Device type	main	main_cgm.parquet	Categorical (multiple)	Text	NaN	Data	Single	10K	tabular	2018-12-27	string
cgm_datapoints_lost_in_qc	CGM datapoints lost in QC	Number of CGM datapoints lost in QC	main	main_cgm.parquet	Integer	integer	NaN	Data	Single	10K	tabular	2018-12-27	int
percentage_of_cgm_datapoints_lost_in_qc	NaN	NaN	NaN	main_cgm.parquet	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	float
number_of_cgm_days_available	Number of CGM days available	Number of CGM days available for the connection	main	main_cgm.parquet	Integer	integer	NaN	Data	Single	10K	tabular	2018-12-27	int
number_of_cgm_datapoints_available	Number of CGM datapoints available	Number of CGM datapoints available for the con...	main	main_cgm.parquet	Integer	integer	NaN	Data	Single	10K	tabular	2018-12-27	int
timezone	Timezone	TImezone of measurement	NaN	main_cgm.parquet	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	datetime64[ns, Asia/Jerusalem]
1st qu_	1st quantile	First quantile of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
3rd qu_	3rd quantile	Third quantile of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
above_140	% above 140	Percent of glucose measures that were larger t...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
above_180	% above 180	Percent of glucose measures that were larger t...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
above_250	% above 250	Percent of glucose measures that were larger t...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
below_54	% below 54	Percent of glucose measures that were lower th...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
below_70	% below 70	Percent of glucose measures that were lower th...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
in_range_63_140	% in range 63-140	Percent of glucose measures that were in a spe...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
in_range_70_180	% in range 70-180	Percent of glucose measures that were in a spe...	main	main_cgm.parquet	Continuous	%	NaN	Data	Single	10K	tabular	2018-12-27	float
adrr	ADRR	Average daily risk range (ADRR) is a variabili...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
auc	AUC	Hourly average AUC. This measure integrates, t...	main	main_cgm.parquet	Continuous	mg/dl*h	NaN	Data	Single	10K	tabular	2018-12-27	float
cogi	COGI	Continuous Glucose Monitoring Index (COGI). CO...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
conga	Conga	Continuous Overall Net Glycemic Action (CONGA)...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
cv	CV	Coefficient of variation of all glucose values.\n	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
cv_measures_mean	CVmean	Mean of all daily CVs.	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
cv_measures_sd	CVsd	Standard deviations of all daily CVs.	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
ea1c	eA1C	A linear transformation of the mean glucose va...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
gmi	GMI	A linear transformation of the mean glucose va...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
grade	GRADE	Glycaemic Risk Assessment Diabetes Equation (G...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
grade_eugly	GRADE eugly	Percentage of the GRADE score that is attribut...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
grade_hyper	GRADE hyper	Percentage of the GRADE score that is attribut...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
grade_hypo	GRADE hypo	Percentage of the GRADE score that is attribut...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
gvp	GVP	Glucose Variability Percentage (GVP), which is...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
hbgi	HBGI	High Blood Glucose Index (HBGI)	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
hyper_index	Hyper index	This is a weighted average of hyperglycemic va...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
hypo_index	Hypo index	This is a weighted average of hypoglycemic val...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
igc	IGC	Index of Glycemic Control (IGC), a sum of the ...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
iqr	IQR	Interquartile range (IQR), calculated as the d...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
j_index	J-index	This index was designed to stress the importan...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
lbgi	LBGI	Low Blood Glucose Index (LBGI)	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
m_value	M value	The M-value is an index aimed to describe the ...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
mad	MAD	Median Absolute Deviation (MAD). This is a mea...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
mag	MAG	Mean Absolute Glucose (MAG). This is a measure...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
mage	MAGE	Mean Amplitude of Glycemic Excursions (MAGE), ...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
min_	Min	Minimum of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
max_	Max	Maximum of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
mean	Mean	Mean of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
median	Median	Median of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
modd	MODD	Mean difference between glucose values obtaine...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
range	Range	Difference between the maximum and minimum glu...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sd	SD	Standard deviation of all glucose values.	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sd_roc	SD.Roc	Standard deviation of all the rate of change (...	main	main_cgm.parquet	Continuous	NaN	NaN	Data	Single	10K	tabular	2018-12-27	float
sdb	SDb	SD between days, within time points. Mean valu...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sdbdm	SDbdm	SD between days, within time points, corrected...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sddm	SDdm	Horizontal SD. SD of the mean glucose values, ...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sdhhmm	SDhhmm	SD between time points. Standard deviation of ...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sdw	SDw	Vertical SD within days. Average value of the ...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
sdwsh	SDwsh	SD within series. Taking hour-long intervals t...	main	main_cgm.parquet	Continuous	mg/dl	NaN	Data	Single	10K	tabular	2018-12-27	float
collection_date	Date	Date of the daily CGM data used to calculate t...	daily iglu	daily_iglu.parquet	Time	Time	NaN	Data	Multiple	10K	tabular	2018-12-27	datetime64[ns, Asia/Jerusalem]
connection_day	Connection day	Day of the CGM connection	daily iglu	daily_iglu.parquet	Integer	integer	NaN	Data	Single	10K	tabular	2018-12-27	int
daily_1st_quartile	Daily 1st quartile	First quantile of daily glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_3rd_quartile	Daily 3rd quartile	Third quantile of daily glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_above_140	Daily % above 140	Percent of daily glucose measures that were la...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_above_180	Daily % above 180	Percent of daily glucose measures that were la...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_above_250	Daily % above 250	Percent of daily glucose measures that were la...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_below_54	Daily % below 54	Percent of daily glucose measures that were lo...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_below_70	Daily % below 70	Percent of daily glucose measures that were lo...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_in_range_63_140	Daily % in range 63-140	Percent of daily glucose measures that were in...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_in_range_70_180	Daily % in range 70-180	Percent of daily glucose measures that were in...	daily iglu	daily_iglu.parquet	Continuous	%	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_adrr	Daily ADRR	Average daily risk range (ADRR) is a variabili...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_auc	Daily AUC	Hourly average AUC. This measure integrates, t...	daily iglu	daily_iglu.parquet	Continuous	mg/dl*h	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_cogi	Daily COGI	Continuous Glucose Monitoring Index (COGI). CO...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_cv	Daily CV	Coefficient of variation of daily glucose values.	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_ea1c	Daily eA1C	A linear transformation of the mean glucose va...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_gmi	Daily GMI	A linear transformation of the mean glucose va...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_grade	Daily GRADE	Glycaemic Risk Assessment Diabetes Equation (G...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_grade_eugly	Daily GRADE_eugly	Percentage of the GRADE score that is attribut...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_grade_hyper	Daily GRADE_hyper	Percentage of the GRADE score that is attribut...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_grade_hypo	Daily GRADE_hypo	Percentage of the GRADE score that is attribut...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_gvp	Daily GVP	Glucose Variability Percentage (GVP), which is...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_hbgi	Daily HBGI	High Blood Glucose Index (HBGI)	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_hyper_index	Daily Hyper index	This is a weighted average of hyperglycemic va...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_hypo_index	Daily Hypo index	This is a weighted average of hypoglycemic val...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_igc	Daily IGC	Index of Glycemic Control (IGC), a sum of the ...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_iqr	Daily IQR	Interquartile range (IQR), calculated as the d...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_j_index	Daily J_index	This index was designed to stress the importan...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_lbgi	Daily LBGI	Low Blood Glucose Index (LBGI)	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_m_value	Daily M value	The M-value is an index aimed to describe the ...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_mad	Daily MAD	Median Absolute Deviation (MAD). This is a mea...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_mag	Daily MAG	Mean Absolute Glucose (MAG). This is a measure...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_mage	Daily MAGE	Mean Amplitude of Glycemic Excursions (MAGE), ...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_min	Daily Min	Minimum of all glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_max	Daily Max	Maximum of all glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_mean	Daily Mean	Mean of all glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_median	Daily Median	Median of all glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_range	Daily Range	Difference between the maximum and minimum glu...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_sd	Daily SD	Standard deviation of all glucose values.	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_sd_roc	Daily SD.Roc	Standard deviation of all the rate of change (...	daily iglu	daily_iglu.parquet	Continuous	NaN	NaN	Data	Multiple	10K	tabular	2018-12-27	float
daily_sdwsh	Daily SDwsh	SD within series. Taking hour-long intervals t...	daily iglu	daily_iglu.parquet	Continuous	mg/dl	NaN	Data	Multiple	10K	tabular	2018-12-27	float