MedLabels Class Reference

A Class which represent time ranges of label values based on registry and labeling method. More...

#include <MedLabels.h>

Public Member Functions
void	prepare_from_registry (const vector< MedRegistryRecord > &reg_records, const vector< MedRegistryRecord > *censor_records=NULL)
bool	has_censor_reg () const
	return true if censor registry was provided
bool	has_censor_reg (int pid) const
	return true if found censor records for patient
void	get_pids (vector< int > &pids) const
	return all availbel pids from registry
void	get_records (int pid, vector< const MedRegistryRecord * > &reg_records, vector< const MedRegistryRecord * > &censor_records) const
	get all registry and censor records for patient
void	calc_signal_stats (const string &repository_path, const string &signal_name, const string &signalHirerchyType, int ageBinValue, MedSamplingStrategy &sampler, const LabelParams &inc_labeling_params, map< float, map< float, vector< int > > > &maleSignalToStats, map< float, map< float, vector< int > > > &femaleSignalToStats, const string &debug_file="", const unordered_set< int > &debug_vals=default_empty_set) const
	calculates table statitics for interrsecting with registry of signal
void	create_incidence_file (const string &file_path, const string &rep_path, int age_bin, int min_age, int max_age, bool use_kaplan_meir=false, const string &sampler_name="yearly", const string &sampler_args="day_jump=365;start_year=2007;end_year=2012;prediction_month_day=101", const string &debug_file="") const
	calculate incidence and writes the result into file with old and new format
SamplingRes	get_samples (int pid, int time, vector< MedSample > &samples, bool show_conflicts=false) const
	returns label value for time point
SamplingRes	get_samples (int pid, const vector< MedSample > &samples, vector< MedSample > &new_samples, bool show_conflicts=false) const
	update outcome and outcomeTime keeping everything else
SamplingRes	get_samples (int pid, const vector< int > &times, vector< MedSample > &samples, bool show_conflicts=false) const
	returns label value for time points
void	create_samples (const MedSamplingStrategy *sampler, MedSamples &samples, bool show_conflicts=true) const
	Creates MedSamples using MedSampling.
void	relabel_samples (MedSamples &samples, bool show_conflicts=true) const
	relabels the samples besed on the labeler
	MedLabels (const LabelParams &params)
	Ctor with labling params.
	MedLabels (const string &labling_params)
	Ctor with labling params as string.

Data Fields
LabelParams	labeling_params
	the labeling parameters - problem definition

Detailed Description

A Class which represent time ranges of label values based on registry and labeling method.

The main procedure is to quety label value using get_label method

Member Function Documentation

calc_signal_stats()

void MedLabels::calc_signal_stats	(	const string &	repository_path,
		const string &	signal_name,
		const string &	signalHirerchyType,
		int	ageBinValue,
		MedSamplingStrategy &	sampler,
		const LabelParams &	inc_labeling_params,
		map< float, map< float, vector< int > > > &	maleSignalToStats,
		map< float, map< float, vector< int > > > &	femaleSignalToStats,
		const string &	debug_file = "",
		const unordered_set< int > &	debug_vals = default_empty_set
	)		const

calculates table statitics for interrsecting with registry of signal

Parameters

repository_path	the repsitory path
signalCode	the signal code to calculate the stats of the registry with
signalHirerchyType	the Hirerchy type: [None, RC, ATC, BNF] for signals with hirerchy
ageBinValue	the age bin size
time_window_from	the minimal time before the event (registry start_time). may be negative to start after event
time_window_to	the maximal time before the event (registry start_time). may be negative to end after event start
sampler	the sampler for how to calc the non appearance of the signal with the registry. You may use MedSamplingAge for example to sample each patient once in each age in the registry dates
debug_file	If provided the output path to write detailed results of the intersection of registry and signal
debug_vals	If not empty and has debug_file. will write the intersection(by the time window) of the registry with those values

Returns

maleSignalToStats The stats for males. the first key in the dictionary is the signal_value. the second key is age_bin and the vector is always of size 4: [signal_not_appear&registry_is_false, signal_not_appear&registry_is_true, signal_appears&registry_is_false, signal_appears&registry_is_true]

femaleSignalToStats The stats for the females. same format as males

create_incidence_file()

void MedLabels::create_incidence_file	(	const string &	file_path,
		const string &	rep_path,
		int	age_bin,
		int	min_age,
		int	max_age,
		bool	use_kaplan_meir = false,
		const string &	sampler_name = "yearly",
		const string &	sampler_args = "day_jump=365;start_year=2007;end_year=2012;prediction_month_day=101",
		const string &	debug_file = ""
	)		const

calculate incidence and writes the result into file with old and new format

Parameters

file_path	the output file path to write the results
rep_path	the repository path to calculate the incidence
age_bin	the age_bin for binning age groups for the incidence
min_age	the minimal age fro the incidence
max_age	the maximal age fro the incidence
use_kaplan_meir	if True will calc using kaplan meier survivol rates
sampler_name	the sampler name for calculating incidence
sampler_args	the sampler args for calculating incidence - may control trail years for example

prepare_from_registry()

void MedLabels::prepare_from_registry	(	const vector< MedRegistryRecord > &	reg_records,
		const vector< MedRegistryRecord > *	censor_records = NULL
	)

prepare MedLabels from registry (and censor if provided) based on labeling rules

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The documentation for this class was generated from the following files:

• Internal/MedUtils/MedUtils/MedLabels.h
• Internal/MedUtils/MedUtils/MedLabels.cpp