.. _stats: ****************** stats - Statistics ****************** .. currentmodule:: gammapy.stats .. _stats-introduction: Introduction ============ gammapy.stats holds statistical estimators, fit statistics and algorithms commonly used in gamma-ray astronomy. It is mostly concerned with the evaluation of one or several observations that count events in a given region and time window, i.e. with Poisson-distributed counts measurements. General notions =============== Counts and fit statistics ------------------------- Gamma-ray measurements are counts, n_on, containing both signal and background events. Estimation of number of signal events or of quantities in physical models is done through Poisson likelihood functions, the fit statistics. In gammapy, they are all log-likelihood functions normalized like chi-squares, i.e. if :math:L is the likelihood function used, they follow the expression :math:2 \times log L. When the expected number of background events, mu_bkg is known, the statistic function is Cash (see :ref:cash). When the number of background events is unknown, one has to use a background estimate n_bkg taken from an OFF measurement where only background events are expected. In this case, the statistic function is WStat (see :ref:wstat). These statistic functions are at the heart of the model fitting approach in gammapy. They are used to estimate the best fit values of model parameters and their associated confidence intervals. They are used also to estimate the excess counts significance, i.e. the probability that a given number of measured events n_on actually contains some signal events :math:n_{excess}, as well as the errors associated to this estimated number of signal counts. Estimating Delta TS ------------------- A classical approach to modeling and fitting relies on hypothesis testing. One wants to estimate whether an hypothesis :math:H_1 is statistically preferred over the reference, or null-hypothesis, :math:H_0. The maximum log-likelihood ratio test provides a way to estimate the p-value of the data following :math:H_1 rather than :math:H_0, when the two hypotheses are nested. We note this ratio :math:\lambda = \frac{max L(X|{H_1})}{max L(X|H_0)} The Wilks theorem shows that under some hypothesis, :math:-2 \log \lambda assymptotically follows a :math:\chi^2 distribution with :math:n_{dof} degrees of freedom, where :math:n_{dof} is the difference of free parameters between :math:H_1 and :math:H_0. With the definition the fit statistics :math:-2 \log \lambda is simply the difference of the fit statistic values for the two hypotheses, the delta TS (for test statistic). Hence, :math:\Delta TS follows :math:\chi^2 distribution with :math:n_{dof} degrees of freedom. In particular, with only one degree of freedom (e.g. intensity of a signal), on can estimate the statistical significance in terms of number of :math:\sigma as :math:\sqrt{\Delta TS}. Counts statistics classes ========================= To estimate the excess counts significance and errors, gammapy uses two classes for Poisson counts with and without known background: ~gammapy.stats.CashCountsStatistic and ~gammapy.stats.WStatCountsStatistic We show below how to use them. Cash counts statistic --------------------- Excess and Significance ^^^^^^^^^^^^^^^^^^^^^^^ Assume one measured :math:n_{on} = 13 counts in a region where one suspects a source might be present. if the expected number of background events is known (here e.g. :math:\mu_{bkg}=9.5), one can use the Cash statistic to estimate the signal or excess number, its statistical significance as well as the confidence interval on the true signal value. .. code-block:: python >>> from gammapy.stats import CashCountsStatistic >>> stat = CashCountsStatistic(n_on=13, mu_bkg=5.5) >>> stat.excess 7.5 >>> stat.error 3.605551275463989 >>> stat.delta_ts 7.365232895800901 >>> stat.significance 2.7138962573762653 >>> stat.p_value 0.006649698694909719 The error is the symmetric error obtained from the covariance of the statistic function, here :math:\sqrt{n_{on}}. The significance is the square root of the :math:\Delta TS, multiplied by the sign of the excess, which is equivalent to the Li & Ma significance for known background. To see how the :math:\Delta TS, relates to the statistic function, we plot below the profile of the Cash statistic as a function of the expected signal events number. .. plot:: stats/plot_cash_significance.py Excess errors ^^^^^^^^^^^^^ You can also compute the confidence interval for the true excess based on the statistic value: If you are interested in 68% (1 :math:\sigma) and 95% (2 :math:\sigma) confidence ranges: .. code-block:: python >>> from gammapy.stats import CashCountsStatistic >>> stat = CashCountsStatistic(n_on=13, mu_bkg=5.5) >>> errn = count_statistic.compute_errn(1.) >>> errp = count_statistic.compute_errp(1.) >>> print(f"68% confidence range: {excess+errn} < mu < {excess+errp}") 68% confidence range: 4.219788441647667 < mu < 11.446309124623102 >>> errn_2sigma = count_statistic.compute_errn(2.) >>> errp_2sigma = count_statistic.compute_errp(2.) >>> print(f"95% confidence range: {excess+errn_2sigma} < mu < {excess+errp_2sigma}") 95% confidence range: 1.5559091942635206 < mu < 16.10168631791818 The 68% confidence interval (1 :math:\sigma) is obtained by finding the expected signal values for which the TS variation is 1. The 95% confidence interval (2 :math:\sigma) is obtained by finding the expected signal values for which the TS variation is :math:2^2 = 4. On the following plot, we show how the 1 :math:\sigma and 2 :math:\sigma confidence errors relate to the Cash statistic profile. .. plot:: stats/plot_cash_errors.py WStat counts statistic ---------------------- Excess and Significance ^^^^^^^^^^^^^^^^^^^^^^^ To measure the significance of an excess, one can directly use the delta TS of the measurement with and without the excess. Taking the square root of the result yields the so-called Li & Ma significance [LiMa1983]_ (see equation 17). As an example, assume you measured :math:n_{on} = 13 counts in a region where you suspect a source might be present and :math:n_{off} = 11 counts in a background control region where you assume no source is present and that is :math:a_{off}/a_{on}=2 times larger than the on-region. Here's how you compute the statistical significance of your detection: .. code-block:: python >>> from gammapy.stats import WStatCountsStatistic >>> stat = WStatCountsStatistic(n_on=13, n_off=11, alpha=1./2) >>> stat.excess >>> stat.significance .. plot:: stats/plot_wstat_significance.py Conversely, if you know that the expected number of background events is :math:\mu_{bkg}=9.5, you can use the Cash statistic and obtain the Li & Ma significance for known background: .. code-block:: python >>> from gammapy.stats import CashCountsStatistic >>> stat = CashCountsStatistic(n_on=13, mu_bkg=5.5) >>> stat.excess >>> stat.significance .. plot:: stats/plot_cash_significance.py Excess errors ^^^^^^^^^^^^^ You can also compute the confidence interval for the true excess based on the statistic value: If you are interested in 68% (1 :math:\sigma) and 95% (1 :math:\sigma) confidence errors: .. code-block:: python >>> from gammapy.stats import CashCountsStatistic >>> stat = CashCountsStatistic(n_on=13, mu_bkg=5.5) >>> stat.compute_errn(1.) -3.91606323 >>> stat.compute_errp(1.) 4.5823187389960225 >>> stat.compute_errn(2.) -3.91606323 >>> stat.compute_errp(2.) 4.5823187389960225 The 68% confidence interval (1 :math:\sigma) is obtained by finding the expected signal values for which the TS variation is 1. The 95% confidence interval (2 :math:\sigma) is obtained by finding the expected signal values for which the TS variation is :math:2^2 = 4. On the following plot, we show how the 1 :math:\sigma and 2 :math:\sigma confidence errors relate to the fit statistic profile. .. plot:: stats/plot_cash_errors.py Note that confidence intervals can be computed in a more robust manner following [Feldman1998]_. See :ref:feldman_cousins. .. _stats_notation: Notations --------- For on-off methods we use the following variable names following the notation in [Cousins2007]_: ================= ====================== ==================================================== Variable Dataset attribute name Definition ================= ====================== ==================================================== n_on counts Total observed counts in the on region n_off counts_off Total observed counts in the off region mu_on npred Total expected counts in the on region mu_off npred_off Total expected counts in the off region mu_sig npred_sig Signal expected counts in the on region mu_bkg npred_bkg Background expected counts in the on region a_on acceptance Relative background exposure in the on region a_off acceptance_off Relative background exposure in the off region alpha alpha Background efficiency ratio a_on / a_off n_bkg background Background estimate in the on region ================= ====================== ==================================================== The ON measurement, assumed to contain signal and background counts, :math:n_{on} follows a Poisson random variable with expected value :math:\mu_{on} = \mu_{sig} + \mu_{bkg}. The OFF measurement is assumed to contain only background counts, with an acceptance to background :math:a_{off}. This OFF measurement can be used to etimate the number of background counts in the ON measurement: :math:n_{bkg} = \alpha\ n_{off} with :math:\alpha = a_{on}/a_{off} the ratio of ON and OFF acceptances. Therefore :math:n_{off} follows a Poisson distribution with expected value :math:\mu_{off} = \mu_{bkg) / \alpha These are references describing the available methods: [LiMa1983]_, [Cash1979]_, [Stewart2009]_, [Rolke2005]_, [Feldman1998]_, [Cousins2007]_. Using gammapy.stats ===================== .. toctree:: :maxdepth: 1 fit_statistics wstat_derivation feldman_cousins Reference/API ============= .. automodapi:: gammapy.stats :no-inheritance-diagram: :include-all-objects: