.. module:: statsmodels.stats :synopsis: Statistical methods and tests .. currentmodule:: statsmodels.stats .. _stats: Statistics :mod:`stats` ======================= This section collects various statistical tests and tools. Some can be used independently of any models, some are intended as extension to the models and model results. API Warning: The functions and objects in this category are spread out in various modules and might still be moved around. We expect that in future the statistical tests will return class instances with more informative reporting instead of only the raw numbers. .. _stattools: Residual Diagnostics and Specification Tests -------------------------------------------- .. module:: statsmodels.stats.stattools :synopsis: Statistical methods and tests that do not fit into other categories .. currentmodule:: statsmodels.stats.stattools .. autosummary:: :toctree: generated/ durbin_watson jarque_bera omni_normtest medcouple robust_skewness robust_kurtosis expected_robust_kurtosis .. module:: statsmodels.stats.diagnostic :synopsis: Statistical methods and tests to diagnose model fit problems .. currentmodule:: statsmodels.stats.diagnostic .. autosummary:: :toctree: generated/ acorr_breusch_godfrey acorr_ljungbox acorr_lm breaks_cusumolsresid breaks_hansen recursive_olsresiduals compare_cox compare_encompassing compare_j het_arch het_breuschpagan het_goldfeldquandt het_white spec_white linear_harvey_collier linear_lm linear_rainbow linear_reset Outliers and influence measures ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. module:: statsmodels.stats.outliers_influence :synopsis: Statistical methods and measures for outliers and influence .. currentmodule:: statsmodels.stats.outliers_influence .. autosummary:: :toctree: generated/ OLSInfluence GLMInfluence MLEInfluence variance_inflation_factor See also the notes on :ref:`notes on regression diagnostics ` Sandwich Robust Covariances --------------------------- The following functions calculate covariance matrices and standard errors for the parameter estimates that are robust to heteroscedasticity and autocorrelation in the errors. Similar to the methods that are available for the LinearModelResults, these methods are designed for use with OLS. .. currentmodule:: statsmodels.stats .. autosummary:: :toctree: generated/ sandwich_covariance.cov_hac sandwich_covariance.cov_nw_panel sandwich_covariance.cov_nw_groupsum sandwich_covariance.cov_cluster sandwich_covariance.cov_cluster_2groups sandwich_covariance.cov_white_simple The following are standalone versions of the heteroscedasticity robust standard errors attached to LinearModelResults .. autosummary:: :toctree: generated/ sandwich_covariance.cov_hc0 sandwich_covariance.cov_hc1 sandwich_covariance.cov_hc2 sandwich_covariance.cov_hc3 sandwich_covariance.se_cov Goodness of Fit Tests and Measures ---------------------------------- some tests for goodness of fit for univariate distributions .. module:: statsmodels.stats.gof :synopsis: Goodness of fit measures and tests .. currentmodule:: statsmodels.stats.gof .. autosummary:: :toctree: generated/ powerdiscrepancy gof_chisquare_discrete gof_binning_discrete chisquare_effectsize .. currentmodule:: statsmodels.stats.diagnostic .. autosummary:: :toctree: generated/ anderson_statistic normal_ad kstest_exponential kstest_fit kstest_normal lilliefors Non-Parametric Tests -------------------- .. module:: statsmodels.sandbox.stats.runs :synopsis: Experimental statistical methods and tests to analyze runs .. currentmodule:: statsmodels.sandbox.stats.runs .. autosummary:: :toctree: generated/ mcnemar symmetry_bowker median_test_ksample runstest_1samp runstest_2samp cochrans_q Runs .. currentmodule:: statsmodels.stats.descriptivestats .. autosummary:: :toctree: generated/ sign_test .. currentmodule:: statsmodels.stats.nonparametric .. autosummary:: :toctree: generated/ rank_compare_2indep rank_compare_2ordinal RankCompareResult cohensd2problarger prob_larger_continuous rankdata_2samp Descriptive Statistics ---------------------- .. module:: statsmodels.stats.descriptivestats :synopsis: Descriptive statistics .. currentmodule:: statsmodels.stats.descriptivestats .. autosummary:: :toctree: generated/ describe Description .. _interrater: Interrater Reliability and Agreement ------------------------------------ The main function that statsmodels has currently available for interrater agreement measures and tests is Cohen's Kappa. Fleiss' Kappa is currently only implemented as a measures but without associated results statistics. .. module:: statsmodels.stats.inter_rater .. currentmodule:: statsmodels.stats.inter_rater .. autosummary:: :toctree: generated/ cohens_kappa fleiss_kappa to_table aggregate_raters Multiple Tests and Multiple Comparison Procedures ------------------------------------------------- `multipletests` is a function for p-value correction, which also includes p-value correction based on fdr in `fdrcorrection`. `tukeyhsd` performs simultaneous testing for the comparison of (independent) means. These three functions are verified. GroupsStats and MultiComparison are convenience classes to multiple comparisons similar to one way ANOVA, but still in development .. module:: statsmodels.sandbox.stats.multicomp :synopsis: Experimental methods for controlling size while performing multiple comparisons .. currentmodule:: statsmodels.stats.multitest .. autosummary:: :toctree: generated/ multipletests fdrcorrection .. currentmodule:: statsmodels.sandbox.stats.multicomp .. autosummary:: :toctree: generated/ GroupsStats MultiComparison TukeyHSDResults .. module:: statsmodels.stats.multicomp :synopsis: Methods for controlling size while performing multiple comparisons .. currentmodule:: statsmodels.stats.multicomp .. autosummary:: :toctree: generated/ pairwise_tukeyhsd .. module:: statsmodels.stats.multitest :synopsis: Multiple testing p-value and FDR adjustments .. currentmodule:: statsmodels.stats.multitest .. autosummary:: :toctree: generated/ local_fdr fdrcorrection_twostage NullDistribution RegressionFDR .. module:: statsmodels.stats.knockoff_regeffects :synopsis: Regression Knock-Off Effects .. currentmodule:: statsmodels.stats.knockoff_regeffects .. autosummary:: :toctree: generated/ CorrelationEffects OLSEffects ForwardEffects OLSEffects RegModelEffects The following functions are not (yet) public .. currentmodule:: statsmodels.sandbox.stats.multicomp .. autosummary:: :toctree: generated/ varcorrection_pairs_unbalanced varcorrection_pairs_unequal varcorrection_unbalanced varcorrection_unequal StepDown catstack ccols compare_ordered distance_st_range ecdf get_tukeyQcrit homogeneous_subsets maxzero maxzerodown mcfdr qcrit randmvn rankdata rejectionline set_partition set_remove_subs tiecorrect .. _tost: Basic Statistics and t-Tests with frequency weights --------------------------------------------------- Besides basic statistics, like mean, variance, covariance and correlation for data with case weights, the classes here provide one and two sample tests for means. The t-tests have more options than those in scipy.stats, but are more restrictive in the shape of the arrays. Confidence intervals for means are provided based on the same assumptions as the t-tests. Additionally, tests for equivalence of means are available for one sample and for two, either paired or independent, samples. These tests are based on TOST, two one-sided tests, which have as null hypothesis that the means are not "close" to each other. .. module:: statsmodels.stats.weightstats :synopsis: Weighted statistics .. currentmodule:: statsmodels.stats.weightstats .. autosummary:: :toctree: generated/ DescrStatsW CompareMeans ttest_ind ttost_ind ttost_paired ztest ztost zconfint weightstats also contains tests and confidence intervals based on summary data .. currentmodule:: statsmodels.stats.weightstats .. autosummary:: :toctree: generated/ _tconfint_generic _tstat_generic _zconfint_generic _zstat_generic _zstat_generic2 Power and Sample Size Calculations ---------------------------------- The :mod:`power` module currently implements power and sample size calculations for the t-tests, normal based test, F-tests and Chisquare goodness of fit test. The implementation is class based, but the module also provides three shortcut functions, ``tt_solve_power``, ``tt_ind_solve_power`` and ``zt_ind_solve_power`` to solve for any one of the parameters of the power equations. .. module:: statsmodels.stats.power :synopsis: Power and size calculations for common tests .. currentmodule:: statsmodels.stats.power .. autosummary:: :toctree: generated/ TTestIndPower TTestPower GofChisquarePower NormalIndPower FTestAnovaPower FTestPower normal_power_het normal_sample_size_one_tail tt_solve_power tt_ind_solve_power zt_ind_solve_power .. _proportion_stats: Proportion ---------- Also available are hypothesis test, confidence intervals and effect size for proportions that can be used with NormalIndPower. .. module:: statsmodels.stats.proportion :synopsis: Tests for proportions .. currentmodule:: statsmodels.stats.proportion .. autosummary:: :toctree: generated proportion_confint proportion_effectsize binom_test binom_test_reject_interval binom_tost binom_tost_reject_interval multinomial_proportions_confint proportions_ztest proportions_ztost proportions_chisquare proportions_chisquare_allpairs proportions_chisquare_pairscontrol proportion_effectsize power_binom_tost power_ztost_prop samplesize_confint_proportion Statistics for two independent samples Status: experimental, API might change, added in 0.12 .. autosummary:: :toctree: generated test_proportions_2indep confint_proportions_2indep power_proportions_2indep tost_proportions_2indep samplesize_proportions_2indep_onetail score_test_proportions_2indep _score_confint_inversion Rates ----- Statistical functions for rates. This currently includes hypothesis tests for two independent samples. Status: experimental, API might change, added in 0.12 .. module:: statsmodels.stats.rates :synopsis: Tests for Poisson rates .. currentmodule:: statsmodels.stats.rates .. autosummary:: :toctree: generated test_poisson_2indep etest_poisson_2indep tost_poisson_2indep Multivariate ------------ Statistical functions for multivariate samples. This includes hypothesis test and confidence intervals for mean of sample of multivariate observations and hypothesis tests for the structure of a covariance matrix. Status: experimental, API might change, added in 0.12 .. module:: statsmodels.stats.multivariate :synopsis: Statistical functions for multivariate samples. .. currentmodule:: statsmodels.stats.multivariate .. autosummary:: :toctree: generated test_mvmean confint_mvmean confint_mvmean_fromstats test_mvmean_2indep test_cov test_cov_blockdiagonal test_cov_diagonal test_cov_oneway test_cov_spherical .. _oneway_stats: Oneway Anova ------------ Hypothesis test, confidence intervals and effect size for oneway analysis of k samples. Status: experimental, API might change, added in 0.12 .. module:: statsmodels.stats.oneway :synopsis: Statistical functions for oneway analysis, Anova. .. currentmodule:: statsmodels.stats.oneway .. autosummary:: :toctree: generated anova_oneway anova_generic equivalence_oneway equivalence_oneway_generic power_equivalence_oneway _power_equivalence_oneway_emp test_scale_oneway equivalence_scale_oneway confint_effectsize_oneway confint_noncentrality convert_effectsize_fsqu effectsize_oneway f2_to_wellek fstat_to_wellek wellek_to_f2 _fstat2effectsize scale_transform simulate_power_equivalence_oneway .. _robust_stats: Robust, Trimmed Statistics -------------------------- Statistics for samples that are trimmed at a fixed fraction. This includes class TrimmedMean for one sample statistics. It is used in `stats.oneway` for trimmed "Yuen" Anova. Status: experimental, API might change, added in 0.12 .. module:: statsmodels.stats.robust_compare :synopsis: Trimmed sample statistics. .. currentmodule:: statsmodels.stats.robust_compare .. autosummary:: :toctree: generated TrimmedMean scale_transform trim_mean trimboth Moment Helpers -------------- When there are missing values, then it is possible that a correlation or covariance matrix is not positive semi-definite. The following functions can be used to find a correlation or covariance matrix that is positive definite and close to the original matrix. Additional functions estimate spatial covariance matrix and regularized inverse covariance or precision matrix. .. module:: statsmodels.stats.correlation_tools :synopsis: Procedures for ensuring correlations are positive semi-definite .. currentmodule:: statsmodels.stats.correlation_tools .. autosummary:: :toctree: generated/ corr_clipped corr_nearest corr_nearest_factor corr_thresholded cov_nearest cov_nearest_factor_homog FactoredPSDMatrix kernel_covariance .. currentmodule:: statsmodels.stats.regularized_covariance .. autosummary:: :toctree: generated/ RegularizedInvCovariance These are utility functions to convert between central and non-central moments, skew, kurtosis and cummulants. .. module:: statsmodels.stats.moment_helpers :synopsis: Tools for converting moments .. currentmodule:: statsmodels.stats.moment_helpers .. autosummary:: :toctree: generated/ cum2mc mc2mnc mc2mvsk mnc2cum mnc2mc mnc2mvsk mvsk2mc mvsk2mnc cov2corr corr2cov se_cov Mediation Analysis ------------------ Mediation analysis focuses on the relationships among three key variables: an 'outcome', a 'treatment', and a 'mediator'. Since mediation analysis is a form of causal inference, there are several assumptions involved that are difficult or impossible to verify. Ideally, mediation analysis is conducted in the context of an experiment such as this one in which the treatment is randomly assigned. It is also common for people to conduct mediation analyses using observational data in which the treatment may be thought of as an 'exposure'. The assumptions behind mediation analysis are even more difficult to verify in an observational setting. .. module:: statsmodels.stats.mediation :synopsis: Mediation analysis .. currentmodule:: statsmodels.stats.mediation .. autosummary:: :toctree: generated/ Mediation MediationResults Oaxaca-Blinder Decomposition ---------------------------- The Oaxaca-Blinder, or Blinder-Oaxaca as some call it, decomposition attempts to explain gaps in means of groups. It uses the linear models of two given regression equations to show what is explained by regression coefficients and known data and what is unexplained using the same data. There are two types of Oaxaca-Blinder decompositions, the two-fold and the three-fold, both of which can and are used in Economics Literature to discuss differences in groups. This method helps classify discrimination or unobserved effects. This function attempts to port the functionality of the oaxaca command in STATA to Python. .. module:: statsmodels.stats.oaxaca :synopsis: Oaxaca-Blinder Decomposition .. currentmodule:: statsmodels.stats.oaxaca .. autosummary:: :toctree: generated/ OaxacaBlinder OaxacaResults Distance Dependence Measures ---------------------------- Distance dependence measures and the Distance Covariance (dCov) test. .. module:: statsmodels.stats.dist_dependence_measures :synopsis: Distance Dependence Measures .. currentmodule:: statsmodels.stats.dist_dependence_measures .. autosummary:: :toctree: generated/ distance_covariance_test distance_statistics distance_correlation distance_covariance distance_variance Meta-Analysis ------------- Functions for basic meta-analysis of a collection of sample statistics. Examples can be found in the notebook * `Meta-Analysis `__ Status: experimental, API might change, added in 0.12 .. module:: statsmodels.stats.meta_analysis :synopsis: Meta-Analysis .. currentmodule:: statsmodels.stats.meta_analysis .. autosummary:: :toctree: generated/ combine_effects effectsize_2proportions effectsize_smd CombineResults The module also includes internal functions to compute random effects variance. .. autosummary:: :toctree: generated/ _fit_tau_iter_mm _fit_tau_iterative _fit_tau_mm