Standard Library Overview ============================== The CosmoSIS standard library is a collection of modules designed for Cosmological parameter estimation. You can couple together pieces of it to build analysis piplines. Background ----------------------- These modules calculate quantities related to the average background expansion of the Universe. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`distances <../reference/standard_library/distances>` - Output cosmological distance measures for dynamical dark energy * - :doc:`growth_factor <../reference/standard_library/growth_factor>` - returns linear growth factor and growth rate for flat cosmology with either const w or variable DE eos w(a) = w + (1-a)*wa * - :doc:`astropy_background <../reference/standard_library/astropy_background>` - Calculate background cosmology using astropy * - :doc:`log_w_model <../reference/standard_library/log_w_model>` - Implement Tripathi, Sangwan, Jassal (2017) w(z) model Boltzmann ----------------------- Boltzmann codes evolve cosmic perturbations from the early Universe through recombination and to late times, and power spectra of matter, the CMB, and other quantities. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`mgcamb <../reference/standard_library/mgcamb>` - Modified Gravity Boltzmann and background integrator for BG, CMB, and matter power * - :doc:`isitgr-camb <../reference/standard_library/isitgr-camb>` - Modified version of CAMB to implement phenomenological modified gravity models * - :doc:`class <../reference/standard_library/class>` - Boltzmann and background integrator for BG, CMB, matter power, and more * - :doc:`camb <../reference/standard_library/camb>` - Boltzmann and background integrator for BG, CMB, and matter power Emulators ----------------------- These modules emulate aspects of cosmic structure based on fits to simulations. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`bacco_emulator <../reference/standard_library/bacco_emulator>` - Emulate the non-linear, baryonified, matter power spectrum * - :doc:`FrankenEmu <../reference/standard_library/FrankenEmu>` - Emulate N-body simulations to compute nonlinear matter power * - :doc:`EuclidEmulator2 <../reference/standard_library/EuclidEmulator2>` - Emulate the boost factors that convert the linear to non-linear power spectrum, including baryon corrections * - :doc:`CosmicEmu <../reference/standard_library/CosmicEmu>` - Emulate N-body simulations to compute nonlinear matter power Structure ----------------------- These modules compute aspects of cosmic structure, for example by integrating over cosmic structure, or calculating halo model quantities. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`sigma_r <../reference/standard_library/sigma_r>` - Compute anisotropy dispersion sigma(R,z) * - :doc:`extract_growth <../reference/standard_library/extract_growth>` - returns growth factor and growth rate by examining small-scale P(k) * - :doc:`NLfactor <../reference/standard_library/NLfactor>` - Compute nonlinear weyl potential (and other) spectrum by multiplying the linear spectrum with matter_power_nl/matter_power_lin * - :doc:`constant_bias <../reference/standard_library/constant_bias>` - Apply a galaxy bias constant with k and z. * - :doc:`sigma_cpp <../reference/standard_library/sigma_cpp>` - Compute anisotropy dispersion sigma(R,z) in cpp * - :doc:`Press_Schechter_MF <../reference/standard_library/Press_Schechter_MF>` - Code to compute the PressSchechter mass function given Pk from CAMB, based on Komatsu's CRL * - :doc:`Extreme_Value_Statistics <../reference/standard_library/Extreme_Value_Statistics>` - PDF of the maximum cluster mass given cosmological parameters * - :doc:`pyhmcode <../reference/standard_library/pyhmcode>` - Compute the non-linear matter power spectrum with pyhalofit * - :doc:`extrapolate <../reference/standard_library/extrapolate>` - Simple log-linear extrapolation of P(k) to high k * - :doc:`CRL_Eisenstein_Hu <../reference/standard_library/CRL_Eisenstein_Hu>` - Komatsu's CRL code to compute the power spectrum using EH fitting formula. * - :doc:`Tinker_MF <../reference/standard_library/Tinker_MF>` - Code to compute the Tinker et al. mass function given Pk from CAMB, based on Komatsu's CRL * - :doc:`Sheth-Tormen MF <../reference/standard_library/Sheth-Tormen MF>` - Code to compute the Sheth-Tormen mass function given Pk from CAMB, based on Komatsu's CRL Two-point Mathemetics ----------------------- These modules perform mathematical claculations associated with two-point statistics, mostly on a sphere. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`cosebis <../reference/standard_library/cosebis>` - Calculate COSEBIs from C_ell power spectra * - :doc:`wl_spectra_ppf <../reference/standard_library/wl_spectra_ppf>` - Compute weak lensing C_ell from P(k,z) and MG D(k,z) with the Limber integral * - :doc:`cl_to_xi_wigner_d <../reference/standard_library/cl_to_xi_wigner_d>` - Compute correlation functions from power spectra * - :doc:`cl_to_corr <../reference/standard_library/cl_to_corr>` - Compute correlation functions xi+, xi-, w, and gamma_t from C_ell * - :doc:`project_2d <../reference/standard_library/project_2d>` - Project 3D power spectra to 2D tomographic bins using the Limber approximation * - :doc:`cl_to_xi_nicaea <../reference/standard_library/cl_to_xi_nicaea>` - Compute WL correlation functions xi+, xi- from C_ell * - :doc:`wl_spectra <../reference/standard_library/wl_spectra>` - Compute various weak lensing C\_ell from P(k,z) with the Limber integral Two-point Systematics ----------------------- These modules compute and apply quantities associated with systematics errors on two-point (and potentially other) quantities. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`shear_bias <../reference/standard_library/shear_bias>` - Modify a set of calculated shear C_ell with a multiplicative bias * - :doc:`add_magnification <../reference/standard_library/add_magnification>` - Add magnification terms to C_ell * - :doc:`clerkin <../reference/standard_library/clerkin>` - Compute galaxy bias as function of k, z for 3-parameter Clerkin et al 2014 model * - :doc:`constant_bias <../reference/standard_library/constant_bias>` - Apply a galaxy bias constant with k and z. * - :doc:`ia_z_powerlaw <../reference/standard_library/ia_z_powerlaw>` - Add redshift dependence to IA model * - :doc:`kappa_beam <../reference/standard_library/kappa_beam>` - Apply smoothing function to cross-correlations with CMB kappa in harmonic space. * - :doc:`no_bias <../reference/standard_library/no_bias>` - Generate galaxy power P(k) as though galaxies were unbiased DM tracers * - :doc:`baryonic <../reference/standard_library/baryonic>` - Apply baryonic effects to nonlinear pk based on hydrodynamic simulation measurements * - :doc:`kappa_ell_cut <../reference/standard_library/kappa_ell_cut>` - Apply minimum and maximum ell to cross-power spectra with CMB kappa. * - :doc:`add_intrinsic <../reference/standard_library/add_intrinsic>` - Sum together intrinsic aligments with shear signal * - :doc:`apply_astrophysical_biases <../reference/standard_library/apply_astrophysical_biases>` - Apply various astrophysical biases to the matter power spectrum P(k,z) * - :doc:`linear_alignments <../reference/standard_library/linear_alignments>` - Compute the terms P_II and P_GI which go into intrinsic aligment calculations Sample Properties ----------------------- These modules compute properties, mostly number density, of galaxy samples. .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`smail <../reference/standard_library/smail>` - Compute window functions for photometric n(z) * - :doc:`photoz_bias <../reference/standard_library/photoz_bias>` - Modify a set of loaded n(z) distributions with a multiplicative or additive bias * - :doc:`Joachimi_Bridle_alpha <../reference/standard_library/Joachimi_Bridle_alpha>` - Calculate the gradient of the galaxy luminosity function at the limiting magnitude of the survey. * - :doc:`gaussian_window <../reference/standard_library/gaussian_window>` - Compute Gaussian n(z) window functions for weak lensing bins * - :doc:`nz_multirank <../reference/standard_library/nz_multirank>` - Load, rank, and sample a set of density n(z) realisations from a FITS file * - :doc:`load_nz <../reference/standard_library/load_nz>` - Load a number density n(z) for weak lensing from a file * - :doc:`load_nz_fits <../reference/standard_library/load_nz_fits>` - Load a number density n(z) from a FITS file Likelihoods ----------------------- These module provide likelihoods that compare theory predictions to data .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`Cluster_mass <../reference/standard_library/Cluster_mass>` - Likelihood of z=1.59 Cluster mass from Santos et al. 2011 * - :doc:`des-y3-bao <../reference/standard_library/des-y3-bao>` - Compute the likelihood of DES Y3 BAO data * - :doc:`eboss_dr16_qso <../reference/standard_library/eboss_dr16_qso>` - Compute the likelihood of eBOSS DR16 from QSO * - :doc:`BOSS <../reference/standard_library/BOSS>` - Compute the likelihood of supplied fsigma8(z=0.57), H(z=0.57), D_a(z=0.57), omegamh2, bsigma8(z=0.57) * - :doc:`h0licow <../reference/standard_library/h0licow>` - * - :doc:`2pt <../reference/standard_library/2pt>` - Generic 2-point measurement Gaussian likelihood * - :doc:`mgs_bao <../reference/standard_library/mgs_bao>` - Compute the likelihood against SDSS MGS data * - :doc:`Riess16 <../reference/standard_library/Riess16>` - Likelihood of hubble parameter H0 from Riess et al 2.4% supernova sample * - :doc:`eboss_dr16_lya <../reference/standard_library/eboss_dr16_lya>` - Compute the likelihood of eBOSS DR16 from Lyman alpha * - :doc:`planck_sz <../reference/standard_library/planck_sz>` - Prior on sigma_8 * Omega_M ** 0.3 from Planck SZ cluster counts * - :doc:`eboss_dr14_lya <../reference/standard_library/eboss_dr14_lya>` - Compute the likelihood of eBOSS DR14 D_m and D_h from Lyman alpha * - :doc:`planck2018 <../reference/standard_library/planck2018>` - Likelihood function of CMB from Planck 2015 data * - :doc:`Riess21 <../reference/standard_library/Riess21>` - Likelihood of hubble parameter H0 from Riess et al supernova sample * - :doc:`WiggleZBao <../reference/standard_library/WiggleZBao>` - Compute the likelihood of the supplied expansion history against WiggleZ BAO data * - :doc:`wmap <../reference/standard_library/wmap>` - Likelihood function of CMB from WMAP * - :doc:`pantheon <../reference/standard_library/pantheon>` - Likelihood of the Pantheon supernova analysis * - :doc:`boss_dr12 <../reference/standard_library/boss_dr12>` - Compute the likelihood of the supplied expansion and growth history against BOSS DR12 data * - :doc:`mgs <../reference/standard_library/mgs>` - Compute the likelihood of MGS BAO and FS as distributed by eBOSS DR16 * - :doc:`jla <../reference/standard_library/jla>` - Supernova likelihood for SDSS-II/SNLS3 * - :doc:`qso <../reference/standard_library/qso>` - Compute the likelihood of eBOSS DR14 D_v from QSO * - :doc:`boss_dr12_lrg_reanalyze <../reference/standard_library/boss_dr12_lrg_reanalyze>` - Compute the likelihood of the supplied expansion and growth history against BOSS DR12 data as reanalyzed by eBOSS DR16 * - :doc:`BBN <../reference/standard_library/BBN>` - Simple prior on Omega_b h^2 from light element abundances * - :doc:`6dFGS <../reference/standard_library/6dFGS>` - Compute the likelihood of supplied D_v or fsigma8(z=0.067) * - :doc:`strong_lens_time_delays <../reference/standard_library/strong_lens_time_delays>` - * - :doc:`act-dr6-lens <../reference/standard_library/act-dr6-lens>` - CMB Lensing from ACT DR6 data. * - :doc:`planck_py <../reference/standard_library/planck_py>` - Lightweight python-based Planck likelihood code * - :doc:`fgas <../reference/standard_library/fgas>` - Likelihood of galaxy cluster gas-mass fractions * - :doc:`eboss_dr16_lrg <../reference/standard_library/eboss_dr16_lrg>` - Compute the likelihood of eBOSS DR16 from LRG * - :doc:`lrg <../reference/standard_library/lrg>` - Compute the likelihood of eBOSS DR14 D_v from LRG * - :doc:`pantheon_plus <../reference/standard_library/pantheon_plus>` - Likelihood of the Pantheon+ supernova analysis optionally combined with the SH0ES H0 measurement * - :doc:`eboss_dr16_elg <../reference/standard_library/eboss_dr16_elg>` - Compute the likelihood of eBOSS DR16 from ELG * - :doc:`JulloLikelihood <../reference/standard_library/JulloLikelihood>` - Likelihood of Jullo et al (2012) measurements of a galaxy bias sample * - :doc:`Riess11 <../reference/standard_library/Riess11>` - Likelihood of hubble parameter H0 from Riess et al supernova sample * - :doc:`balmes <../reference/standard_library/balmes>` - * - :doc:`wmap_shift <../reference/standard_library/wmap_shift>` - Massively simplified WMAP9 likelihood reduced to just shift parameter * - :doc:`BICEP2 <../reference/standard_library/BICEP2>` - Compute the likelihood of the supplied CMB power spectra Misc & Utilities ----------------------- These modules supply special utilities or calculation tools .. list-table:: :header-rows: 1 * - Name - Purpose * - :doc:`fast_pt <../reference/standard_library/fast_pt>` - Compute various 1-loop perturbation theory quantities * - :doc:`sigma8_rescale <../reference/standard_library/sigma8_rescale>` - Rescale structure measures to use a specified sigma_8 * - :doc:`stop <../reference/standard_library/stop>` - Enters python debugger. * - :doc:`copy <../reference/standard_library/copy>` - Copy a section to a new section * - :doc:`BBN-Consistency <../reference/standard_library/BBN-Consistency>` - Compute consistent Helium fraction from baryon density given BBN * - :doc:`rename <../reference/standard_library/rename>` - Rename a section to a new name * - :doc:`correlated_priors <../reference/standard_library/correlated_priors>` - Include correlations between nusiance parameters * - :doc:`w0wa_sum_prior <../reference/standard_library/w0wa_sum_prior>` - Skip parameter sample without failing if w0+wa>0. * - :doc:`delete <../reference/standard_library/delete>` - Enters python debugger. * - :doc:`consistency <../reference/standard_library/consistency>` - Deduce missing cosmological parameters and check consistency