*.cf                    Divide two cf objects by each other measurement
                        by measurement
*.raw_cf                multiply two 'raw_cf' objects
+.cf                    Arithmetically add correlators
+.raw_cf                add two 'raw_cf' objects
-.cf                    Arithmetically subtract correlators
-.raw_cf                add two 'raw_cf' objects
/.raw_cf                divide two 'raw_cf' objects
CExp                    Cosh Or Sinh Build Out Of Two Exps
add.cf                  Arithmetically adds two correlation functions
add.raw_cf              add two 'raw_cf' objects
addConfIndex2cf         add a configuration index to an 'cf' object
addStat.cf              Combine statistics of two cf objects
addStat.raw_cf          Extend statistics of an existing 'raw_cf'
                        container
alphas                  compute alpha strong at given scale
analysis_gradient_flow
                        analysis_gradient_flow
analysis_online         analysis_online
avg.cbt.cf              average close-by-times in a correlation
                        function
block.raw_cf            Block average correlation function data
bootstrap.analysis      Performs a Bootstrap with Blocking Analysis of
                        a Timeseries
bootstrap.cf            bootstrap a set of correlation functions
bootstrap.effectivemass
                        Computes effective masses with bootstrapping
                        errors
bootstrap.gevp          perform a bootstrap analysis of a GEVP
bootstrap.hankel        GEVP method based on Hankel matrices.
bootstrap.hankel_summed
                        GEVP method based on Hankel matrices.
bootstrap.meanerror     Compute the bootstrap error of the mean
bootstrap.nlsfit        Bootstrap a non-linear least-squares fit
c.cf                    Concatenate correlation function objects
c.raw_cf                Concatenate 'raw_cf' correlation function
                        objects
cA2.09.48_3pi_I3_0_A1u_1_pc
                        A three pion correlator with significant
                        thermal states.
cdh                     finite size corrections a la Colangelo, Duerr,
                        Haefeli
cdhnew                  finite size corrections a la Colangelo, Duerr,
                        Haefeli, but re-expanded as series in the quark
                        mass
cf                      Correlation function container
cf_boot                 Bootstrapped CF mixin constructor
cf_key_meson_2pt        Generate key string to identify a meson 2pt
                        function
cf_key_meson_3pt        Generate HDF5 key for CVC 'correlators' meson
                        3pt function with a local or derivative
                        insertion The key for a meson three-point
                        function has the form:
                        /sud+-g-u-g/t10/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D.../gi5/pix0piy0piz0
                        where, from left to right: • 'u' is the flavour
                        of the "backward" propagator • 'd' is the
                        flavour of the "sequential" propagator • '+'
                        indicates that 'sud' is daggered • 'g'
                        indicates a gamma insertion • 'u' is the
                        flavour of the foward propagator • 'g'
                        indicates a Dirac structure at the source •
                        'tXX' is the source time slice • 'dtYY' is the
                        source-sink separation • 'gfN' gamma structure
                        at the sink in CVC indexing • 'pfxXpfyYpfzZ' is
                        the sink momentum in CVC convention (sink and
                        source phases are both e^ipx) • 'gcN' gamma
                        structure at the current insertion point in CVC
                        indexing • 'DdimJ_dirK' covariant displacement
                        applied in dimension 'J', direction 'K' where
                        it should be noted that this is. in operator
                        notation, i.e., the right-most displacement is
                        the one applied first.  • ...  • 'giN' gamma
                        structure at the souce in CVC indexing •
                        'pixXpiyYpizZ' at the source in CVC convention
cf_meta                 CF metadata mixin constructor
cf_orig                 Original data CF mixin constructor
cf_principal_correlator
                        Principal correlator CF mixin constructor
cf_shifted              Shifted CF mixin constructor
cf_smeared              Smeared CF mixin constructor
cf_subtracted           Subtracted CF mixin constructor
cf_weighted             Weighted CF mixin constructor
compute.plotlims        compute.plotlims
computeDisc             computes a disconnected correlation function
                        from loops
computeacf              Computes The ACF and Integrated AC Time
computefps              Computes the pseudoscalar decay constant for
                        the twisted mass case from the pseudoscalar
                        amplitude and mass
computefpsOS            Computes the pseudoscalar decay constant for
                        the Osterwalder Seiler case from the
                        pseudoscalar amplitude and mass
concat.cf               Concatenate two correlation function objects
concat.raw_cf           Concatenate two 'raw_cf' correlation function
                        objects
conj_raw_cf             Take the complex conjugate of a 'raw_cf' object
construct_onlinemeas_rundir
                        Construct a run directory string for
                        analysis_online
correlatormatrix        Sample correlator matrix
correlators_key_meson_2pt
                        Generate HDF5 key for CVC 'correlators' meson
                        2pt function
correlators_key_meson_3pt
                        Generate HDF5 key for CVC 'correlators' meson
                        3pt function with a local or derivative
                        insertion The key for a meson three-point
                        function has the form:
                        /sud+-g-u-g/t10/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D.../gi5/pix0piy0piz0
                        where, from left to right: • 'u' is the flavour
                        of the "backward" propagator • 'd' is the
                        flavour of the "sequential" propagator • '+'
                        indicates that 'sud' is daggered • 'g'
                        indicates a gamma insertion • 'u' is the
                        flavour of the foward propagator • 'g'
                        indicates a Dirac structure at the source •
                        'tXX' is the source time slice • 'dtYY' is the
                        source-sink separation • 'gfN' gamma structure
                        at the sink in CVC indexing • 'pfxXpfyYpfzZ' is
                        the sink momentum in CVC convention (sink and
                        source phases are both e^ipx) • 'gcN' gamma
                        structure at the current insertion point in CVC
                        indexing • 'DdimJ_dirK' covariant displacement
                        applied in dimension 'J', direction 'K' where
                        it should be noted that this is. in operator
                        notation, i.e., the right-most displacement is
                        the one applied first.  • ...  • 'giN' gamma
                        structure at the souce in CVC indexing •
                        'pixXpiyYpizZ' at the source in CVC convention
create_displ_chains     create list of chains of displacements Multilpe
                        covariant displacements, when applied in order,
                        form a list of displacments. Each consists of a
                        direction and a dimension.
cvc_local_loop_key      Generate HDF5 key for a momentum and
                        spin-projected CVC loop
cvc_read_loops          read HDF5 loop files in the CVC loop format
cvc_to_raw_cf           Convert correlation function read from CVC HDF5
                        or AFF format to 'raw_cf'
cyprus_make_key_scalar
                        HDF5 key for Cyprus CalcLoops scalar-type loops
cyprus_make_key_vector
                        HDF5 key for Cyprus CalcLoops derivative-type
                        loops
cyprus_read_loops       read HDF5 loop files in the Cyprus CalcLoops
                        format
disc_3pt                disconnected contribution to current insertion
                        three-point function
dispersion_relation     Continuum dispersion relation for CM to lattice
                        frame
effectivemass           effectivemass
effectivemass.cf        Computes effective mass values for a
                        correlation function
effmass                 effmass
effmass2                effmass2
escapeLatexSpecials     Escape special LaTeX characters for use in
                        LaTeX labels
extract.loop            Extract a single loop from an object of class
                        'cmiloop'
extract.obs             Extract One or More Gamma Combinations from am
                        CMI Correlator
extractSingleCor.cf     extract one single correlator object as 'cf'
                        object from a large 'cf' object.
extract_mass            generic function to extract a fitted mass
extract_mass.effectivemassfit
                        specialisation of extract_mass to objects of
                        type 'effectivemassfit'
extract_mass.matrixfit
                        specialisation of extract_mass to objects of
                        type 'matrixfit'
fit.cosh                Fits a sum of several 'cosh'-functions
fit.effectivemass       Fits a constant to effective mass data
fit.plateau2cf          fits a plateau to an object of class 'cf'
foldr1                  Folds the non-empty list with the binary
                        function
fs.a0                   Finite Size Corrections to qcotdelta for I=2
                        pipi near threshold
fs.mpia0                Finite Size Corrections to qcotdelta for I=2
                        pipi near threshold
fs.qcotdelta            Finite Size Corrections to qcotdelta for I=2
                        pipi near threshold
g1                      g1
get_plotdata_raw_cf     extract data from 'raw_cf' in format convenient
                        to plot
getorderedconfignumbers
                        Creates an ordered vector of gauge config file
                        numbers
getorderedfilelist      Creates an ordered filelist from a basename and
                        a path
gevp                    solve GEVP for correlator matrix
gevp.hankel             GEVP method based on Hankel matrices.
gevp.hankel_summed      GEVP method based on Hankel matrices.
gevp2amplitude          Extracts physical amplitudes from a GEVP
gevp2cf                 Extracts a principle correlator from a GEVEP
gm                      List of arrays of gamma structures
gm_mu                   Accessor function for 'gm'
h5_get_dataset          get dataset from HDF5 file
h5_names_exist          check if group names exist in HDF5 file
hadron                  The Hadron Package
hankel2cf               hankel2cf
hankel2effectivemass    hankel2effectivemass
hankeldensity2effectivemass
                        hankeldensity2effectivemass
has_icf                 Checks whether the cf object contains an
                        imaginary part
idx_matrix.raw_cf       Construct the tensor index set for the entire
                        raw correlator
int_idx_matrix.raw_cf   Construct tensor index set for the internal
                        degrees of freedom
invalidate.samples.cf   Invalidate samples
invcosh                 numerically invert the cosh function for the
                        mass
invertCovMatrix         Inverts the covariance matrix for noisy data
is.cf                   Checks whether an object is a cf
is.raw_cf               check if an object is of class 'raw_cf'
is_empty.cf             Checks whether the cf object contains no data
is_empty.raw_cf         check if an obect is of class 'raw_cf' and
                        empty otherwise
jackknife.cf            jackknife a set of correlation functions
jackknife_cov           jackknife_cov
jackknife_error         Estimates error from jackknife samples
loop_2pt                compute two-point correlation function between
                        quark loops
loop_spin_project       spin projection of quark loop data
loop_stochav            average over stochastic samples of loop
loop_vev_subtract       subtract vev from loop data
loopdata                Sample loop data
make_parind             Create a parameter index matrix for 'matrixfit'
make_parlist            Create a parameter list for 'matrixfit'
matrixModel             Correlator matrix model.
matrixfit               Routine For A Factorising Matrix Fit
mom_combinations        Generate table of momentum component
                        combinations
mul.cf                  Arithmetically scale a correlator by a scalar a
mul.raw_cf              scale 'raw_cf' data
new_matrixfit           perform a factorising fit of a matrix of
                        correlation functions
old_removeTemporal.cf   Remove temporal states
onlinemeas              determines pion mass and pcac mass from online
                        measured correlator of the HMC code
overview_plot_raw_cf    create convenient overview plots for a 'raw_cf'
                        object
parametric.bootstrap    Parametric bootstrap
parametric.bootstrap.cov
                        Parametric bootstrap with covariance
parametric.nlsfit       NLS fit with parametric bootstrap
parametric.nlsfit.cov   parametric.nlsfit.cov
pcModel                 Principal correlator two state model.
pcac                    Computes the pcac mass
pcacfit                 pcacfit
plaq.sample             Sample plaquette time series
plot.averx              Plots averx data
plot.bootstrapfit       Plot a bootstrap NLS fit
plot.cf                 Plot a correlation function
plot.cfit               plot.c1fit
plot.coshfit            Plot a cosh-fit
plot.effectivemass      plot.effectivemass
plot.effmass            plot.effmass
plot.gevp.amplitude     plot.gevp.amplitude
plot.hadronacf          plot.hadronacf
plot.massfit            plot.massfit
plot.matrixfit          Plot a matrixfit
plot.ofit               plot.ofit
plot.outputdata         Plot Command For Class Ouputdata
plot.pionff             plot.pionff
plot.raw_cf             plot all correlators in 'raw_cf' object
plot.uwerr              Plot Command For Class UWerr
plot_eigenvalue_timeseries
                        plot_eigenvalue_timeseries
plot_hankel_spectrum    plot_hankel_spectrum
plot_timeseries         plot_timeseries
plothlinewitherror      plothlinewitherror
plotwitherror           Plot Command For XY Plots With Error Bars
pointswithslantederror
                        pointswithslantederror
print.bootstrapfit      Print a bootstrap NLS fit
print.cf                print.cf
print.effectivemassfit
                        print.effectivemassfit
print.ofit              print.ofit
print.raw_cf            Print summary of data contained in 'raw_cf'
                        container
pscor.sample            Sample pseudoscalar correlator
raw_cf                  Container for raw correlation functions
raw_cf_data             Original data mixin constructor for 'raw_cf'
raw_cf_meta             'raw_cf' metadata mixin constructor
raw_cf_to_cf            Extract a particular internal component of a
                        'raw_cf' into a 'cf'
readbinarycf            read correlation function from binary files
readbinarydisc          read disconnected loops from binary files
readbinarysamples       Read binary correlation function by sample
readcmidisc             reads disconnected loops in cmi format
readcmifiles            Read Single Data Files in Chris Michael Format
readgradflow            Read Gradient Flow Output Files in tmLQCD
                        format
readhlcor               readhlcor
readnissatextcf         reader for Nissa text format correlation
                        functions
readoutputdata          Read Data In output.data Format of tmLQCD
readtextcf              Read correlator data from single file
removeTemporal.cf       Remove Thermal States by Weighting and Shifting
resample_hankel         Resample bootstrap samples in Hankel effmass
resampling_is_compatible
                        Checks whether the resampling of two cf objects
                        is compatible
resampling_is_concatenable
                        Checks whether the resampling of two cf objects
                        is concatenable
residual_plot           residual_plot
restore_seed            Restore random number generator state
samplecf                Sample cf data
shift.cf                shift a correlation function by 'places'
                        time-slices
shift.raw_cf            shift a 'raw_cf' correlation function by
                        'places' time-slices
simple.nlsfit           NLS fit with without bootstrap
store_correl            Store a 'raw_cf' correlator in an associative
                        array together with a description The object
                        'cf' will be stored as an element of 'cmap'
                        under key 'out_key' in the member 'obj' of
                        'cmap'. The data frame passed via 'desc' will
                        be appended as a row to 'cmap[[out_key]]$map'.
                        If 'out_key' does not exist as a key in 'cmap',
                        a new element will be created. If it already
                        exists, 'addStat.raw_cf' is called to add
                        statistics to the existing 'raw_cf'. Requires
                        the 'hash' package.
string2error            string2error
subtract.excitedstates
                        Substract excited states.
summary.bootstrapfit    Summarize a bootstrap NLS fit
summary.cf              summary.cf
summary.coshfit         Summarize a cosh-fit
summary.effectivemass   summary.effectivemass
summary.effectivemassfit
                        summary.effectivemassfit
summary.gevp.amplitude
                        summary.gevp.amplitude
summary.hadronacf       summary.hadronacf
summary.hankel_summed   summary.hankel_summed
summary.matrixfit       summary.matrixfit
summary.ofit            summary.ofit
summary.raw_cf          Print summary of data contained in 'raw_cf'
                        container
summary.uwerr           summary.uwerr
swap_seed               Set seed and store a seed which can be used to
                        reset the random number generator
symmetrise.cf           Average backward and forward-dominated parts of
                        the correlation function
takeTimeDiff.cf         Take time difference
tex.catwitherror        paste a number with error in tex-ready format
tikz.finalize           tikz.finalize
tikz.init               tikz.init
unsymmetrise.cf         Unfold a correlation function which has been
                        symmetrised
uwerr                   Time Series Analysis With Gamma Method
uwerr.cf                uwerr.cf
uwerr.raw_cf            Gamma method analysis on all time-slices in a
                        'raw_cf' object
weight.cf               Weight a correlation function
weight_shift_reweight.cf
                        Weight-shift-reweight a correlation function
zetazp                  Computes the running of Z_P from scale mu0 to
                        scale mu2
