# Analysis Framework for Monte Carlo Simulation Data in Physics

## Documentation for package ‘hadron’ version 3.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J L M N O P R S T U W Z misc

## -- A --

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

## -- B --

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 --

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
CExp | Cosh Or Sinh Build Out Of Two Exps
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
computeacf | Computes The ACF and Integrated AC Time
computeDisc | computes a disconnected correlation function from loops
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

## -- D --

disc_3pt | disconnected contribution to current insertion three-point function
dispersion_relation | Continuum dispersion relation for CM to lattice frame

## -- E --

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'

## -- F --

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

## -- G --

g1 | g1
getorderedconfignumbers | Creates an ordered vector of gauge config file numbers
getorderedfilelist | Creates an ordered filelist from a basename and a path
get_plotdata_raw_cf | extract data from 'raw_cf' in format convenient to plot
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'

## -- H --

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

## -- I --

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

## -- J --

jackknife.cf | jackknife a set of correlation functions
jackknife_cov | jackknife_cov
jackknife_error | Estimates error from jackknife samples

## -- L --

loopdata | Sample loop data
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

## -- M --

make_parind | Create a parameter index matrix for 'matrixfit'
make_parlist | Create a parameter list for 'matrixfit'
matrixfit | Routine For A Factorising Matrix Fit
matrixModel | Correlator matrix model.
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

## -- N --

new_matrixfit | perform a factorising fit of a matrix of correlation functions

## -- O --

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

## -- P --

parametric.bootstrap | Parametric bootstrap
parametric.bootstrap.cov | Parametric bootstrap with covariance
parametric.nlsfit | NLS fit with parametric bootstrap
parametric.nlsfit.cov | parametric.nlsfit.cov
pcac | Computes the pcac mass
pcacfit | pcacfit
pcModel | Principal correlator two state model.
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
plothlinewitherror | plothlinewitherror
plotwitherror | Plot Command For XY Plots With Error Bars
plot_eigenvalue_timeseries | plot_eigenvalue_timeseries
plot_hankel_spectrum | plot_hankel_spectrum
plot_timeseries | plot_timeseries
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

## -- R --

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
readcmicor | Read Single Data Files in Chris Michael Format
readcmidatafiles | Read Single Data Files in Chris Michael Format
readcmidisc | reads disconnected loops in cmi format
readcmifiles | Read Single Data Files in Chris Michael Format
readcmiloopfiles | 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

## -- S --

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

## -- T --

takeTimeDiff.cf | Take time difference
tex.catwitherror | paste a number with error in tex-ready format
tikz.finalize | tikz.finalize
tikz.init | tikz.init

## -- U --

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
uwerrderived | Time Series Analysis With Gamma Method
uwerrprimary | Time Series Analysis With Gamma Method

## -- W --

weight.cf | Weight a correlation function
weight_shift_reweight.cf | Weight-shift-reweight a correlation function

## -- Z --

zetazp | Computes the running of Z_P from scale mu0 to scale mu2

## -- misc --

*.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
/.cf | Divide two cf objects by each other measurement by measurement
/.raw_cf | divide two 'raw_cf' objects