Analysis Framework for Monte Carlo Simulation Data in Physics


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Documentation for package ‘hadron’ version 3.2.0

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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
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
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 --

jab.cf jackknife-after-bootstrap analysis
jab.cf.derived jackknife-after-bootstrap analysis
jab.effectivemass jackknife-after-bootstrap analysis
jab.effectivemassfit jackknife-after-bootstrap analysis
jab.matrixfit jackknife-after-bootstrap analysis
jackknife-after-bootstrap jackknife-after-bootstrap analysis
jackknife.cf jackknife a set of correlation functions
jackknifeafterboot jackknife-after-bootstrap analysis
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
predict.bootstrapfit Predict values for bootstrapfit
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