LatAnalyze is a C++11 library for statistical data analysis based on bootstrap resampling. It has been written with lattice QCD data analysis in mind (hence the name), but its features are not lattice specific and can be used more general statistical context.
Sadly a proper documentation was never written, but some comprehensive examples covering most features can be found in the examples directory.
The main features are the following:
- Array and matrix types with fast arithmetic operations based on Eigen.
- High-level types for bootstrap sample manipulation (including various statistical estimators and histogramming).
- Mathematical expression parser for runtime defined functions.
- Data I/O in ASCII and HDF5 (optional).
- High-level wrappers to minimisation routines from the GSL, Minuit (optional) and NLopt.
- Non-linear regression with error on independent variables (through total least squares).
- High-level wrappers to numerical integrator and non-linear solver from the GSL.
- High-level functional types for function of model. General functions can be defined from C pointers, C++ objects, strings of mathematical expressions or tabulated data.
- High-level plotting functions based on gnuplot, with the possibility of generating and saving plot scripts.
The head of the master branch always points to the latest stable release. The develop branch is the main unstable branch of LatAnalyze.
LatAnalyze is written in C++11 and requires a rather recent C++ compiler to be built. It has been successfully built on various Linux and OS X platforms using clang (from 3.7), GCC (from 4.9) and the Intel C++ compiler (2016). The only strict dependencies is the GSL. Additionally, autoconf, automake (from 1.11), libtool, bison (from 3.0) and flex are necessary to build the library. Unless you use a very exotic system, these tools are standard on any Unix platform and should be already present or easy to install through a package manager. Optional dependencies are HDF5 (built with C++ support), Minuit and NLopt.
Below are instructions for a quick installation. For a more customised installation, one first needs to generate the build system by running ./bootstrap.sh in the root directory. Then the library can be built and installed through the usual GNU mantra ./configure <options> && make && make install. Use ./configure --help to obtain a list of possible options for ./configure. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the CXXFLAGS variable to -O3 -march=native -mtune=native.
For a quick installation with all possible extensions execute:
./install-latan.sh <prefix>
in the ci-scripts directory where <prefix> is where you want LatAnalyze (and its dependencies) to be installed. This script will automatically download, build and install GSL, HDF5, Minuit, and NLopt.
All the dependencies of LatAnalyze can be installed through the Homebrew package manager.
brew install automake autoconf libtool bison flex gsl minuit2 nlopt hdf5
Then generate the build system in LatAnalyze main directory by running the ./bootstrap.sh script. Finally, build the library
mkdir build
cd build
../configure --prefix=<prefix> --with-minuit=/usr/local --with-nlopt=/usr/local \
--with-hdf5=/usr/local --with-gsl=/usr/local \
CXXFLAGS='-g -O3 -march=native -mtune=native'
make -j <n>
make install
where <prefix> should be replaced by the desired prefix for LatAnalyze installation, and <n> is the number of parallel build processes (typically twice your number of cores).
Various fixes and cleaning of outdated code.
Additions:
- 'Impulse' & line type plots
- Plot line width & dash modifiers
- Plot palettes (
category10by default) - Multivariate Gaussian RNG
- 2-pt fitter 'scan' mode over all possible fit ranges
- Command line utility for plotting data
Changes:
- Complete overhaul of the header structure
- Integration of LatCore in LatAnalyze
- p-value is now a 2-sided chi^2 test, 1-sided value kept as 'chi^2 CCDF'
Fixes:
- Matrix plot data now saving correctly
- Many compatibility fixes
Additions:
latan-configutility to easily compile LatAnalyze-based programs- Linear and constant models to the 2-point fitter
Changes:
- HDF5 is now a compulsory dependency
Fixes:
- Variance matrix computation fix.
Additions:
- Sample plot CL utility.
- Infinity as a math constant.
- Option to dump bootstrap sequence while resampling.
- FFT through the GSL.
Changes:
- GSL integrator accepts infinite bounds.
latan-sample-combineaccepts mixes ofDSampleandDMatSample.- More general
latan-sample-elementcommand.
Additions:
- The math interpreter supports
inffor infinity.
Changes:
- Vector version of
setUnidimData.
Fixes:
- Variance matrix computation fix.
Fixes:
- Wrong argument number check in
latan-resample
Additions:
- 2-pt function fitter
latan-2pt-fit - Tool to extract one element of a matrix sample
latan-sample-element - Band plotting
Changes:
- Sample utilities renamed
latan-sample-* - Resample utility renamed
latan-resample
Fixes:
- HDF5 archive URL update in build scripts
Fixes:
- Minuit precision fixed
- Minor fit interface fixes
Additions:
- Wrappers to NLopt and GSL minimisers.
- Command-line tool to plot the correlation heatmap of a boostrap sample file.
- I/O functions for
DSampletype.
Changes:
- Internal random generator removed (obsolete because of C++11 pseudo-random generators).
- Fit interface and
XY*Dataclasses rewritten from scratch for improved flexibility and performance.
Fixes:
- Loads of portability and compatibility fixes and CI with Travis.
Commit 7b4f2884a5e99bbfab4d4bd7623f609a55403c39.
First 'stable' version of LatAnalyze in C++. The v2.0 refers to the C version and v1.0 to an old undistributed version.
This version compiles fine on OS X with clang but does have many portability issues to other platforms/compilers, v3.1 is the first real release.