w_stateprobs

WARNING: w_stateprobs is being deprecated. Please use w_direct instead.

usage:

w_stateprobs trace [-h] [-W WEST_H5FILE] [--first-iter N_ITER] [--last-iter N_ITER]
                         [--step-iter STEP] [-a ASSIGNMENTS] [-o OUTPUT] [-k KINETICS]
                         [--disable-bootstrap] [--disable-correl] [--alpha ALPHA]
                         [--autocorrel-alpha ACALPHA] [--nsets NSETS] [-e {cumulative,blocked,none}]
                         [--window-frac WINDOW_FRAC] [--disable-averages]

Calculate average populations and associated errors in state populations from weighted ensemble data. Bin assignments, including macrostate definitions, are required. (See “w_assign –help” for more information).

Output format

The output file (-o/–output, usually “direct.h5”) contains the following dataset:

/avg_state_probs [state]
  (Structured -- see below) Population of each state across entire
  range specified.

/avg_color_probs [state]
  (Structured -- see below) Population of each ensemble across entire
  range specified.

If –evolution-mode is specified, then the following additional datasets are available:

/state_pop_evolution [window][state]
  (Structured -- see below). State populations based on windows of
  iterations of varying width.  If --evolution-mode=cumulative, then
  these windows all begin at the iteration specified with
  --start-iter and grow in length by --step-iter for each successive
  element. If --evolution-mode=blocked, then these windows are all of
  width --step-iter (excluding the last, which may be shorter), the first
  of which begins at iteration --start-iter.

/color_prob_evolution [window][state]
  (Structured -- see below). Ensemble populations based on windows of
  iterations of varying width.  If --evolution-mode=cumulative, then
  these windows all begin at the iteration specified with
  --start-iter and grow in length by --step-iter for each successive
  element. If --evolution-mode=blocked, then these windows are all of
  width --step-iter (excluding the last, which may be shorter), the first
  of which begins at iteration --start-iter.

The structure of these datasets is as follows:

iter_start
  (Integer) Iteration at which the averaging window begins (inclusive).

iter_stop
  (Integer) Iteration at which the averaging window ends (exclusive).

expected
  (Floating-point) Expected (mean) value of the observable as evaluated within
  this window, in units of inverse tau.

ci_lbound
  (Floating-point) Lower bound of the confidence interval of the observable
  within this window, in units of inverse tau.

ci_ubound
  (Floating-point) Upper bound of the confidence interval of the observable
  within this window, in units of inverse tau.

stderr
  (Floating-point) The standard error of the mean of the observable
  within this window, in units of inverse tau.

corr_len
  (Integer) Correlation length of the observable within this window, in units
  of tau.

Each of these datasets is also stamped with a number of attributes:

mcbs_alpha
  (Floating-point) Alpha value of confidence intervals. (For example,
  *alpha=0.05* corresponds to a 95% confidence interval.)

mcbs_nsets
  (Integer) Number of bootstrap data sets used in generating confidence
  intervals.

mcbs_acalpha
  (Floating-point) Alpha value for determining correlation lengths.

Command-line options

optional arguments:

-h, --help            show this help message and exit

WEST input data options:

-W WEST_H5FILE, --west-data WEST_H5FILE
                      Take WEST data from WEST_H5FILE (default: read from the HDF5 file specified in
                      west.cfg).

iteration range:

--first-iter N_ITER   Begin analysis at iteration N_ITER (default: 1).
--last-iter N_ITER    Conclude analysis with N_ITER, inclusive (default: last completed iteration).
--step-iter STEP      Analyze/report in blocks of STEP iterations.

input/output options:

-a ASSIGNMENTS, --assignments ASSIGNMENTS
                      Bin assignments and macrostate definitions are in ASSIGNMENTS (default:
                      assign.h5).
-o OUTPUT, --output OUTPUT
                      Store results in OUTPUT (default: stateprobs.h5).

input/output options:

-k KINETICS, --kinetics KINETICS
                      Populations and transition rates are stored in KINETICS (default: assign.h5).

confidence interval calculation options:

--disable-bootstrap, -db
                      Enable the use of Monte Carlo Block Bootstrapping.
--disable-correl, -dc
                      Disable the correlation analysis.
--alpha ALPHA         Calculate a (1-ALPHA) confidence interval' (default: 0.05)
--autocorrel-alpha ACALPHA
                      Evaluate autocorrelation to (1-ACALPHA) significance. Note that too small an
                      ACALPHA will result in failure to detect autocorrelation in a noisy flux signal.
                      (Default: same as ALPHA.)
--nsets NSETS         Use NSETS samples for bootstrapping (default: chosen based on ALPHA)

calculation options:

-e {cumulative,blocked,none}, --evolution-mode {cumulative,blocked,none}
                      How to calculate time evolution of rate estimates. ``cumulative`` evaluates rates
                      over windows starting with --start-iter and getting progressively wider to --stop-
                      iter by steps of --step-iter. ``blocked`` evaluates rates over windows of width
                      --step-iter, the first of which begins at --start-iter. ``none`` (the default)
                      disables calculation of the time evolution of rate estimates.
--window-frac WINDOW_FRAC
                      Fraction of iterations to use in each window when running in ``cumulative`` mode.
                      The (1 - frac) fraction of iterations will be discarded from the start of each
                      window.

misc options:

--disable-averages, -da
                      Whether or not the averages should be printed to the console (set to FALSE if flag
                      is used).