doc: fix doc following recent changes

doc/dynare.texi

@@ -7088,23 +7088,25 @@ calibrated model.
 @xref{nobs}.
 
 @item use_shock_groups [= @var{SHOCK_GROUPS_NAME}]
-@anchor{use_shock_groups}. Uses groups of shocks instead of individual shocks in
+@anchor{use_shock_groups} Uses groups of shocks instead of individual shocks in
-the decomposition. Groups of shocks are defined in @xref{shock_groups} block.
+the decomposition. Groups of shocks are defined in the @ref{shock_groups} block.
 
 @item colormap = @var{COLORMAP_NAME}
-@anchor{colormap}. Controls the colormap used for the shocks decomposition
+@anchor{colormap} Controls the colormap used for the shocks decomposition
 graphs. See @code{colormap} in Matlab/Octave manual.
 
 @item nograph
-@xref{nograph}. Suppresses the display and creation only within the @code{shock_decomposition}-command
+@xref{nograph} Suppresses the display and creation only within the
-but does not affect other commands. See also @xref{plot_shock_decomposition} for plotting graphs.
+@code{shock_decomposition}-command but does not affect other commands.
+@xref{plot_shock_decomposition} for plotting graphs.
 
 @item init_state = @var{INTEGER}
-@anchor{init_state}. It can take values of 0 (=default) and 1. 
+@anchor{init_state} It can take values of @math{0} or @math{1}. If equal to
-If @code{init_state= 0}, the shock decomposition is computed conditional on the smoothed state variables
+@math{0}, the shock decomposition is computed conditional on the smoothed state
-in period 0, i.e. the smoothed shocks starting in period 1 are used.
+variables in period @math{0}, @i{i.e.} the smoothed shocks starting in period
-If @code{init_state= 1}, the shock decomposition is computed conditional on the smoothed state variables
+@math{1} are used.  If equal to @math{1}, the shock decomposition is computed
-in period 1.
+conditional on the smoothed state variables in period @math{1}. Default:
+@math{0}
 @end table
 
 @outputhead
@@ -7172,13 +7174,21 @@ shocks_decomposition(use_shock_groups=group1);
 
 @descriptionhead
 
-This command computes the realtime historical shock decomposition for a given sample based on 
+This command computes the realtime historical shock decomposition for a given
-the Kalman smoother. For each period @code{T=presample:nobs}, it computes 
+sample based on the Kalman smoother. For each period
-- realtime historical shock decomposition Y(t|T) for t=1:T, i.e. without observing data in [T+1:nobs];
+@math{T=[@code{presample}@dots{}@code{nobs}]}, it computes the:
-- conditional shock decomposition Y(T|T) CONDITIONAL on Y(T|T-1), i.e. Y(t|T) for t=T-1:T;
+@itemize @bullet
-- forecast shock decomposition Y(T|T-1).
+@item
+realtime historical shock decomposition @math{Y(t|T)} for @math{t=[1@dots{}T]},
+@i{i.e.} without observing data in @math{[T+1@dots{}@code{nobs}]};
+@item
+conditional shock decomposition @math{Y(T|T)} conditional on @math{Y(T|T-1)},
+@i{i.e.} @math{Y(t|T)} for @math{t=[T-1@dots{}T]};
+@item
+forecast shock decomposition @math{Y(T|T-1)}.
+@end itemize
 
-Like @xref{shock_decomposition} it decomposes the historical deviations of the endogenous 
+Like @ref{shock_decomposition} it decomposes the historical deviations of the endogenous 
 variables from their respective steady state values into the contribution coming 
 from the various shocks. The @code{variable_names} provided govern for which 
 variables the decomposition is plotted.
@@ -7192,7 +7202,7 @@ model).
 @table @code
 
 @item parameter_set = @var{PARAMETER_SET}
-Specify the parameter set to use for running the smoother. The
+Specify the parameter set to use for running the smoother.
 @var{PARAMETER_SET} can take one of the following seven values:
 @code{calibration}, @code{prior_mode}, @code{prior_mean},
 @code{posterior_mode}, @code{posterior_mean},
@@ -7210,12 +7220,13 @@ calibrated model.
 @xref{nobs}.
 
 @item use_shock_groups [= @var{SHOCK_GROUPS_NAME}]
-@anchor{use_shock_groups_realtime}. Uses groups of shocks instead of individual shocks in
+@anchor{use_shock_groups_realtime} Uses groups of shocks instead of individual
-the decomposition. Groups of shocks are defined in @xref{shock_groups} block.
+shocks in the decomposition. Groups of shocks are defined in the
+@ref{shock_groups} block.
 
 @item colormap = @var{COLORMAP_NAME}
-@anchor{colormap_realtime}. Controls the colormap used for the shocks decomposition
+@anchor{colormap_realtime} Controls the colormap used for the shocks
-graphs. See @code{colormap} in Matlab/Octave manual.
+decomposition graphs. See @code{colormap} in Matlab/Octave manual.
 
 @item nograph
 @xref{nograph}. Only shock decompositions are computed and stored in @code{oo_.realtime_shock_decomposition},
@@ -7223,36 +7234,48 @@ graphs. See @code{colormap} in Matlab/Octave manual.
 (@xref{plot_shock_decomposition}).
 
 @item presample
-@anchor{presample_shock_decomposition}. First data point from which recursive realtime shock decompositions are computed, i.e. for T=(presample:nobs).
+@anchor{presample_shock_decomposition} First data point from which recursive
+realtime shock decompositions are computed, @i{i.e.} for
+@math{T=[@code{presample}@dots{}@code{nobs}]}.
 
 @item forecast
-@anchor{forecast_shock_decomposition}. Compute shock decompositions up to T+k periods, i.e. get shock contributions to k-step ahead forecasts.
+@anchor{forecast_shock_decomposition} Compute shock decompositions up to
+@math{T+k} periods, @i{i.e.} get shock contributions to k-step ahead forecasts.
 
 @item save_realtime = [@var{integer1} ... @var{integern}]
-@anchor{save_realtime}. Choose for which vintages to save the full realtime shock decomposition. Default = 0.
+@anchor{save_realtime} Choose for which vintages to save the full realtime
+shock decomposition. Default: @math{0}.
 @end table
 
 @outputhead
 
 @vindex oo_.realtime_shock_decomposition
-The results of realtime historical decompositions are stored in the field @code{oo_.realtime_shock_decomposition}, which is a structure.
+The results of realtime historical decompositions are stored in the field
-Field @code{pool} stores the pooled decomposition @xref{plot_shock_decomposition}.
+@code{oo_.realtime_shock_decomposition}, which is a structure. Field
-Fields @code{time_*} store the vintages of realtime historical shock decompositions.
+@code{pool} stores the pooled decomposition (@xref{plot_shock_decomposition}).
+Fields @code{time_*} store the vintages of realtime historical shock
+decompositions.
 
 @vindex oo_.conditional_shock_decomposition
-The results of realtime conditional decompositions are stored in the field @code{oo_.conditional_shock_decomposition}, which is a structure.
+The results of realtime conditional decompositions are stored in the field
-Field @code{pool} stores the pooled decomposition Y(t|T) for t=T-1:T @xref{plot_shock_decomposition}.
+@code{oo_.conditional_shock_decomposition}, which is a structure. Field
-Conditional shock decomposition sets the initial condition in T-1, so only computes the effect of shocks in period T, 
+@code{pool} stores the pooled decomposition @math{Y(t|T)} for
-i.e. it is just a 1-period shock decomposition from T-1 to T. In practice it decomposes the update step of the Kalman filter.
+@math{t=T-1@dots{}T} @xref{plot_shock_decomposition}. Conditional shock
-Fields @code{time_*} store the vintages of k-step conditional forecast shock decompositions Y(t|T+k), for t=T:T+k.
+decomposition sets the initial condition in @math{T-1}, so only computes the
-See also @xref{vintage}.
+effect of shocks in period @math{T}, @i{i.e.} it is just a @math{1}-period
+shock decomposition from @math{T-1} to @math{T}. In practice it decomposes the
+update step of the Kalman filter. Fields @code{time_*} store the vintages of
+@math{k}-step conditional forecast shock decompositions @math{Y(t|T+k)}, for
+@math{t=[T@dots{}T+k}. @xref{vintage}.
 
 @vindex oo_.realtime_forecast_shock_decomposition
-The results of realtime forecast decompositions are stored in the field @code{oo_.realtime_forecast_shock_decomposition}, which is a structure.
+The results of realtime forecast decompositions are stored in the field
-Field @code{pool} stores the pooled decomposition @xref{plot_shock_decomposition}.
+@code{oo_.realtime_forecast_shock_decomposition}, which is a structure. Field
-Forecast shock decomposition computes the 1-step ahead effect of shocks on the 1-step ahead prediction, i.e. Y(T|T-1).
+@code{pool} stores the pooled decomposition @xref{plot_shock_decomposition}.
-Fields @code{time_*} store the vintages of k-step out-of-sample forecast shock decompositions, i.e. Y(t|T), for t=T:T+k.
+Forecast shock decomposition computes the @math{1}-step ahead effect of shocks
-See also @xref{vintage}.
+on the @math{1}-step ahead prediction, @i{i.e.} @math{Y(T|T-1)}. Fields
+@code{time_*} store the vintages of @math{k}-step out-of-sample forecast shock
+decompositions, @i{i.e.} @math{Y(t|T)}, for @math{t=[T@dots{}T+k]}. @xref{vintage}.
 
 @end deffn
 
@@ -7274,11 +7297,12 @@ Note that this command must come after @code{shock_decomposition} or @code{realt
 @table @code
 
 @item use_shock_groups [= @var{SHOCK_GROUPS_NAME}]
-@anchor{use_shock_groups_plot}. Uses groups of shocks instead of individual shocks in
+@anchor{use_shock_groups_plot} Uses groups of shocks instead of individual
-the decomposition. Groups of shocks are defined in @xref{shock_groups} block.
+shocks in the decomposition. Groups of shocks are defined in the
+@ref{shock_groups} block.
 
 @item colormap = @var{COLORMAP_NAME}
-@anchor{colormap_plot}. Controls the colormap used for the shocks decomposition
+@anchor{colormap_plot} Controls the colormap used for the shocks decomposition
 graphs. See @code{colormap} in Matlab/Octave manual.
 
 @item nodisplay
@@ -7288,56 +7312,94 @@ graphs. See @code{colormap} in Matlab/Octave manual.
 @xref{graph_format}.
 
 @item detailed 
-@anchor{detailed}. Plots shock contributions using subplots, one per shock (or group of shocks).
+@anchor{detailed} Plots shock contributions using subplots, one per shock (or group of shocks).
 
 @item interactive 
-@anchor{interactive}. Under MATLAB, add uimenu's for detailed group plots.
+@anchor{interactive} Under MATLAB, add uimenu's for detailed group plots.
 
 @item screen
-@anchor{screen}. For large models [i.e. for models with more than 16 shocks], plots only the shocks 
+@anchor{screen} For large models (@i{i.e.} for models with more than @math{16}
-that have the largest historical contribution for chosen selected @code{variable_names}. 
+shocks), plots only the shocks that have the largest historical contribution
-Historical contribution is ranked by the mean absolute value of all historical contributions.
+for chosen selected @code{variable_names}.  Historical contribution is ranked
+by the mean absolute value of all historical contributions.
 
 @item steadystate = @var{INTEGER}
-@anchor{steadystate}. 0=default. 
+@anchor{steadystate} If equal to @math{1}, the the @math{y}-axis value of the
-If =1, the the y-axis value of the zero line in the shock decomposition plot is translated to the steady state level.
+zero line in the shock decomposition plot is translated to the steady state
+level. Default: @math{0}
 
 @item type = @var{TYPE_NAME}
-@anchor{type}. For quarterly data, the @var{TYPE_NAME} can take one of the following values:
+@anchor{type} For quarterly data, @var{TYPE_NAME} can take one of the
-@code{qoq} for quarter-on-quarter plots, 
+following values: @code{qoq} for quarter-on-quarter plots, @code{yoy} for
-@code{yoy} for year-on-year plots of growth rates, 
+year-on-year plots of growth rates, @code{aoa} for annualized variables,
-@code{aoa} for annualized variables, i.e. the value in the last quarter for each year is plotted.
+@i{i.e.} the value in the last quarter for each year is plotted.  Default
-Default value: @code{empty}, i.e. standard period-on-period plots [qoq for quarterly data].
+value: @code{empty}, @i{i.e.} standard period-on-period plots (@code{qoq} for
+quarterly data).
 
 @item fig_name = @var{FIG_NAME}
-@anchor{fig_name}. Specifies a user-defined keyword to be appended to the default figure name set by @code{plot_shock_decomposition}.
+@anchor{fig_name} Specifies a user-defined keyword to be appended to the
-This can avoid to overwrite plots in case of sequential calls to @code{plot_shock_decomposition}.
+default figure name set by @code{plot_shock_decomposition}.  This can avoid to
+overwrite plots in case of sequential calls to @code{plot_shock_decomposition}.
 
 @item write_xls 
-@anchor{write_xls}. Saves shock decompositions to excel.
+@anchor{write_xls} Saves shock decompositions to excel.
 
 @item realtime = @var{INTEGER}
-@anchor{realtime}. Which kind of shock decomposition to plot. @var{INTEGER} can take following values:
+@anchor{realtime} Which kind of shock decomposition to plot. @var{INTEGER} can take following values:
-@code{0}: historical shock decomposition: Y(t|T) for t=1:T, T=nobs full sample [DEFAULT]
+@itemize @bullet
-@code{1}: realtime historical shock decomposition: for T=1:nobs, realtime shock decomposition Y(t|T) for t=1:T
+@item
-@code{2}: conditional shock decomposition: for T=1:nobs, realtime shock decomposition of Y(T|T) CONDITIONAL on Y(T|T-1), i.e. Y(t|T) for t=T-1:T
+@code{0}: historical shock decomposition: @math{Y(t|T)} for
-@code{3}: forecast shock decomposition: for T=1:nobs, realtime shock decomposition of Y(T|T-1)
+@math{t=[1@dots{}T]}, @math{T=} @code{nobs} full sample
+@item
+@code{1}: realtime historical shock decomposition: for
+@math{T=[1@dots{}@code{nobs}]}, realtime shock decomposition @math{Y(t|T)} for
+@math{t=[1@dots{}T]}
+@item
+@code{2}: conditional shock decomposition: for @code{T=1:nobs}, realtime shock
+decomposition of @math{Y(T|T)} conditional on @math{Y(T|T-1)}, @i{i.e.}
+@math{Y(t|T)} for @math{t=[T-1@dots{}T]}
+@item
+@code{3}: forecast shock decomposition: for @math{T=[1@dots{}@code{nobs}]},
+realtime shock decomposition of @math{Y(T|T-1)}
+@end itemize
+Default: @math{0}
 
 @item vintage = @var{INTEGER}
-@anchor{vintage}. Applies if @code{realtime}>0. @var{INTEGER} can take following values:
+@anchor{vintage} Applies if @code{realtime}@math{>0}. Can take following values:
-
+@itemize @bullet
-@code{0}: plots 1step pooled shock decompositions [DEFAULT]
+@item
-@code{realtime=1}: pooled realtime shock decomposition. For T=1:nobs, plots last time point Y(T|T) of each vintage shock decomposition Y(1:T|T)
+@code{0}: plots @math{1}-step pooled shock decompositions
-@code{realtime=2}: pooled conditional shock decomposition. For T=1:nobs, realtime 1-step shock decomposition of Y(T|T) CONDITIONAL on Y(T|T-1)
+@item
-[i.e. decomposition of 1-step filter updates of each vintage T]
+@code{1}: pooled realtime shock decomposition. For @math{T=[1@dots{}@code{nobs}]}, plots last
-@code{realtime=3}: pooled forecast shock decomposition. For T=1:nobs, realtime 1-step ahead shock decomposition of Y(T|T-1) 
+time point @math{Y(T|T)} of each vintage shock decomposition @math{Y(1:T|T)}
-[i.e. decomposition of shock contributions to 1-step ahead forecasts of each vintage T]
+@item
-
+@code{2}: pooled conditional shock decomposition. For
-@code{>0}: plots shock decompositions for vintage T=@code{vintage} under the following scenarios
+@math{T=[1@dots{}@code{nobs}]}, realtime @math{1}-step shock decomposition of
-@code{realtime=1}: the full vintage shock decomposition Y(t|T) for t=1:T
+@math{Y(T|T)} conditional on @math{Y(T|T-1)} (@i{i.e.} decomposition of
-@code{realtime=2}: plots conditional forecast shock decomposition from T, i.e. plots Y(T+j|T+j) 
+@math{1}-step filter updates of each vintage @math{T}}
-and the shock contributions needed to get to the data Y(T+j) CONDITIONAL on T=@code{vintage}, with j=(0:@code{forecast}).
+@item
-@code{realtime=3}: plots unconditional forecast shock decomposition from T, i.e. Y(T+j|T), where T=@code{vintage} and j=(0:@code{forecast}).
+@code{3}: pooled forecast shock decomposition. For
+@math{T=[1@dots{}@code{nobs}]}, realtime @math{1}-step ahead shock
+decomposition of @math{Y(T|T-1)} (@i{i.e.}  decomposition of shock
+contributions to @math{1}-step ahead forecasts of each vintage @math{T})
+@end itemize
+When the value passed is greater than @math{0}, it plots the shock
+decompositions for vintage @math{T=@code{vintage}} under the following scenarios:
+@itemize @bullet
+@item
+@code{realtime=1}: the full vintage shock decomposition @math{Y(t|T)} for
+@math{t=[1@dots{}T]}
+@item
+@code{realtime=2}: the conditional forecast shock decomposition from @math{T},
+@i{i.e.} plots @math{Y(T+j|T+j)} and the shock contributions needed to get to
+the data @math{Y(T+j)} conditional on @math{T=}@code{vintage}, with
+@math{j=[0@dots{}@code{forecast}]}.
+@item
+@code{realtime=3}: plots unconditional forecast shock decomposition from
+@math{T}, @i{i.e.} @math{Y(T+j|T)}, where @math{T=@code{vintage}} and
+@math{j=[0@dots{}@code{forecast}]}.
+@end itemize
+Default: @math{0}
 @end table
 
 @end deffn