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Daniel Weschke
2026-04-05 20:00:27 +02:00
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@@ -1,8 +1,8 @@
This is ess.info, produced by makeinfo version 7.2 from ess.texi.
This is ess.info, produced by makeinfo version 7.3 from ess.texi.
INFO-DIR-SECTION Emacs
START-INFO-DIR-ENTRY
* ESS: (ess). Emacs Speaks Statistics (R/S/S+, SAS, BUGS/JAGS and Stata).
* ESS: (ess). Emacs Speaks Statistics (R/S/S+, SAS, BUGS/NIMBLE and Stata).
END-INFO-DIR-ENTRY
ESS -- Emacs Speaks Statistics
@@ -14,7 +14,7 @@ File: ess.info, Node: Top, Next: Introduction, Up: (dir)
ESS: Emacs Speaks Statistics
****************************
ESS version 25.01.0
ESS version 26.01.0
by A.J. Rossini,
R.M. Heiberger,
@@ -30,7 +30,7 @@ ESS version 25.01.0
Emacs Speaks Statistics (ESS) provides an intelligent, consistent
interface between the user and the software. ESS interfaces with
R, SAS, S-PLUS, BUGS/JAGS and other statistical analysis packages
R, SAS, S-PLUS, BUGS/NIMBLE and other statistical analysis packages
on GNU/Linux, other Unix-like systems such as macOS, and Microsoft
Windows. ESS is itself a package within the Emacs text editor and
uses Emacs features to streamline the creation and use of
@@ -66,7 +66,6 @@ the file COPYING in the same directory as this file for more details.
* ESS for R:: Overview of ESS features for the S family
* ESS for SAS::
* ESS for BUGS::
* ESS for JAGS::
* Mailing lists/bug reports:: How to get assistance with ESS
* Customization:: Customizing ESS
* Indices::
@@ -79,7 +78,7 @@ File: ess.info, Node: Introduction, Next: Installation, Prev: Top, Up: Top
ESS provides a generic interface, through Emacs, to statistical
packages. It currently supports R (and the rest of the S family), SAS,
BUGS/JAGS, Stata, and Julia with the level of support roughly in that
BUGS/NIMBLE, Stata, and Julia with the level of support roughly in that
order.
Throughout this manual, _Emacs_ refers to _GNU Emacs_ by the Free
@@ -249,7 +248,14 @@ File: ess.info, Node: New features, Next: Credits, Prev: Features, Up: Intro
1.2 New features in ESS
=======================
Changes and New Features in 25.01.0:
Changes and New Features in 26.01.0:
• ESS[BUGS] is still relevant due to NIMBLE keeping the language
alive. However, only syntax highlighting and key-presses will be
supported moving forward. For example, the ‘<’ key now generates
‘<-’ rather than the former ‘=’ since equals is a valid character
in NIMBLE BUGS.
Changes and New Features in 25.01.0:
• polymode: In our transition from literate libraries (such as noweb
documented below with respect to 19.04), we now recommend the
@@ -3510,29 +3516,48 @@ File: ess.info, Node: Outline, Next: Toolbar, Prev: Imenu, Up: Extras
R editing buffers integrate with ‘outline-minor-mode’. When you toggle
the minor mode (for example via ‘M-x outline-minor-mode’ or by adding it
to ‘ess-r-mode-hook’), ESS assigns ‘ess-r-outline-level’ to
‘outline-level’ and installs ‘ess-r-outline-regexp’ so that comment
headings drive folding. Lines that begin with one or more ‘#’, followed
by text and a trailing marker of ‘----’, ‘====’, or ‘####’, are treated
as outline headings. This matches the section markers convention
adopted by RStudio.
‘outline-level’ and configures ‘outline-regexp’ according to
‘ess-r-outline-style’ so that comment headings drive folding. By
default, outline support is disabled (‘none’), but you can enable it by
setting ‘ess-r-outline-style’ to ‘RStudio’ or ‘Org-like’. With the
‘RStudio’ style, lines that begin with one or more ‘#’, followed by text
and a trailing marker of ‘----’, ‘====’, or ‘####’, are treated as
outline headings. This matches the section markers convention adopted
by RStudio.
# Setup ----
## Data ----
### Models ====
#### Helpers ####
The number of leading ‘#’ characters sets the outline depth. Use
standard Outline commands (such as ‘C-c C-t’) to cycle visibility once
the minor mode is active. To enable Outlining automatically, add it to
the R mode hook:
The number of leading ‘#’ characters sets the outline depth. When
using the RStudio outline style, ‘ess-indent-with-fancy-comments’ is
automatically set to ‘nil’ locally in the buffer to prevent single-hash
comments from being treated as right-margin comments with
‘comment-column’ 40. When switching back to a different outline style,
the original local binding is restored; if the variable was not
buffer-local, the current global default applies.
Use standard Outline commands (such as ‘C-c C-t’) to cycle
visibility once the minor mode is active. To enable Outlining
automatically, add it to the R mode hook:
(add-hook 'ess-r-mode-hook #'outline-minor-mode)
-- User Option: ess-r-outline-regexp
Regular expression used by ESS to recognise outline headings in R
buffers. The default matches the RStudio-style sections shown
above, but you can customise it if you prefer a different comment
convention.
-- User Option: ess-r-outline-style
Select which outline convention ‘ess-r-mode’ should use. The
default ‘none’ disables outline support to preserve backward
compatibility. Set to ‘RStudio’ to recognise the comment rulers
shown above, or choose ‘Org-like’ to match the ‘### * Section’
pattern, inspired from org-mode:
### * Setup
### ** Data
### *** Models
### **** Helpers
You can switch styles via ‘M-x ess-r-set-outline-style’ or by
customizing this option.

File: ess.info, Node: Toolbar, Next: Xref, Prev: Outline, Up: Extras
@@ -3662,48 +3687,6 @@ polymode <https://github.com/polymode/poly-R/>,
<https://polymode.github.io/>, or markdown-mode with edit-indirect
<https://jblevins.org/projects/markdown-mode>.
ESS provides support for writing and processing Sweave
(<https://leisch.userweb.mwn.de/Sweave/>), building up on Emacs'
ess-noweb-mode for literate programming. When working on an Sweave
document, the following key bindings are available:
-- Command: ess-swv-weave CHOOSE
‘M-n s’ Run Sweave on the current .Rnw file. If CHOOSE is
non-‘nil’, offer a menu of available weavers.
-- Command: ess-swv-latex
‘M-n l’ Run LaTeX after Sweave'ing.
-- Command: ess-swv-PS
‘M-n p’ Generate and display a postscript file after LaTeX'ing.
-- Command: ess-swv-PDF PDFLATEX-CMD
‘M-n P’ Generate and display a PDF file after LaTeX'ing. Optional
argument PDFLATEX-CMD is the command to use, which by default, is
the command used to generate the PDF file is the first element of
‘ess-swv-pdflatex-commands’.
-- User Option: ess-swv-pdflatex-commands
Commands used by ‘ess-swv-PDF’ to run a version of pdflatex; the
first entry is the default command.
Sweave'ing with ‘ess-swv-weave’ starts an inferior-ESS process, if
one is not available. Other commands are available from the ‘Sweaving,
Tangling, ...’ submenu of the Noweb menu.
AUCTeX (<https://www.gnu.org/software/auctex>) users may prefer to
set the variable ‘ess-swv-plug-into-AUCTeX-p’ (available from the "ESS
Sweave" customization group) to t. Alternatively, the same can be
achieved by activating the entry "AUCTeX Interface" from the ‘Sweaving,
Tangling, ...’ submenu, which toggles this variable on or off. When the
interface is activated, new entries for Sweave'ing and LaTeX'ing
thereafter are available from AUCTeX's "Command" menu. Sweave'ing can,
thus, be done by ‘C-c C-c Sweave RET’ without an inferior-ESS process.
Similarly, LaTeX'ing can be done by ‘C-c C-c LaTeXSweave RET’. In both
cases, the process can be monitored with ‘C-c C-l’
(‘TeX-recenter-output-buffer’). Open the viewer with ‘C-c C-v’
(‘TeX-view’), as usual in AUCTeX.

File: ess.info, Node: ESS for R, Next: ESS for SAS, Prev: Extras, Up: Top
@@ -4403,120 +4386,26 @@ File: ess.info, Node: ESS(SAS)--Windows, Prev: ESS(SAS)--Graphics, Up: ESS fo
'submit-region' or paste them into SAS Display Manager.

File: ess.info, Node: ESS for BUGS, Next: ESS for JAGS, Prev: ESS for SAS, Up: Top
File: ess.info, Node: ESS for BUGS, Next: Mailing lists/bug reports, Prev: ESS for SAS, Up: Top
14 ESS for BUGS
***************
ESS[BUGS] provides 5 features. First, BUGS syntax is described to allow
for proper fontification of statements, distributions, functions,
commands and comments in BUGS model files, command files and log files.
Second, ESS creates templates for the command file from the model file
so that a BUGS batch process can be defined by a single file. Third,
ESS provides a BUGS batch script that allows ESS to set BUGS batch
parameters. Fourth, key sequences are defined to create a command file
and submit a BUGS batch process. Lastly, interactive submission of BUGS
commands is also supported.
ESS[BUGS] NIMBLE has re-vitalized the BUGS language. All previous
instances of BUGS such as OpenBUGS and JAGS are now deprecated.
Therefore, ESS suppors BUGS syntax to allow for proper fontification of
statements, distributions, functions, commands and comments in
BUGS/NIMBLE model files.
14.1 ESS[BUGS]-Model files
==========================
Model files with the ‘.bug’ extension are edited in ESS[BUGS] mode.
Three keys are bound for your use in ESS[BUGS], ‘F2’, ‘C-c C-c’ and ‘=’.
‘F2’ performs the same action as it does in ESS[SAS], *Note
ESS(SAS)--Function keys for batch processing::. ‘C-c C-c’ performs the
function ‘ess-bugs-next-action’ which you will use a lot. Pressing it
in an empty buffer for a model file will produce a template for you.
‘=’ inserts the set operator, ‘<-’.
14.2 ESS[BUGS]-Command files
============================
Files ending in ‘.bmd’ are used for BUGS command files. When you have
finished editing your model file and press ‘C-c C-c’, a command file is
created if one does not already exist. When you are finished editing
your command file, pressing ‘C-c C-c’ again will submit your command
file as a batch job.
14.3 ESS[BUGS]-Log files
========================
The ‘.bog’ extension is used for BUGS log files. The command line
generated by ESS creates the ‘.bog’ transcript file.

File: ess.info, Node: ESS for JAGS, Next: Mailing lists/bug reports, Prev: ESS for BUGS, Up: Top
File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: ESS for BUGS, Up: Top
15 ESS for JAGS
***************
ESS[JAGS] provides 4 features. First, JAGS syntax is described to allow
for proper fontification of statements, distributions, functions,
commands and comments in JAGS model files, command files and log files.
Second, ESS creates templates for the command file from the model file
so that a JAGS batch process can be defined by a single file. Third,
ESS provides a JAGS batch script that allows ESS to set JAGS batch
parameters. Fourth, key sequences are defined to create a command file
and submit a JAGS batch process.
15.1 ESS[JAGS]-Model files
==========================
Files with the ‘.jag’ extension are edited in ESS[JAGS] mode. Three
keys are bound for your use in ESS[JAGS], ‘F2’, ‘C-c C-c’ and ‘=’. ‘F2’
performs the same action as it does in ESS[SAS], *Note
ESS(SAS)--Function keys for batch processing::. ‘C-c C-c’ performs the
function ‘ess-bugs-next-action’ which you will use a lot. Pressing it
in an empty buffer for a model file will produce a template for you.
‘=’ inserts the set operator, ‘<-’.
The first press of ‘C-c C-c’ will set up a template, including some
necessary file-local variables in an empty buffer. These variables are
‘ess-jags-chains’, ‘ess-jags-monitor’, ‘ess-jags-thin’,
‘ess-jags-burnin’ and ‘ess-jags-update’; they appear in the ‘Local
Variables’ section. When you are finished editing your model file,
pressing ‘C-c C-c’ will perform the necessary actions to build your
command file for you.
The ‘ess-jags-chains’ variable is the number of chains that you want
to initialize and sample from; defaults to 1. The ‘ess-jags-monitor’
variable is a list of variables that you want monitored: encase each
variable in double quotes. When you press ‘C-c C-c’, the appropriate
statements are created in the command file to monitor the list of
variables. By default, no variables are explicitly monitored which
means JAGS will implicitly monitor all "default" variables. The
‘ess-jags-thin’ variable is the thinning parameter. By default, the
thinning parameter is set to 1, i.e. no thinning. The
‘ess-jags-burnin’ variable is the number of initial samples to discard.
By default, the burnin parameter is set to 10000. The ‘ess-jags-update’
variable is the number of post-burnin samples to keep. By default, the
update parameter is set to 10000. Both ‘ess-jags-burnin’ and
‘ess-jags-update’ are multiplied by ‘ess-jags-thin’ since JAGS does not
do it automatically.
15.2 ESS[JAGS]-Command files
============================
Files ending in ‘.jmd’ are for JAGS command files. For your ‘.jmd’
file, there is only one variable, ‘ess-jags-command’, in the ‘Local
Variables’ section. When you have finished editing your model file and
press ‘C-c C-c’, a command file is created if one does not already
exist. When you are finished editing your command file, pressing ‘C-c
C-c’ again will submit your command file as a batch job. The
‘ess-jags-command’ variable allows you to specify a different JAGS
program to use to run your model; defaults to "jags".
15.3 ESS[JAGS]-Log files
========================
The ‘.jog’ extension is used for JAGS log files. You may find ‘F2’
useful to refresh the ‘.jog’ if the batch process over-writes or appends
it.

File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: ESS for JAGS, Up: Top
16 Bugs and Bug Reporting, Mailing Lists
15 Bugs and Bug Reporting, Mailing Lists
****************************************
* Menu:
@@ -4529,7 +4418,7 @@ File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: E

File: ess.info, Node: Bugs, Next: Reporting Bugs, Up: Mailing lists/bug reports
16.1 Bugs
15.1 Bugs
=========
• Commands like ‘ess-display-help-on-object’ and list completion
@@ -4569,7 +4458,7 @@ File: ess.info, Node: Bugs, Next: Reporting Bugs, Up: Mailing lists/bug repor

File: ess.info, Node: Reporting Bugs, Next: Mailing Lists, Prev: Bugs, Up: Mailing lists/bug reports
16.2 Reporting Bugs
15.2 Reporting Bugs
===================
Please post bug reports, suggestions etc. on our github issue tracker
@@ -4594,7 +4483,7 @@ donations are also more than welcome.

File: ess.info, Node: Mailing Lists, Next: Help with Emacs, Prev: Reporting Bugs, Up: Mailing lists/bug reports
16.3 Mailing Lists
15.3 Mailing Lists
==================
There is a mailing list for discussions and announcements relating to
@@ -4614,7 +4503,7 @@ this is a fairly low-volume mailing list.

File: ess.info, Node: Help with Emacs, Prev: Mailing Lists, Up: Mailing lists/bug reports
16.4 Help with Emacs
15.4 Help with Emacs
====================
Emacs is a complex editor with many abilities that we do not have space
@@ -4726,9 +4615,6 @@ Key index
* M-;: Indenting. (line 65)
* M-?: Object names. (line 33)
* M-C-q: Indenting. (line 49)
* M-n l: Sweave and AUCTeX. (line 24)
* M-n P: Sweave and AUCTeX. (line 30)
* M-n s: Sweave and AUCTeX. (line 20)
* M-RET: Resubmit. (line 10)
* RET: Command-line editing. (line 10)
* RET <1>: Resubmit. (line 18)
@@ -4770,7 +4656,7 @@ Function and program index
* dump(): Edit buffer. (line 35)
* ess-change-directory: Package listing. (line 29)
* ess-cleanup: Hot keys. (line 71)
* ess-cleanup <1>: Help. (line 170)
* ess-cleanup <1>: Help. (line 169)
* ess-complete-object-name: Object names. (line 32)
* ess-describe-help-mode: Help. (line 21)
* ess-display-help-on-object: Hot keys. (line 65)
@@ -4810,7 +4696,7 @@ Function and program index
* ess-parse-errors: Hot keys. (line 54)
* ess-parse-errors <1>: Error Checking. (line 9)
* ess-quit: Hot keys. (line 70)
* ess-quit <1>: Help. (line 170)
* ess-quit <1>: Help. (line 169)
* ess-R-complete-object-name: roxygen2. (line 80)
* ess-r-outline-level: Outline. (line 6)
* ess-r-package-list-available-packages: Package listing. (line 12)
@@ -4843,10 +4729,6 @@ Function and program index
* ess-submit-bug-report: Reporting Bugs. (line 6)
* ess-switch-to-end-of-ESS: Help. (line 117)
* ess-switch-to-inferior-or-script-buffer: Other. (line 12)
* ess-swv-latex: Sweave and AUCTeX. (line 23)
* ess-swv-PDF: Sweave and AUCTeX. (line 29)
* ess-swv-PS: Sweave and AUCTeX. (line 26)
* ess-swv-weave: Sweave and AUCTeX. (line 19)
* ess-tracebug: ESS tracebug. (line 6)
* ess-transcript-clean-region: Clean. (line 10)
* ess-transcript-copy-command: Resubmit. (line 13)
@@ -4913,14 +4795,13 @@ Variable index
* ess-r-flymake-linters: ESS Flymake. (line 16)
* ess-r-flymake-lintr-cache: ESS Flymake. (line 23)
* ess-R-font-lock-keywords: Highlighting. (line 19)
* ess-r-outline-regexp: Outline. (line 6)
* ess-r-outline-regexp <1>: Outline. (line 27)
* ess-r-outline-style: Outline. (line 6)
* ess-r-outline-style <1>: Outline. (line 37)
* ess-search-list: Source Directories. (line 62)
* ess-source-directory: Source Directories. (line 22)
* ess-style: Styles. (line 21)
* ess-style-alist: Styles. (line 28)
* ess-switch-to-end-of-proc-buffer: Other. (line 21)
* ess-swv-pdflatex-commands: Sweave and AUCTeX. (line 35)
* ess-use-eldoc: ESS ElDoc. (line 13)
* ess-use-flymake: ESS Flymake. (line 12)
* iESS program arguments: Customizing startup. (line 48)
@@ -5091,111 +4972,110 @@ Concept Index

Tag Table:
Node: Top268
Node: Introduction2906
Node: Features5692
Node: Current Features6518
Node: New features10065
Node: Credits37885
Node: Manual41544
Node: Installation44254
Node: Installing from a third-party repository45191
Node: Installing from source46138
Node: Activating and Loading ESS47762
Node: Check Installation48844
Node: Interactive ESS49068
Node: Starting up49913
Node: Multiple ESS processes50673
Node: ESS processes on Remote Computers51786
Node: Customizing startup56013
Node: Controlling buffer display58995
Node: Entering commands61632
Node: Command-line editing62794
Node: Transcript64059
Node: Last command65856
Node: Process buffer motion67314
Node: Transcript resubmit68857
Node: Saving transcripts70854
Node: Command History72688
Node: Saving History76189
Node: History expansion76970
Node: Hot keys80361
Node: Statistical Process running in ESS?84531
Node: Emacsclient85878
Node: Other86698
Node: Evaluating code87741
Node: Transcript Mode91673
Node: Resubmit92846
Node: Clean93921
Node: Editing objects94921
Node: Edit buffer96039
Node: Loading98129
Node: Error Checking99184
Node: Indenting100257
Node: Styles103409
Node: Other edit buffer commands105911
Node: Source Files107623
Node: Source Directories112339
Node: Help115548
Node: Completion120250
Node: Object names120465
Node: Function arguments123179
Node: Minibuffer completion124158
Node: Company124656
Node: Icicles125055
Node: Developing with ESS126431
Node: ESS tracebug126877
Node: Getting started with tracebug129934
Node: Editing documentation132220
Node: R documentation files132772
Node: roxygen2136587
Node: Namespaced Evaluation141110
Node: Extras143124
Node: ESS ElDoc144216
Node: ESS Flymake145796
Node: Handy commands146926
Node: Highlighting148203
Node: Parens149254
Node: Graphics149730
Node: printer150401
Node: X11151173
Node: winjava151512
Node: Imenu151924
Node: Outline152779
Node: Toolbar154091
Node: Xref154501
Node: Rdired154831
Node: Package listing155910
Node: Org157358
Node: Sweave and AUCTeX158312
Node: ESS for R160944
Node: ESS(R)--Editing files161244
Node: iESS(R)--Inferior ESS processes161749
Node: Philosophies for using ESS(R)164468
Node: Example ESS usage165395
Node: ESS for SAS166799
Node: ESS(SAS)--Design philosophy167526
Node: ESS(SAS)--Editing files168463
Node: ESS(SAS)--TAB key170407
Node: ESS(SAS)--Batch SAS processes171821
Node: ESS(SAS)--Function keys for batch processing177041
Node: iESS(SAS)--Interactive SAS processes186948
Node: iESS(SAS)--Common problems190890
Node: ESS(SAS)--Graphics192504
Node: ESS(SAS)--Windows193303
Node: ESS for BUGS193887
Node: ESS for JAGS195699
Node: Mailing lists/bug reports199195
Node: Bugs199459
Node: Reporting Bugs201135
Node: Mailing Lists202054
Node: Help with Emacs202792
Node: Customization203328
Node: Indices204106
Node: Key index204281
Node: Function and program index209413
Node: Variable index218979
Node: Concept index222686
Node: Top270
Node: Introduction2893
Node: Features5681
Node: Current Features6507
Node: New features10054
Node: Credits38231
Node: Manual41890
Node: Installation44600
Node: Installing from a third-party repository45537
Node: Installing from source46484
Node: Activating and Loading ESS48108
Node: Check Installation49190
Node: Interactive ESS49414
Node: Starting up50259
Node: Multiple ESS processes51019
Node: ESS processes on Remote Computers52132
Node: Customizing startup56359
Node: Controlling buffer display59341
Node: Entering commands61978
Node: Command-line editing63140
Node: Transcript64405
Node: Last command66202
Node: Process buffer motion67660
Node: Transcript resubmit69203
Node: Saving transcripts71200
Node: Command History73034
Node: Saving History76535
Node: History expansion77316
Node: Hot keys80707
Node: Statistical Process running in ESS?84877
Node: Emacsclient86224
Node: Other87044
Node: Evaluating code88087
Node: Transcript Mode92019
Node: Resubmit93192
Node: Clean94267
Node: Editing objects95267
Node: Edit buffer96385
Node: Loading98475
Node: Error Checking99530
Node: Indenting100603
Node: Styles103755
Node: Other edit buffer commands106257
Node: Source Files107969
Node: Source Directories112685
Node: Help115894
Node: Completion120596
Node: Object names120811
Node: Function arguments123525
Node: Minibuffer completion124504
Node: Company125002
Node: Icicles125401
Node: Developing with ESS126777
Node: ESS tracebug127223
Node: Getting started with tracebug130280
Node: Editing documentation132566
Node: R documentation files133118
Node: roxygen2136933
Node: Namespaced Evaluation141456
Node: Extras143470
Node: ESS ElDoc144562
Node: ESS Flymake146142
Node: Handy commands147272
Node: Highlighting148549
Node: Parens149600
Node: Graphics150076
Node: printer150747
Node: X11151519
Node: winjava151858
Node: Imenu152270
Node: Outline153125
Node: Toolbar155358
Node: Xref155768
Node: Rdired156098
Node: Package listing157177
Node: Org158625
Node: Sweave and AUCTeX159579
Node: ESS for R160176
Node: ESS(R)--Editing files160476
Node: iESS(R)--Inferior ESS processes160981
Node: Philosophies for using ESS(R)163700
Node: Example ESS usage164627
Node: ESS for SAS166031
Node: ESS(SAS)--Design philosophy166758
Node: ESS(SAS)--Editing files167695
Node: ESS(SAS)--TAB key169639
Node: ESS(SAS)--Batch SAS processes171053
Node: ESS(SAS)--Function keys for batch processing176273
Node: iESS(SAS)--Interactive SAS processes186180
Node: iESS(SAS)--Common problems190122
Node: ESS(SAS)--Graphics191736
Node: ESS(SAS)--Windows192535
Node: ESS for BUGS193119
Node: Mailing lists/bug reports193675
Node: Bugs193939
Node: Reporting Bugs195615
Node: Mailing Lists196534
Node: Help with Emacs197272
Node: Customization197808
Node: Indices198586
Node: Key index198761
Node: Function and program index203674
Node: Variable index212948
Node: Concept index216582

End Tag Table