#LyX 2.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 417
+\lyxformat 445
\begin_document
\begin_header
\textclass scrbook
\font_roman default
\font_sans default
\font_typewriter default
+\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
-
\graphics default
\default_output_format default
-\output_sync 0
+\output_sync 1
\bibtex_command default
\index_command default
\paperfontsize 12
\pdf_quoted_options "linkcolor=black, citecolor=black, urlcolor=blue, filecolor=blue, pdfpagelayout=OneColumn, pdfnewwindow=true, pdfstartview=XYZ, plainpages=false"
\papersize default
\use_geometry false
-\use_amsmath 1
-\use_esint 0
-\use_mhchem 1
-\use_mathdots 1
-\use_undertilde 1
+\use_package amsmath 1
+\use_package amssymb 1
+\use_package esint 0
+\use_package mathdots 1
+\use_package mathtools 0
+\use_package mhchem 1
+\use_package undertilde 0
\cite_engine basic
+\cite_engine_type numerical
+\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
+\justification true
\use_refstyle 0
\notefontcolor #0000ff
\index Index
\papercolumns 1
\papersides 2
\paperpagestyle headings
-\tracking_changes false
+\tracking_changes true
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict true
+\author 274215730 "scott"
\end_header
\begin_body
User's Guide\SpecialChar \@.
\emph default
- The reason for separating this document out is simple: the
+ The reason for separating the two documents is simple: the
\emph on
User's Guide
\emph default
TeX Code
\end_layout
+\end_inset
+
+ or the keyboard shortcut
+\begin_inset Info
+type "shortcut"
+arg "ert-insert"
\end_inset
.
\begin_inset Newline newline
\end_inset
-This is an example for a minipage environment.
+This is an example of a minipage environment.
You
\begin_inset Newline newline
\end_inset
box containing this text is directly after this paragraph.
Those of you reading the manual in LyX will only see the TeX code inset.
Those reading a printed version of the manuals will see the actual results:
+\begin_inset VSpace bigskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
\begin_inset ERT
-status collapsed
+status open
\begin_layout Plain Layout
\begin_layout Plain Layout
-This is an example for a minipage environment.
+This is an example of a minipage environment.
You can put nearly everything in it, even (non-floating) figures and tables.
\end_layout
\end_inset
+\begin_inset VSpace bigskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
\end_layout
\begin_layout Itemize
-Beware reinventing the wheel.
+Beware of reinventing the wheel.
\end_layout
\begin_layout Standard
LaTeX packages provide special commands, which are only available within
a document when the package has been declared in the preamble.
+ In addition to providing special commands, the inclusion of a package can
+ change the document.
For example, the package
\begin_inset Flex Code
status collapsed
\begin_inset Newline newline
\end_inset
-There are several LaTeX counters and variables which
+There are several LaTeX counters and variables that
\emph on
must
\emph default
be set globally from within the preamble in order to have the desired effect.
- (There are variables which you can set and reset inside the document, too.)
- Margins are a good example of something which must be set in the preamble.
+ (There are variables that you can set and reset inside the document, too.)
+ Margins are a good example of something that must be set in the preamble.
Another example is the label format for lists.
You can actually set these just about anywhere, but it's best to do it
just once, inside the preamble.
When LyX calls LaTeX, it tells LaTeX to blithely ignore any errors and keep
going.
It then uses the logfile from the LaTeX run to do a post-mortem.
- After analyzing the logfile,LyX displays a dialog listing the errors.
+ After analyzing the logfile, LyX displays a dialog listing the errors.
Clicking on any one of them will take you to the position in your LyX file
where the error occurred.
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
- LaTeX Error: File
+LaTeX Error: File
\begin_inset Quotes els
\end_inset
\end_inset
-, than the established
+, then the established
\begin_inset Flex Code
status collapsed
.
You are free to use the same or different styles for each section.
- Additionally, you can chose if the bibliography section should contain
+ Additionally, you can choose if the bibliography section should contain
\begin_inset Quotes eld
\end_inset
\end_inset
- removes the bibliography title, you have manually re-add that, too (as
+ removes the bibliography title, you have to manually re-add that, too (as
a chapter* or section*, for instance).
\end_layout
\end_inset
(those commands have to be inserted as TeX code).
- The bibliography will contain all references which have been cited in the
+ The bibliography will contain all references that have been cited in the
current
\begin_inset Flex Code
status collapsed
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\end_inset
is really only meaningful to LaTeXperts, but the practical difference is
- that files which are
+ that files that are
\begin_inset Quotes eld
\end_inset
\begin_inset Quotes erd
\end_inset
- are typeset beginning on a new page, while files which are
+ are typeset beginning on a new page, while files that are
\begin_inset Quotes eld
\end_inset
\begin_layout Standard
Generally, the master file is converted into a full LaTeX file before typesettin
-g, while the included files are converted to LaTeX files which do not have
+g, while the included files are converted to LaTeX files that do not have
all the preamble information.
\end_layout
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
First, open all the files in question: let's call them A and B in a two
file example, where B is included in A.
Let's say you insert a label in A, then want to reference it in B.
- Open the cross-reference dialog in whilst in document B, and you can select
+ Open the cross-reference dialog whilst in document B, and you can select
the
\begin_inset Quotes eld
\end_inset
\end_layout
\begin_layout Standard
-As the bibliography list is in a comment, LaTeX won't use use it and the
- references will look like this: [?], instead of like this: [1].
+As the bibliography list is in a comment, LaTeX won't use it and the references
+ will look like this: [?], instead of like this: [1].
One solution is to use the LaTeX-package
\begin_inset Flex Code
status collapsed
\begin_layout Standard
You will now see your name in the upper left.
If a field has a default entry that you would like to get rid of (often
- the page number appears in the central footer, simply include a command
+ the page number appears in the central footer) simply include a command
with a blank argument, e.
\begin_inset space \thinspace{}
\end_inset
\begin_layout Standard
The six panels are divided up by the packages they require.
- The following table shows the mappings from button name to LaTeX packages.
+ The following table shows the mappings from button name to LaTeX package.
\end_layout
\begin_layout Standard
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
-<features tabularvalignment="middle">
+<features rotate="0" tabularvalignment="middle">
<column alignment="center" valignment="top" width="0pt">
<column alignment="center" valignment="top" width="0pt">
<row>
\begin_inset CommandInset href
LatexCommand href
name "accessed online"
-target "http://www.lyx.org/trac/browser/lyx-devel/trunk/development/HTML/HTML.notes"
+target "http://www.lyx.org/trac/browser/lyxgit/development/HTML/HTML.notes?rev=master"
\end_inset
\end_layout
\begin_layout Standard
-Another useful tool is command-line based client you will find in
+Another useful tool is the command-line based clientfound in
\begin_inset Flex Code
status collapsed
\end_inset
- select Ly
-\begin_inset ERT
+ choose
+\begin_inset Flex MenuItem
status collapsed
\begin_layout Plain Layout
+custom
+\end_layout
-{}
+\end_inset
+
+ preset and enter command
+\begin_inset Flex MenuItem
+status collapsed
+
+\begin_layout Plain Layout
+/Applications/LyX.app/Contents/MacOS/lyxeditor
\end_layout
\end_inset
-X.
+.
\end_layout
\begin_layout Standard
\begin_inset Quotes erd
\end_inset
- to reverse search.
+ of reverse search.
It allows you to let the viewer jump to a given position from within LyX.
If forward search is set up (as described in what follows), you can put
the cursor anywhere in your LyX document, and hit
\end_inset
-: name of the (temporary) exported .tex file
+: name of the (temporary) exported .tex file (without path)
+\end_layout
+
+\begin_layout Itemize
+\noindent
+\begin_inset Flex Code
+status collapsed
+
+\begin_layout Plain Layout
+$$f
+\end_layout
+
+\end_inset
+
+: name of the (temporary) exported .tex file (including path)
\end_layout
\begin_layout Itemize
\end_inset
.
- These latter functionality is provided by an external call of synctex (see
+ This latter functionality is provided by an external call of synctex (see
the predefined example configurations).
\end_layout
\end_inset
- module, which is loaded by default when when you select one of the AMS
- classes.
+ module, which is loaded by default when you select one of the AMS classes.
(It can also be used with other classes and can be removed, if you would
rather use something else.) Less commonly used environments are in the
\begin_inset Flex Code
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\emph on
\begin_inset space \space{}
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\end_inset
-, lots will probably never, due to the limitations of LyX's framework.
+, lots will probably never be supported, due to the limitations of LyX's
+ framework.
Of course you can still use all features with the help of some native LaTeX
commands (TeX code
\begin_inset Foot
\end_inset
).
- In this section, we can only list those features which are natively supported
+ In this section, we can only list those features that are natively supported
by LyX.
For detailed descriptions (and for the rest of features) we recommend you
have a look at the detailed manual of the Memoir class
\begin_inset Quotes erd
\end_inset
-, i.
-\begin_inset space \thinspace{}
-\end_inset
-
-g.
-\begin_inset space \space{}
-\end_inset
-
-without pagina).
+).
If you want an empty title page, type
\family typewriter
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\family typewriter
chktex
\family default
- it from CTAN,
+ from CTAN,
\begin_inset CommandInset href
LatexCommand href
target "http://www.ctan.org/tex-archive/help/Catalogue/entries/chktex.html"
\begin_inset Newline newline
\end_inset
-In you are in bad luck, the text will break right between the referenced
- text and reference number, and that's a pity.
+If you have bad luck, the text will break right between the referenced text
+ and reference number, and that's a pity.
See section
\begin_inset CommandInset ref
LatexCommand ref
\family sans
ChkTeX
\family default
-, and this gap can make some warnings seem arcane or just right down plain
- silly.
+, and this gap can make some warnings seem arcane or just plain silly.
\end_layout
\begin_layout Standard
\end_inset
- to the internal document structure, some of the warnings will not seen
- to appear correctly.
+ to the internal document structure, some of the warnings will not appear
+ correctly.
There are two things you can do about this:
\end_layout
ChkTeX
\family default
invocation command line in
-\family sans
-Preferences
-\family default
- (tabs
-\family sans
-Outputs
-\family default
-,
-\family sans
-Misc
-\family default
-), or the global
+\begin_inset Flex MenuItem
+status collapsed
+
+\begin_layout Plain Layout
+Tools\SpecialChar \menuseparator
+Preferences\SpecialChar \menuseparator
+Output\SpecialChar \menuseparator
+LaTeX\SpecialChar \menuseparator
+CheckTeX command
+\end_layout
+
+\end_inset
+
+, or the global
\family sans
ChkTeX
\family default
).
See below to learn what warnings can be enabled and disabled on the command
line.
-
\end_layout
\begin_layout Itemize
\end_layout
\begin_layout Standard
-A friend of mine wanted to try LyX for a group project.
- When he didn't find support for version control or file locking, he dropped
- it.
- This angered me a bit, so I thought that I should at least make support
- for RCS (with the possibility of CVS and/or SCCS as a future improvement.)
- This has been done.
- LyX now supports some of the most basic RCS/CVS/SVN commands.
+LyX supports some of the most basic RCS/CVS/SVN commands.
If you need something a bit more sophisticated you will have to do that
manually in a terminal.
\end_layout
\begin_layout Standard
-Also note that CVS support is not as good as subversion support so we advice
+Also note that CVS support is not as good as subversion support so we advise
using SVN instead.
- Good place to start with Subversion is SVN Book
+ A good place to start learning Subversion is SVN Book
\begin_inset Foot
status open
\end_inset
.
- In case of RCS you should read
+ In the case of RCS you should read
\begin_inset Quotes eld
\end_inset
The implementation in LyX assumes a recent version of the GNU RCS or CVS/SVN
package—no guarantees are made for older versions.
Most of the log messages are not currently displayed after operations —
- you can check them in Messages pane if unsure.
+ you can check them in the Messages pane if unsure.
+ Regular users of version control will appreciate VC toolbar, which can
+ be enabled via
+\family sans
+View\SpecialChar \menuseparator
+Toolbars\SpecialChar \menuseparator
+Version
+\begin_inset space ~
+\end_inset
+
+Control
+\family default
+.
\end_layout
\begin_layout Standard
Control
\family default
submenu.
- LyX was tested against RCS 5.7/5.8.
+ LyX was tested against RCS 5.7/5.8
+\begin_inset Foot
+status open
+
+\begin_layout Plain Layout
+Note that old DOS / MS Windows builds (5.7) need to setup environment variables
+ in order to work properly with LyX.
+ In particular time zone (TZ) should be set and more importantly RCSINIT
+ in order to change default archive location ("SET RCSINIT=-x,v/") --- LyX
+ expects archive to be found in file.lyx,v within the original document directory.
+ See also README shipped with Windows RCS binaries.
+\end_layout
+
+\end_inset
+
+.
\end_layout
\begin_layout Subsubsection
\end_inset
- in case you have already the documents directory under CVS control (in
- particular
+ in the case you have already the documents directory under CVS control
+ (in particular
\family typewriter
CVS/Entries
\family default
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="2">
-<features tabularvalignment="middle">
+<features rotate="0" tabularvalignment="middle">
<column alignment="center" valignment="top" width="0">
<column alignment="center" valignment="top" width="0">
<row>
\end_layout
\begin_layout Standard
-Compared with Linux setting up svn client to communicate over ssh under
+Compared with Linux setting up an svn client to communicate over ssh under
Windows is a rather troublesome task.
We will at least offer some hints how to setup the client side but prior
knowledge about ssh and the Windows command line is needed, also be prepared
\end_layout
\begin_layout Enumerate
-Get a svn client for windows, as described in the previous sections.
+Get an svn client for windows, as described in the previous sections.
When it is a fresh install run some svn command (e.g.
\begin_inset Flex Code
\end_layout
\begin_layout Enumerate
-Choose a ssh client for Windows.
+Choose an ssh client for Windows.
There are several possibilities, we will use the one from Putty tools
\begin_inset Foot
status open
\end_inset
-/
+ /
\begin_inset Flex Code
status collapsed
dumps.
While this is useful for plain text files, it is much less useful in the
- case of LyX files, which have more complicated structure.
+ case of LyX files, which have more a complicated structure.
Hence we provide binding to the Document comparison feature.
- They are two ways of calling this feature - either by direct call of
+ There are two ways of calling this feature - either by direct call of
\begin_inset Flex Code
status collapsed
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\begin_layout Subsection
LyX and Literate Programming
+\change_inserted 274215730 1350434640
+ with Noweb
+\change_unchanged
+
\end_layout
\begin_layout Standard
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\begin_inset space \thinspace{}
\end_inset
-g.
+e.
\begin_inset space \space{}
\end_inset
\end_layout
\begin_layout Standard
-The down side of the Scrap paragraph layout is that consecutive paragraphs
- of code will be spaced with one empty line in the source code and also
- in the printed documentation.
+The down
+\change_deleted 274215730 1350432842
+
+\change_unchanged
+side of the Scrap paragraph layout is that consecutive paragraphs of code
+ will be spaced with one empty line in the source code and also in the printed
+ documentation.
The work around is to enter each line of code within a single Scrap, with
a newline (ctrl-return).
The example above will look like this:
\family typewriter
build-script $$i
\family default
-
+ $$r
\begin_inset Quotes erd
\end_inset
\end_inset
(a program or script) with the name of the Noweb file (normally a file
- in the LyX temp directory).
+ in the LyX temp directory) and the directory path of the original LyX file.
\end_layout
\end_layout
\begin_layout LyX-Code
-notangle -Rbuild-script $1 | env NOWEB_SOURCE=$1 sh
+notangle -Rbuild-script $1 | env NOWEB_SOURCE=$1 NOWEB_OUTPUT_DIR=$2 sh
\end_layout
\begin_layout Standard
\family typewriter
-parselog=listerrors
+parselog=$$s/scripts/listerrors
\family default
\begin_inset Quotes erd
program.
\end_layout
-\begin_layout Standard
-The converter code looks in
-\emph on
-MYLYXDIR/scripts
-\emph default
- first, then in
-\emph on
-LIBDIR/scripts
-\emph default
- then on the path for the
-\begin_inset Quotes eld
-\end_inset
-
-listerrors
-\begin_inset Quotes erd
-\end_inset
-
- program.
-\end_layout
-
\begin_layout Standard
The build will normally take place in LyX's temporary directory, so the
files produced by the conversion will be in that directory.
\family default
conversion may produce several files, and so most of these would then be
deleted when LyX was closed.
- The present solution is to use a `copier',
-\begin_inset Foot
-status collapsed
-
-\begin_layout Plain Layout
-See section
-\emph on
-Copiers
-\emph default
- of the
-\emph on
-Customization
-\emph default
- manual for information on these.
-\end_layout
-
-\end_inset
-
- in this case, the
-\family typewriter
-ext_copy.py
-\family default
- script in its default mode, so that the entire contents of the temporary
- directory is copied.
- More will get copied than is needed, to be sure, but nothing will be lost.
- If, however, you know what extensions the generated files will have, this
- can be improved by using the
-\family typewriter
--e
-\family default
- option to
-\family typewriter
-ext_copy
-\family default
-.
- This option takes a comma-separated list of extensions to copy.
- So, for example, if the conversion will generate only files with the extensions
-
-\family typewriter
-.c
-\family default
- and
-\family typewriter
-.h
-\family default
-, then the correct definition would be:
-\end_layout
-
-\begin_layout LyX-Code
-python -tt $$s/scripts/ext_copy.py -e c,h $$i $$o
-\end_layout
-
-\begin_layout Standard
-The result will be that only files with these two extensions will be copied
- out.
+ This is why we pass in the NOWEB_OUTPUT_DIR environment variable so that
+ the build-script scrap can place the generated files in that location.
\end_layout
\begin_layout Paragraph
\end_inset
[...
- code to extract files ...]
+ code to extract files ...
+ use NOWEB_OUTPUT_DIR here ...]
\begin_inset Newline newline
\end_inset
\begin_inset Quotes eld
\end_inset
-Conversion
+File Handling
\begin_inset Quotes erd
\end_inset
\begin_inset Quotes eld
\end_inset
-literate
+NoWeb
\begin_inset Quotes erd
\end_inset
\begin_inset space ~
\end_inset
-format Set up via the Formats tab, this is where the Noweb-specific pieces
- are set up.
+format Set up via the File Formats tab, this is where the Noweb-specific
+ pieces are set up.
The
\family sans
GUI Name
\family typewriter
build-script $$i
\family default
-
+ $$r
\begin_inset Quotes erd
\end_inset
\family typewriter
-originaldir,parselog=listerrors
+parselog=$$s/scripts/listerrors
\family default
\begin_inset Quotes erd
\end_layout
\begin_layout Standard
-I take advantage of the new created LyX server function and this ddd feature,
- and set
+I take advantage of the new
+\change_inserted 274215730 1350432999
+ly
+\change_unchanged
+ created LyX server function and this ddd feature, and set
\begin_inset Quotes eld
\end_inset
\begin_layout Standard
With this, whenever you are using ddd and find a point in the program that
you want to edit, you just press shift-ctrl-V (in the ddd window), and
- ddd you forward this information to LyX through the LyX server and then
- the LyX window will show the same file with the cursor at the same position
- ddd was pointing to.
+ ddd
+\change_deleted 274215730 1350433047
+you
+\change_inserted 274215730 1350433047
+will
+\change_unchanged
+ forward this information to LyX through the LyX server and then the LyX
+ window will show the same file with the cursor at the same position ddd
+ was pointing to.
No more guessing or long scrolling to locate a point in the program back
from debugging !
\end_layout
I recommend you choosing a color that is close to the background but not
equal, that way you still can see it is there, but it is not bothering
you anymore.
+
+\change_deleted 274215730 1350434691
+\change_inserted 274215730 1350434708
+
+\end_layout
+
+\begin_layout Subsection
+
+\change_inserted 274215730 1350434732
+LyX and knitr/Sweave
+\end_layout
+
+\begin_layout Standard
+
+\change_inserted 274215730 1350434777
+Support for knitr and Sweave is documented in the knitr.lyx example file
+ and in the Sweave manual (in the Help > Specific Manuals submenu).
+\change_unchanged
+
\end_layout
\begin_layout Chapter
For other special things you can do with figures, tables, floats, boxes
and notes, have a look at the
\emph on
-EmbeddedObjects
+Embedded
+\begin_inset space ~
+\end_inset
+
+Objects
\emph default
manual.
\end_layout
\backslash
setlength
\series default
- will be used for all following multiple columns until to change them again.
+ will be used for all following multiple columns until you change them again.
\end_layout
\end_inset