Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 One more question:
 I found Elsarticle-harv the style which comes quite close to what the
 editor/Springer wants, except
 
 it gives me for citations (Author, 2004) instead of (Author 2004)
 in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
 in the citation style selection.
 
 For \citealt there is a selection for Author 2004 (no comma).
 
 How could I get this right?
 
 Simply, instead of  looking only at what the citation style selection
 offers, looking at the pdf output. It is what you describe. No comma
 between author and year.
 
 The Elsarticle-harv style works with the natbib package.
 Whatever you set in natbib will be valid. The citation style is
 determined by natbib package, not by the style (bst) file.
 The bst file determines the bibliography style.
 
 By the way the Elsarticle-harv bibliography style is not what you
 described in your opening post. The year is not in parenthesis.
 
 I attach the lyx file and the pdf output made by using
 Elsarticle-harv.bst.
 
 bcsikos
Thanks, Csikos

my 
%setcitestyle{round,aysep={}}
\setcitestyle{comma,aysep={}}
-- 
-
Wolfgang Engelmann
Schlossgartenstrasse 22
D-72070 Tübingen
Tel 07071 68325

Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 One more question:
 I found Elsarticle-harv the style which comes quite close to what the
 editor/Springer wants, except
 
 it gives me for citations (Author, 2004) instead of (Author 2004)
 in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
 in the citation style selection.
 
 For \citealt there is a selection for Author 2004 (no comma).
 
 How could I get this right?
 
 Simply, instead of  looking only at what the citation style selection
 offers, looking at the pdf output. It is what you describe. No comma
 between author and year.
 
 The Elsarticle-harv style works with the natbib package.
 Whatever you set in natbib will be valid. The citation style is
 determined by natbib package, not by the style (bst) file.
 The bst file determines the bibliography style.
 
 By the way the Elsarticle-harv bibliography style is not what you
 described in your opening post. The year is not in parenthesis.
 
 I attach the lyx file and the pdf output made by using
 Elsarticle-harv.bst.
 
 bcsikos

Thanks, Csikos

instead of 
\setcitestyle{comma,aysep={}}
I had used
\setcitestyle{round,aysep={}}

changing it to comma gives me what I need.
I have to get familiar with the natbib package and its explanations. For 
the time being I am glad the chapter is now ready to be sent away.

I appreciated your help a lot.

Sorry for a mail sent a few minutes ago incidently and incomplete. 

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 One more question:
 I found Elsarticle-harv the style which comes quite close to what the
 editor/Springer wants, except
 
 it gives me for citations (Author, 2004) instead of (Author 2004)
 in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
 in the citation style selection.
 
 For \citealt there is a selection for Author 2004 (no comma).
 
 How could I get this right?
 
 Simply, instead of  looking only at what the citation style selection
 offers, looking at the pdf output. It is what you describe. No comma
 between author and year.
 
 The Elsarticle-harv style works with the natbib package.
 Whatever you set in natbib will be valid. The citation style is
 determined by natbib package, not by the style (bst) file.
 The bst file determines the bibliography style.
 
 By the way the Elsarticle-harv bibliography style is not what you
 described in your opening post. The year is not in parenthesis.
 
 I attach the lyx file and the pdf output made by using
 Elsarticle-harv.bst.
 
 bcsikos
Thanks, Csikos

my 
%setcitestyle{round,aysep={}}
\setcitestyle{comma,aysep={}}
-- 
-
Wolfgang Engelmann
Schlossgartenstrasse 22
D-72070 Tübingen
Tel 07071 68325

Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 One more question:
 I found Elsarticle-harv the style which comes quite close to what the
 editor/Springer wants, except
 
 it gives me for citations (Author, 2004) instead of (Author 2004)
 in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
 in the citation style selection.
 
 For \citealt there is a selection for Author 2004 (no comma).
 
 How could I get this right?
 
 Simply, instead of  looking only at what the citation style selection
 offers, looking at the pdf output. It is what you describe. No comma
 between author and year.
 
 The Elsarticle-harv style works with the natbib package.
 Whatever you set in natbib will be valid. The citation style is
 determined by natbib package, not by the style (bst) file.
 The bst file determines the bibliography style.
 
 By the way the Elsarticle-harv bibliography style is not what you
 described in your opening post. The year is not in parenthesis.
 
 I attach the lyx file and the pdf output made by using
 Elsarticle-harv.bst.
 
 bcsikos

Thanks, Csikos

instead of 
\setcitestyle{comma,aysep={}}
I had used
\setcitestyle{round,aysep={}}

changing it to comma gives me what I need.
I have to get familiar with the natbib package and its explanations. For 
the time being I am glad the chapter is now ready to be sent away.

I appreciated your help a lot.

Sorry for a mail sent a few minutes ago incidently and incomplete. 

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
> Wolfgang Engelmann  írta:
> >One more question:
> >I found Elsarticle-harv the style which comes quite close to what the
> >editor/Springer wants, except
> >
> >it gives me for citations (Author, 2004) instead of (Author 2004)
> >in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
> >in the citation style selection.
> >
> >For \citealt there is a selection for Author 2004 (no comma).
> >
> >How could I get this right?
> 
> Simply, instead of  looking only at what the citation style selection
> offers, looking at the pdf output. It is what you describe. No comma
> between author and year.
> 
> The Elsarticle-harv style works with the natbib package.
> Whatever you set in natbib will be valid. The citation style is
> determined by natbib package, not by the style (bst) file.
> The bst file determines the bibliography style.
> 
> By the way the Elsarticle-harv bibliography style is not what you
> described in your opening post. The year is not in parenthesis.
> 
> I attach the lyx file and the pdf output made by using
> Elsarticle-harv.bst.
> 
> bcsikos
Thanks, Csikos

my 
%setcitestyle{round,aysep={}}
\setcitestyle{comma,aysep={}}
-- 
-
Wolfgang Engelmann
Schlossgartenstrasse 22
D-72070 Tübingen
Tel 07071 68325

Re: Citation and reference style

[Wolfgang Engelmann]

Am Sunday, 25. August 2013, 23:19:32 schrieb Csikos Bela:
> Wolfgang Engelmann  írta:
> >One more question:
> >I found Elsarticle-harv the style which comes quite close to what the
> >editor/Springer wants, except
> >
> >it gives me for citations (Author, 2004) instead of (Author 2004)
> >in the \citep case. There is no offer for (Author 2004) (i.e. no comma)
> >in the citation style selection.
> >
> >For \citealt there is a selection for Author 2004 (no comma).
> >
> >How could I get this right?
> 
> Simply, instead of  looking only at what the citation style selection
> offers, looking at the pdf output. It is what you describe. No comma
> between author and year.
> 
> The Elsarticle-harv style works with the natbib package.
> Whatever you set in natbib will be valid. The citation style is
> determined by natbib package, not by the style (bst) file.
> The bst file determines the bibliography style.
> 
> By the way the Elsarticle-harv bibliography style is not what you
> described in your opening post. The year is not in parenthesis.
> 
> I attach the lyx file and the pdf output made by using
> Elsarticle-harv.bst.
> 
> bcsikos

Thanks, Csikos

instead of 
\setcitestyle{comma,aysep={}}
I had used
\setcitestyle{round,aysep={}}

changing it to comma gives me what I need.
I have to get familiar with the natbib package and its explanations. For 
the time being I am glad the chapter is now ready to be sent away.

I appreciated your help a lot.

Sorry for a mail sent a few minutes ago incidently and incomplete. 

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 
 I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.
 
 For clarification I include a small lyx file and bib file with which I
 tried out your authdate.bst file you had sent, but it did not work (??
 instead of citations, no references, no error message.
 
 It works perfectly. In your sample lyx file you have loaded natbib
 twice, probably that was the reason for fail. If you load natbib
 through lyx GUI you must not load it again in your preamble.
 
 I modified your sample lyx file and I attach it here with the output
 pdf.
 
 bcsikos

Thanks again, Csikos. 

I do not quite understand 
documentbibliography

there are only 3 citation styles:

default (numerical)
Natbib with style Author-year and numerical
and 
Jurabib

How would I modify Natbib with something else besides Author-year (eg 
round, comma)? In the preamble, and would this overwrite the bibliography 
setting? (eg with your \setcitestyle{comma,aysep={}}? 
Why is default only numerical? What if I want Kluwer style or something 
else? I can't leave everything unchecked in Bibliography, I have to check 
one. 

Wolfgang

Re: Citation and reference style

[Julien Rioux]

On 24/08/2013 3:13 AM, Wolfgang Engelmann wrote:

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:

  Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

 

  I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.

 

  For clarification I include a small lyx file and bib file with which I

  tried out your authdate.bst file you had sent, but it did not work (??

  instead of citations, no references, no error message.

 

  It works perfectly. In your sample lyx file you have loaded natbib

  twice, probably that was the reason for fail. If you load natbib

  through lyx GUI you must not load it again in your preamble.

 

  I modified your sample lyx file and I attach it here with the output

  pdf.

 

  bcsikos

Thanks again, Csikos.

I do not quite understand

documentbibliography

there are only 3 citation styles:

default (numerical)

Natbib with style Author-year and numerical

and

Jurabib

How would I modify Natbib with something else besides Author-year (eg
round, comma)? In the preamble, and would this overwrite the
bibliography setting? (eg with your \setcitestyle{comma,aysep={}}?

Why is default only numerical? What if I want Kluwer style or something
else? I can't leave everything unchecked in Bibliography, I have to
check one.



The file kluwer.bst is used with harvard.sty or natbib.sty. If you watn 
to use harvard.sty, select the default bibliography and put


\usepackage{harvard}

in your document preamble. If you want to use natbib.sty instead 
(recommended), select the natbib author-year setting. If you need 
additional customization of natbib options, do it in the document 
preamble as Csikos explained.


kluwer.bst supports full author citation, so you're good to use it with 
all the natbib features.


Cheers,
Julien

Re: Citation and reference style

[Julien Rioux]

On 23/08/2013 3:08 AM, Wolfgang Engelmann wrote:

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:

  So I select under toolsoutputlatex Bibliography Processor  bibtex

  (or custom? or bibtex8?)

 

  It seems you are using an older lyx version. It should work with it,

  still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.

I am using 2.0.6

May be I should upgrade, but I am always afraid I do something wrong and
can't work with it afterward. There is a deadline for a book chapter
waiting...

 

  Set bibliography processor to bibtex. bibtex8 might work as well, I

  never tried it. If you select bibtex, make sure those fields in the bib

  database file that will be in the output do have only ASCII or latin-1

  encoded characters. Special characters should be replaced by latex

  commands (eg. ö is \{o} etc.).

 

  Since I have over 700 citations, I used Jabref for my bibliography and

  clicked the references via the lyx-export of jabref to the

  corresponding places of my document. If I use \setcitestyle{aysep={}}

  instead of your proposed \setcitestyle{round,aysep={}}, and if I put

  () around the citation, I get what I need.

 

  Do not add manually '(' and ')' around citations. The opening and

  closing braces (rounded, square, or other) are part of the citation.

  And it is better to add the citations within lyx.

 

  I don't know if jabref can handle the two different types of citations:

  ' and 'text (Author year) text'. Can it make a

  difference? If you insert the citations within lyx you can select which

  type you want. If you look at the source you can see that the latex

  command for the two types are different, \citet and \citep.

 

  Also, if you have several citations in a group, lyx can handle it.

  Can jabref handle that?

###I do it via lyx (add)

 

  Unfortunately you have to go through all the citations and adjust them

  manually. Or you can work on the .lyx source file directly using a text

  editor and replacing all cite* command with citep. (Make a backup

  of the original file before editing!) After this open your edited file

  in lyx, find the few (I suppose) occasions of 'text Author (year) text'

  type citations and adjust them manually.

 

  The \setcitestyle{round,aysep={}} and \setcitestyle{aysep={}}

  commands in the preamble have the same effect, as round is the

  default option in case of author-year citation. Removing or adding it

  does not make any difference.

 

  But what about eg: (Praschak-Rieder and Willeit 2012) and in case

  of three authors and more (Crosthwait et al. 1997)?

 

  I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!)
reference:

author 1

author 1 and author 2

author 1 et all (3 authors or more)

  Unfortunately latex handles citations in goups. One group is all

  the citations selected and added at the same time. All these citations

  will be between the same pair of parentheses. If you add neighboring

  citations separately, they will be within different parentheses pairs.

 

  The source also shows the difference. For example.

 

  3 citations in one group:

 

  \citep{citation1,citation2,citaton3}

 

  The output will be:

 

  (author1 year1, author2 year2, author3 year3)

 

  However if you add them separately, like this:

 

  \citep{citation1} \citep{citation2} \cite{citaton3}

 

  the output will be:

 

  (author1 year1) (author2 year2) (author3 year3)

 

  You can adjust the opening and closing braces and the seperators

  between authors etc using \setcitestyle.

 

  Read the natbib manual (available at CTAN) section 2.9 Selecting

  citation punctuation.

 

  Where in the .lyx file (or elsewhere) would I place the authdate.bst

  file you kindly supplied?

 

  You can put it anywhere you want, but the best place is the directory

  where your .lyx file is. You select the bst file by clicking 'BibTeX

  Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts



The .bst file has to be found by *bibtex*, so .lyx/layouts isn't a 
particularly good choice (unless you additionally tell bibtex to look 
there). The document directory, as suggested by Csikos, works just fine.


Cheers,
Julien

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:


I do not quite understand
documentbibliography

there are only 3 citation styles:


OK, I try to explain.
These 3 options are not citation styles.

LaTex has its own default command set and what it can do. 
However this set is limited. Therefore your can load packages 
(you could call them modules or plugins as well) which add 
further options (possibilities) to what you can do with LaTeX. 
That is loading packages increase the capabilities of LaTeX. 
These packages add new commands and/or modify basic 
commands. 

default (numerical) 
Natbib with style Author-year and numerical 
and Jurabib

When you select default, LyX does not load any package. 
In this case you can use only the default LaTeX bibliography 
capabilities, which is very limited. It only support numeric type 
citations (if I am correct).

If you want different citation/bibliography types you can load
packages (sty files). There are many of them, one is  jurabib, 
another one is  natbib package. These packages change 
LaTex default behavior and add new commands. 
All these packages are different. If you want to use one of them 
you have to learn how to use that specific one. The package manuals
describe how to use the given package. I only use the natbib 
package because it is very flexible.

Along with the package (sty file) bibliography generation requires 
a .bst file which defines the style (look) of the citations and the
bibliography (references). The bst style file has to support a given
package. Generally the sty files are accompanied with different
bst files you can use with them. For example the natbib package
comes with abbrvnat.bst, plainnat.bst, and unsrtnat.bst styles,
which are guaranteed to work with natbib package.


What if I want Kluwer style or something else?

In optimal case there should be a Kluwer.sty file and a Kluwer.bst 
file which  together make the correct output. If there are no such 
files you have to find another pair which makes the same output.


How would I modify Natbib with something else besides Author-year (eg 
round, comma)?

When you select natbib in Document-Settings-Bibliography, lyx
loads natbib package in the preamble:

\usepackage[authoryear]{natbib}

or

\usepackage[numbers]{natbib}

depending on your selection.

Turn on source view (View-View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


In the preamble, and would this overwrite the bibliography 
setting? (eg with your \setcitestyle{comma,aysep={}}?

Yes. Since the package is already loaded, you can not load it
again, or you'll get errors.

Instead modify the package options (without loading it again)
by  \setcitestyle command. Options and keywords are described 
in the natbib manual.


Why is default only numerical?

This is how LaTeX was written. It is not a problem, since there
are many packages that extends it.


I can't leave everything unchecked in Bibliography, I have to check 
one.

Yes, but if you check default (numerical) no additional package is 
 loaded. It equals to not selecting anything.

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Saturday, 24. August 2013, 16:01:01 schrieb Csikos Bela:

Thanks for this very illustrative and comprehensive explanation. I was not 
aware of this possibility: 
 Turn on source view (View-View Source), set it to showing
 Preamble Only. Note that you have to insert at least one citation
 for the command to be inserted.
good to know. Thanks.

One more question:
I found Elsarticle-harv the style which comes quite close to what the 
editor/Springer wants, except

it gives me for citations
(Author, 2004)
instead of 
(Author 2004)
in the \citep case.
There is no offer for 
(Author 2004) (i.e. no comma)
in the citation style selection.

For \citealt there is a selection for Author 2004 (no comma).

How could I get this right?

Wolfgang

Re: Citation and reference style

[John Kane]

 From: Csikos Bela bcsikos...@freemail.hu
To: lyx-users@lists.lyx.org 
Sent: Saturday, August 24, 2013 10:01:01 AM
Subject: Re: Citation and reference style
 



Turn on source view (View-View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


bcsikos

Ah thank you. I have been wondering how to do that and kept forgetting to ask.

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 
 I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.
 
 For clarification I include a small lyx file and bib file with which I
 tried out your authdate.bst file you had sent, but it did not work (??
 instead of citations, no references, no error message.
 
 It works perfectly. In your sample lyx file you have loaded natbib
 twice, probably that was the reason for fail. If you load natbib
 through lyx GUI you must not load it again in your preamble.
 
 I modified your sample lyx file and I attach it here with the output
 pdf.
 
 bcsikos

Thanks again, Csikos. 

I do not quite understand 
documentbibliography

there are only 3 citation styles:

default (numerical)
Natbib with style Author-year and numerical
and 
Jurabib

How would I modify Natbib with something else besides Author-year (eg 
round, comma)? In the preamble, and would this overwrite the bibliography 
setting? (eg with your \setcitestyle{comma,aysep={}}? 
Why is default only numerical? What if I want Kluwer style or something 
else? I can't leave everything unchecked in Bibliography, I have to check 
one. 

Wolfgang

Re: Citation and reference style

[Julien Rioux]

On 24/08/2013 3:13 AM, Wolfgang Engelmann wrote:

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:

  Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

 

  I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.

 

  For clarification I include a small lyx file and bib file with which I

  tried out your authdate.bst file you had sent, but it did not work (??

  instead of citations, no references, no error message.

 

  It works perfectly. In your sample lyx file you have loaded natbib

  twice, probably that was the reason for fail. If you load natbib

  through lyx GUI you must not load it again in your preamble.

 

  I modified your sample lyx file and I attach it here with the output

  pdf.

 

  bcsikos

Thanks again, Csikos.

I do not quite understand

documentbibliography

there are only 3 citation styles:

default (numerical)

Natbib with style Author-year and numerical

and

Jurabib

How would I modify Natbib with something else besides Author-year (eg
round, comma)? In the preamble, and would this overwrite the
bibliography setting? (eg with your \setcitestyle{comma,aysep={}}?

Why is default only numerical? What if I want Kluwer style or something
else? I can't leave everything unchecked in Bibliography, I have to
check one.



The file kluwer.bst is used with harvard.sty or natbib.sty. If you watn 
to use harvard.sty, select the default bibliography and put


\usepackage{harvard}

in your document preamble. If you want to use natbib.sty instead 
(recommended), select the natbib author-year setting. If you need 
additional customization of natbib options, do it in the document 
preamble as Csikos explained.


kluwer.bst supports full author citation, so you're good to use it with 
all the natbib features.


Cheers,
Julien

Re: Citation and reference style

[Julien Rioux]

On 23/08/2013 3:08 AM, Wolfgang Engelmann wrote:

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:

  So I select under toolsoutputlatex Bibliography Processor  bibtex

  (or custom? or bibtex8?)

 

  It seems you are using an older lyx version. It should work with it,

  still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.

I am using 2.0.6

May be I should upgrade, but I am always afraid I do something wrong and
can't work with it afterward. There is a deadline for a book chapter
waiting...

 

  Set bibliography processor to bibtex. bibtex8 might work as well, I

  never tried it. If you select bibtex, make sure those fields in the bib

  database file that will be in the output do have only ASCII or latin-1

  encoded characters. Special characters should be replaced by latex

  commands (eg. ö is \{o} etc.).

 

  Since I have over 700 citations, I used Jabref for my bibliography and

  clicked the references via the lyx-export of jabref to the

  corresponding places of my document. If I use \setcitestyle{aysep={}}

  instead of your proposed \setcitestyle{round,aysep={}}, and if I put

  () around the citation, I get what I need.

 

  Do not add manually '(' and ')' around citations. The opening and

  closing braces (rounded, square, or other) are part of the citation.

  And it is better to add the citations within lyx.

 

  I don't know if jabref can handle the two different types of citations:

  ' and 'text (Author year) text'. Can it make a

  difference? If you insert the citations within lyx you can select which

  type you want. If you look at the source you can see that the latex

  command for the two types are different, \citet and \citep.

 

  Also, if you have several citations in a group, lyx can handle it.

  Can jabref handle that?

###I do it via lyx (add)

 

  Unfortunately you have to go through all the citations and adjust them

  manually. Or you can work on the .lyx source file directly using a text

  editor and replacing all cite* command with citep. (Make a backup

  of the original file before editing!) After this open your edited file

  in lyx, find the few (I suppose) occasions of 'text Author (year) text'

  type citations and adjust them manually.

 

  The \setcitestyle{round,aysep={}} and \setcitestyle{aysep={}}

  commands in the preamble have the same effect, as round is the

  default option in case of author-year citation. Removing or adding it

  does not make any difference.

 

  But what about eg: (Praschak-Rieder and Willeit 2012) and in case

  of three authors and more (Crosthwait et al. 1997)?

 

  I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!)
reference:

author 1

author 1 and author 2

author 1 et all (3 authors or more)

  Unfortunately latex handles citations in goups. One group is all

  the citations selected and added at the same time. All these citations

  will be between the same pair of parentheses. If you add neighboring

  citations separately, they will be within different parentheses pairs.

 

  The source also shows the difference. For example.

 

  3 citations in one group:

 

  \citep{citation1,citation2,citaton3}

 

  The output will be:

 

  (author1 year1, author2 year2, author3 year3)

 

  However if you add them separately, like this:

 

  \citep{citation1} \citep{citation2} \cite{citaton3}

 

  the output will be:

 

  (author1 year1) (author2 year2) (author3 year3)

 

  You can adjust the opening and closing braces and the seperators

  between authors etc using \setcitestyle.

 

  Read the natbib manual (available at CTAN) section 2.9 Selecting

  citation punctuation.

 

  Where in the .lyx file (or elsewhere) would I place the authdate.bst

  file you kindly supplied?

 

  You can put it anywhere you want, but the best place is the directory

  where your .lyx file is. You select the bst file by clicking 'BibTeX

  Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts



The .bst file has to be found by *bibtex*, so .lyx/layouts isn't a 
particularly good choice (unless you additionally tell bibtex to look 
there). The document directory, as suggested by Csikos, works just fine.


Cheers,
Julien

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:


I do not quite understand
documentbibliography

there are only 3 citation styles:


OK, I try to explain.
These 3 options are not citation styles.

LaTex has its own default command set and what it can do. 
However this set is limited. Therefore your can load packages 
(you could call them modules or plugins as well) which add 
further options (possibilities) to what you can do with LaTeX. 
That is loading packages increase the capabilities of LaTeX. 
These packages add new commands and/or modify basic 
commands. 

default (numerical) 
Natbib with style Author-year and numerical 
and Jurabib

When you select default, LyX does not load any package. 
In this case you can use only the default LaTeX bibliography 
capabilities, which is very limited. It only support numeric type 
citations (if I am correct).

If you want different citation/bibliography types you can load
packages (sty files). There are many of them, one is  jurabib, 
another one is  natbib package. These packages change 
LaTex default behavior and add new commands. 
All these packages are different. If you want to use one of them 
you have to learn how to use that specific one. The package manuals
describe how to use the given package. I only use the natbib 
package because it is very flexible.

Along with the package (sty file) bibliography generation requires 
a .bst file which defines the style (look) of the citations and the
bibliography (references). The bst style file has to support a given
package. Generally the sty files are accompanied with different
bst files you can use with them. For example the natbib package
comes with abbrvnat.bst, plainnat.bst, and unsrtnat.bst styles,
which are guaranteed to work with natbib package.


What if I want Kluwer style or something else?

In optimal case there should be a Kluwer.sty file and a Kluwer.bst 
file which  together make the correct output. If there are no such 
files you have to find another pair which makes the same output.


How would I modify Natbib with something else besides Author-year (eg 
round, comma)?

When you select natbib in Document-Settings-Bibliography, lyx
loads natbib package in the preamble:

\usepackage[authoryear]{natbib}

or

\usepackage[numbers]{natbib}

depending on your selection.

Turn on source view (View-View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


In the preamble, and would this overwrite the bibliography 
setting? (eg with your \setcitestyle{comma,aysep={}}?

Yes. Since the package is already loaded, you can not load it
again, or you'll get errors.

Instead modify the package options (without loading it again)
by  \setcitestyle command. Options and keywords are described 
in the natbib manual.


Why is default only numerical?

This is how LaTeX was written. It is not a problem, since there
are many packages that extends it.


I can't leave everything unchecked in Bibliography, I have to check 
one.

Yes, but if you check default (numerical) no additional package is 
 loaded. It equals to not selecting anything.

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Saturday, 24. August 2013, 16:01:01 schrieb Csikos Bela:

Thanks for this very illustrative and comprehensive explanation. I was not 
aware of this possibility: 
 Turn on source view (View-View Source), set it to showing
 Preamble Only. Note that you have to insert at least one citation
 for the command to be inserted.
good to know. Thanks.

One more question:
I found Elsarticle-harv the style which comes quite close to what the 
editor/Springer wants, except

it gives me for citations
(Author, 2004)
instead of 
(Author 2004)
in the \citep case.
There is no offer for 
(Author 2004) (i.e. no comma)
in the citation style selection.

For \citealt there is a selection for Author 2004 (no comma).

How could I get this right?

Wolfgang

Re: Citation and reference style

[John Kane]

 From: Csikos Bela bcsikos...@freemail.hu
To: lyx-users@lists.lyx.org 
Sent: Saturday, August 24, 2013 10:01:01 AM
Subject: Re: Citation and reference style
 



Turn on source view (View-View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


bcsikos

Ah thank you. I have been wondering how to do that and kept forgetting to ask.

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:
> Wolfgang Engelmann  írta:
> 
> I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.
> 
> >For clarification I include a small lyx file and bib file with which I
> >tried out your authdate.bst file you had sent, but it did not work (??
> >instead of citations, no references, no error message.
> 
> It works perfectly. In your sample lyx file you have loaded natbib
> twice, probably that was the reason for fail. If you load natbib
> through lyx GUI you must not load it again in your preamble.
> 
> I modified your sample lyx file and I attach it here with the output
> pdf.
> 
> bcsikos

Thanks again, Csikos. 

I do not quite understand 
document>bibliography

there are only 3 citation styles:

default (numerical)
Natbib with style Author-year and numerical
and 
Jurabib

How would I modify Natbib with something else besides Author-year (eg 
round, comma)? In the preamble, and would this overwrite the bibliography 
setting? (eg with your \setcitestyle{comma,aysep={}}? 
Why is default only numerical? What if I want Kluwer style or something 
else? I can't leave everything unchecked in Bibliography, I have to check 
one. 

Wolfgang

Re: Citation and reference style

[Julien Rioux]

On 24/08/2013 3:13 AM, Wolfgang Engelmann wrote:

Am Friday, 23. August 2013, 20:41:37 schrieb Csikos Bela:

 > Wolfgang Engelmann  írta:

 >

 > I haven't tried 2.1 beta yet. 2.0.6 should work in your case perfectly.

 >

 > >For clarification I include a small lyx file and bib file with which I

 > >tried out your authdate.bst file you had sent, but it did not work (??

 > >instead of citations, no references, no error message.

 >

 > It works perfectly. In your sample lyx file you have loaded natbib

 > twice, probably that was the reason for fail. If you load natbib

 > through lyx GUI you must not load it again in your preamble.

 >

 > I modified your sample lyx file and I attach it here with the output

 > pdf.

 >

 > bcsikos

Thanks again, Csikos.

I do not quite understand

document>bibliography

there are only 3 citation styles:

default (numerical)

Natbib with style Author-year and numerical

and

Jurabib

How would I modify Natbib with something else besides Author-year (eg
round, comma)? In the preamble, and would this overwrite the
bibliography setting? (eg with your \setcitestyle{comma,aysep={}}?

Why is default only numerical? What if I want Kluwer style or something
else? I can't leave everything unchecked in Bibliography, I have to
check one.



The file kluwer.bst is used with harvard.sty or natbib.sty. If you watn 
to use harvard.sty, select the "default" bibliography and put


\usepackage{harvard}

in your document preamble. If you want to use natbib.sty instead 
(recommended), select the "natbib author-year" setting. If you need 
additional customization of natbib options, do it in the document 
preamble as Csikos explained.


kluwer.bst supports full author citation, so you're good to use it with 
all the natbib features.


Cheers,
Julien

Re: Citation and reference style

[Julien Rioux]

On 23/08/2013 3:08 AM, Wolfgang Engelmann wrote:

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:

 > >So I select under tools>output>latex> Bibliography Processor > bibtex

 > >(or custom? or bibtex8?)

 >

 > It seems you are using an older lyx version. It should work with it,

 > still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.

I am using 2.0.6

May be I should upgrade, but I am always afraid I do something wrong and
can't work with it afterward. There is a deadline for a book chapter
waiting...

 >

 > Set bibliography processor to bibtex. bibtex8 might work as well, I

 > never tried it. If you select bibtex, make sure those fields in the bib

 > database file that will be in the output do have only ASCII or latin-1

 > encoded characters. Special characters should be replaced by latex

 > commands (eg. ö is \"{o} etc.).

 >

 > >Since I have over 700 citations, I used Jabref for my bibliography and

 > >clicked the references via the lyx-export of jabref to the

 > >corresponding places of my document. If I use \setcitestyle{aysep={}}

 > >instead of your proposed \setcitestyle{round,aysep={}}, and if I put

 > >() around the citation, I get what I need.

 >

 > Do not add manually '(' and ')' around citations. The opening and

 > closing braces (rounded, square, or other) are part of the citation.

 > And it is better to add the citations within lyx.

 >

 > I don't know if jabref can handle the two different types of citations:

 > ' and 'text (Author year) text'. Can it make a

 > difference? If you insert the citations within lyx you can select which

 > type you want. If you look at the source you can see that the latex

 > command for the two types are different, \citet and \citep.

 >

 > Also, if you have several citations in a group, lyx can handle it.

 > Can jabref handle that?

###I do it via lyx (add)

 >

 > Unfortunately you have to go through all the citations and adjust them

 > manually. Or you can work on the .lyx source file directly using a text

 > editor and replacing all cite* command with citep. (Make a backup

 > of the original file before editing!) After this open your edited file

 > in lyx, find the few (I suppose) occasions of 'text Author (year) text'

 > type citations and adjust them manually.

 >

 > The \setcitestyle{round,aysep={}} and \setcitestyle{aysep={}}

 > commands in the preamble have the same effect, as round is the

 > default option in case of author-year citation. Removing or adding it

 > does not make any difference.

 >

 > >But what about eg: (Praschak-Rieder and Willeit 2012) and in case

 > >of three authors and more (Crosthwait et al. 1997)?

 >

 > I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!)
reference:

author 1

author 1 and author 2

author 1 et all (3 authors or more)

 > Unfortunately latex handles citations in goups. One group is all

 > the citations selected and added at the same time. All these citations

 > will be between the same pair of parentheses. If you add neighboring

 > citations separately, they will be within different parentheses pairs.

 >

 > The source also shows the difference. For example.

 >

 > 3 citations in one group:

 >

 > \citep{citation1,citation2,citaton3}

 >

 > The output will be:

 >

 > (author1 year1, author2 year2, author3 year3)

 >

 > However if you add them separately, like this:

 >

 > \citep{citation1} \citep{citation2} \cite{citaton3}

 >

 > the output will be:

 >

 > (author1 year1) (author2 year2) (author3 year3)

 >

 > You can adjust the opening and closing braces and the seperators

 > between authors etc using \setcitestyle.

 >

 > Read the natbib manual (available at CTAN) section 2.9 Selecting

 > citation punctuation.

 >

 > >Where in the .lyx file (or elsewhere) would I place the authdate.bst

 > >file you kindly supplied?

 >

 > You can put it anywhere you want, but the best place is the directory

 > where your .lyx file is. You select the bst file by clicking 'BibTeX

 > Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts



The .bst file has to be found by *bibtex*, so .lyx/layouts isn't a 
particularly good choice (unless you additionally tell bibtex to look 
there). The document directory, as suggested by Csikos, works just fine.


Cheers,
Julien

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann  írta:


>I do not quite understand
>document>bibliography
>
>there are only 3 citation styles:


OK, I try to explain.
These 3 options are not citation styles.

LaTex has its own default command set and what it can do. 
However this set is limited. Therefore your can load packages 
(you could call them modules or plugins as well) which add 
further options (possibilities) to what you can do with LaTeX. 
That is loading packages increase the capabilities of LaTeX. 
These packages add new commands and/or modify basic 
commands. 

>default (numerical) 
>Natbib with style Author-year and numerical 
>and Jurabib

When you select default, LyX does not load any package. 
In this case you can use only the default LaTeX bibliography 
capabilities, which is very limited. It only support numeric type 
citations (if I am correct).

If you want different citation/bibliography types you can load
packages (sty files). There are many of them, one is  jurabib, 
another one is  natbib package. These packages change 
LaTex default behavior and add new commands. 
All these packages are different. If you want to use one of them 
you have to learn how to use that specific one. The package manuals
describe how to use the given package. I only use the natbib 
package because it is very flexible.

Along with the package (sty file) bibliography generation requires 
a .bst file which defines the style (look) of the citations and the
bibliography (references). The bst style file has to support a given
package. Generally the sty files are accompanied with different
bst files you can use with them. For example the natbib package
comes with abbrvnat.bst, plainnat.bst, and unsrtnat.bst styles,
which are guaranteed to work with natbib package.


>What if I want Kluwer style or something else?

In optimal case there should be a Kluwer.sty file and a Kluwer.bst 
file which  together make the correct output. If there are no such 
files you have to find another pair which makes the same output.


>How would I modify Natbib with something else besides Author-year (eg 
>round, comma)?

When you select natbib in Document->Settings->Bibliography, lyx
loads natbib package in the preamble:

\usepackage[authoryear]{natbib}

or

\usepackage[numbers]{natbib}

depending on your selection.

Turn on source view (View->View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


>In the preamble, and would this overwrite the bibliography 
>setting? (eg with your \setcitestyle{comma,aysep={}}?

Yes. Since the package is already loaded, you can not load it
again, or you'll get errors.

Instead modify the package options (without loading it again)
by  \setcitestyle command. Options and keywords are described 
in the natbib manual.


>Why is default only numerical?

This is how LaTeX was written. It is not a problem, since there
are many packages that extends it.


>I can't leave everything unchecked in Bibliography, I have to check 
>one.

Yes, but if you check default (numerical) no additional package is 
 loaded. It equals to not selecting anything.

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Saturday, 24. August 2013, 16:01:01 schrieb Csikos Bela:

Thanks for this very illustrative and comprehensive explanation. I was not 
aware of this possibility: 
> Turn on source view (View->View Source), set it to showing
> Preamble Only. Note that you have to insert at least one citation
> for the command to be inserted.
good to know. Thanks.

One more question:
I found Elsarticle-harv the style which comes quite close to what the 
editor/Springer wants, except

it gives me for citations
(Author, 2004)
instead of 
(Author 2004)
in the \citep case.
There is no offer for 
(Author 2004) (i.e. no comma)
in the citation style selection.

For \citealt there is a selection for Author 2004 (no comma).

How could I get this right?

Wolfgang

Re: Citation and reference style

[John Kane]

 From: Csikos Bela <bcsikos...@freemail.hu>
To: lyx-users@lists.lyx.org 
Sent: Saturday, August 24, 2013 10:01:01 AM
Subject: Re: Citation and reference style
 



Turn on source view (View->View Source), set it to showing
Preamble Only. Note that you have to insert at least one citation 
for the command to be inserted.


bcsikos

Ah thank you. I have been wondering how to do that and kept forgetting to ask.

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:
 So I select under toolsoutputlatex Bibliography Processor  bibtex
 (or custom? or bibtex8?)
 
 It seems you are using an older lyx version. It should work with it,
 still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.
I am using 2.0.6
May be I should upgrade, but I am always afraid I do something wrong and 
can't work with it afterward. There is a deadline for a book chapter 
waiting...

 
 Set bibliography processor to bibtex. bibtex8 might work as well, I
 never tried it. If you select bibtex, make sure those fields in the bib
 database file that will be in the output do have only ASCII or latin-1
 encoded characters. Special characters should be replaced by latex
 commands (eg. ö is \{o} etc.).
 
 Since I have over 700 citations, I used Jabref for my bibliography and
 clicked the references via the lyx-export of jabref to the
 corresponding places of my document. If I use 
\setcitestyle{aysep={}}
 instead of your proposed \setcitestyle{round,aysep={}}, and if I put
 () around the citation, I get what I need.
 
 Do not add manually '(' and ')' around citations. The opening and
 closing braces (rounded, square, or other) are part of the citation.
 And it is better to add the citations within lyx.
 
 I don't know if jabref can handle the two different types of citations:
  ' and 'text (Author year) text'. Can it make a
 difference? If you insert the citations within lyx you can select which
 type you want. If you look at the source you can see that the latex
 command for the two types are different, \citet and \citep.
 
 Also, if you have several citations in a group, lyx can handle it.
 Can jabref handle that?
###I do it via lyx (add)
 
 Unfortunately you have to go through all the citations and adjust them
 manually. Or you can work on the .lyx source file directly using a text
 editor and replacing all cite* command with citep. (Make a backup
 of the original file before editing!) After this open your edited file
 in lyx, find the few (I suppose) occasions of 'text Author (year) text'
 type citations and adjust them manually.
 
 The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
 commands in the preamble have the same effect, as round is the
 default option in case of author-year citation. Removing or adding it
 does not make any difference.
 
 But what about eg: (Praschak-Rieder and Willeit 2012) and in case
 of three authors and more (Crosthwait et al. 1997)?
 
 I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!) 
reference:
author 1
author 1 and author 2
author 1 et all (3 authors or more)

 Unfortunately latex handles citations in goups. One group is all
 the citations selected and added at the same time. All these citations
 will be between the same pair of parentheses. If you add neighboring
 citations separately, they will be within different parentheses pairs.
 
 The source also shows the difference. For example.
 
 3 citations in one group:
 
 \citep{citation1,citation2,citaton3}
 
 The output will be:
 
 (author1 year1, author2 year2, author3 year3)
 
 However if you add them separately, like this:
 
 \citep{citation1} \citep{citation2} \cite{citaton3}
 
 the output will be:
 
 (author1 year1) (author2 year2) (author3 year3)
 
 You can adjust the opening and closing braces and the seperators
 between authors etc using \setcitestyle.
 
 Read the natbib manual (available at CTAN) section 2.9 Selecting
 citation punctuation.
 
 Where in the .lyx file (or elsewhere) would I place the authdate.bst
 file you kindly supplied?
 
 You can put it anywhere you want, but the best place is the directory
 where your .lyx file is. You select the bst file by clicking 'BibTeX
 Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts
 
 If you still have questions don't hesitate to ask, but be specific,
 please.

Hope I was this time.

Thanks,
Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

I am using 2.0.6

That is the latest stable version. I thought you worked with older version
since there is no toolsoutputlatex Bibliography Processor menu
in lyx 2.0.6. Now I see you only left out 'Preferences' step.


### here I meant the 'et al' after more then 2 authors in a (one!)
reference:
author 1
author 1 and author 2
author 1 et all (3 authors or more)

I still don't get it. Could you please give some real example embedded
in text? Anyway the et al. is handled automatically by bibtex.
If there is only one author the output is: (author year)
2 authors, output: (author1 and author2 year)
3 author, output: (author1 et al. year).

You find more examples in the natbib manual, Section 2.3 Basic
Citation Commands.

I suggest that you create a new file and insert only short text in it with
different citations and look at the output. Experience with it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts

I always keep the specific style along with the document.
I keep different documents in separate directories with the necessary
files (images, bibtex database and style file etc.).

So if I want to transfer/copy the document to another computer I transfer
the whole document directory. 

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 I am using 2.0.6
 
 That is the latest stable version. I thought you worked with older
 version since there is no toolsoutputlatex Bibliography Processor
 menu in lyx 2.0.6. Now I see you only left out 'Preferences' step.

Thanks again for your help, Csikos.

I tried for quite some time this morning to get the Lyx2.1beta installed by 
using LinuxMint Debian 15, but without success. I used 
http://ppa.launchpad.net/lyx-
devel/daily/ubuntu/dists/debian/main/source/Sources
so I gave up and used my lyx 2.0.6
(error: it could not find the lyx2.1 package
 
 ### here I meant the 'et al' after more then 2 authors in a (one!)
 reference:
 author 1
 author 1 and author 2
 author 1 et all (3 authors or more)
 
 I still don't get it. Could you please give some real example embedded
 in text? Anyway the et al. is handled automatically by bibtex.
 If there is only one author the output is: (author year)
 2 authors, output: (author1 and author2 year)
 3 author, output: (author1 et al. year).

For clarification I include a small lyx file and bib file with which I tried 
out your authdate.bst file you had sent, but it did not work (?? instead of 
citations, no references, no error message.
Instead I tried the authordate1, 2, 3 and 4 bst files from within lyx
and found authordate1 useful, but not adequate. 
So I have to fiddle around with it (I tried many other bst files from the 
dropdown menu, but none was as I need it). 

 
 You find more examples in the natbib manual, Section 2.3 Basic
 Citation Commands.

will read that and try to set up a correct one for my needs via makebst or 
something alike.
 
 I suggest that you create a new file and insert only short text in it
 with different citations and look at the output. Experience with it.
 
 ### I guess there is a 'normal' place? I have it now in .lyx/layouts
 
 I always keep the specific style along with the document.
 I keep different documents in separate directories with the necessary
 files (images, bibtex database and style file etc.).

So did I, except the style files. 

 
 So if I want to transfer/copy the document to another computer I
 transfer the whole document directory.

Yes.

Thanks for your patience.
I was hoping to get some help from the publisher (sv), but nothing so far.

Wolfgang
 
 bcsikos
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Bruce1972,
  author = {Bruce, V. G.},
  title = {Mutants of the biological clock in \emph{{C}hlamydomonas reinhardi}},
  journal = {Genetics},
  year = {1972},
  volume = {70},
  pages = {537--548},
  abstract = {A genetic analysis of the biological clock in Chlamydomonas reinhardi
	has been initiated. Of six wild-type strains tested (3 mt(+) and
	3 mt(-)), five had periods close to 24 hr whereas one had a 21-hr
	period. Mutants with altered clock period have been isolated. The
	periods of 3 of these variant strains are temperature compensated.
	Genetic crosses involving a long-period mutant suggest that a single
	gene confers the long-period character, and in general clock-period
	length seems to be a useful phenotypic measure of alterations in
	the clock due to genetic differences. One phase mutant was found
	but its behavior was variable and the phase of the rhythm, relative
	to a light-dark transition which initiates the rhythm, does not seem
	to be reliable as a parameter of clock differences. No markers have
	yet been mapped.},
  keywords = {Biological Clocks; Cell Movement; Chlamydomonas; Chlorophyta; Circadian
	Rhythm; Crosses, Genetic; Genotype; Methods; Mutation, drug effects;
	Nitrosoguanidines, pharmacology; Phenotype; Photic Stimulation; Temperature;
	Time Factors},
  language = {eng},
  medline-pst = {ppublish},
  owner = {wolfgang},
  pmid = {5034771},
  timestamp = {2012.03.02}
}

@ARTICLE{Gaskill2010,
  author = {Christa Gaskill and Jennifer Forbes-Stovall and Bruce Kessler and
	Mike Young and Claire A Rinehart and Sigrid Jacobshagen},
  title = {Improved automated monitoring and new analysis algorithm for circadian
	phototaxis rhythms in \emph{{C}hlamydomonas}},
  journal = {Plant Physiol Bioch},
  year = {2010},
  volume = {48},
  pages = {239--246},
  abstract = {Automated monitoring of circadian rhythms is an efficient way of gaining
	insight into oscillation parameters like period and phase for the
	underlying pacemaker of the circadian clock. 
	
	
	Measurement of the circadian rhythm of phototaxis (swimming towards
	light) exhibited by the green alga Chlamydomonas reinhardtii has
	been automated by directing a narrow and dim light beam through a
	culture at regular intervals and determining the decrease in light
	transmittance due to the accumulation of cells in the beam. 
	
	
	In this study, the monitoring process was optimized by constructing
	a new computer-controlled measuring machine that limits the test
	beam to wavelengths reported to be specific for 

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:

Hi, 

I think all my problems are solved. One of the authors of the chapters of 
the book insisted to send in a latex file to Springer publisher, and this 
was accepted. So he probably has the correct bst style file which I could 
use. And I don't need to convert to rtf or whatever. Heureka. One should be 
more courages in respect to the publishers (and editors). 

Thanks all for valuable help and making me learn quite a bit again.

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:
 So I select under toolsoutputlatex Bibliography Processor  bibtex
 (or custom? or bibtex8?)
 
 It seems you are using an older lyx version. It should work with it,
 still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.
I am using 2.0.6
May be I should upgrade, but I am always afraid I do something wrong and 
can't work with it afterward. There is a deadline for a book chapter 
waiting...

 
 Set bibliography processor to bibtex. bibtex8 might work as well, I
 never tried it. If you select bibtex, make sure those fields in the bib
 database file that will be in the output do have only ASCII or latin-1
 encoded characters. Special characters should be replaced by latex
 commands (eg. ö is \{o} etc.).
 
 Since I have over 700 citations, I used Jabref for my bibliography and
 clicked the references via the lyx-export of jabref to the
 corresponding places of my document. If I use 
\setcitestyle{aysep={}}
 instead of your proposed \setcitestyle{round,aysep={}}, and if I put
 () around the citation, I get what I need.
 
 Do not add manually '(' and ')' around citations. The opening and
 closing braces (rounded, square, or other) are part of the citation.
 And it is better to add the citations within lyx.
 
 I don't know if jabref can handle the two different types of citations:
  ' and 'text (Author year) text'. Can it make a
 difference? If you insert the citations within lyx you can select which
 type you want. If you look at the source you can see that the latex
 command for the two types are different, \citet and \citep.
 
 Also, if you have several citations in a group, lyx can handle it.
 Can jabref handle that?
###I do it via lyx (add)
 
 Unfortunately you have to go through all the citations and adjust them
 manually. Or you can work on the .lyx source file directly using a text
 editor and replacing all cite* command with citep. (Make a backup
 of the original file before editing!) After this open your edited file
 in lyx, find the few (I suppose) occasions of 'text Author (year) text'
 type citations and adjust them manually.
 
 The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
 commands in the preamble have the same effect, as round is the
 default option in case of author-year citation. Removing or adding it
 does not make any difference.
 
 But what about eg: (Praschak-Rieder and Willeit 2012) and in case
 of three authors and more (Crosthwait et al. 1997)?
 
 I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!) 
reference:
author 1
author 1 and author 2
author 1 et all (3 authors or more)

 Unfortunately latex handles citations in goups. One group is all
 the citations selected and added at the same time. All these citations
 will be between the same pair of parentheses. If you add neighboring
 citations separately, they will be within different parentheses pairs.
 
 The source also shows the difference. For example.
 
 3 citations in one group:
 
 \citep{citation1,citation2,citaton3}
 
 The output will be:
 
 (author1 year1, author2 year2, author3 year3)
 
 However if you add them separately, like this:
 
 \citep{citation1} \citep{citation2} \cite{citaton3}
 
 the output will be:
 
 (author1 year1) (author2 year2) (author3 year3)
 
 You can adjust the opening and closing braces and the seperators
 between authors etc using \setcitestyle.
 
 Read the natbib manual (available at CTAN) section 2.9 Selecting
 citation punctuation.
 
 Where in the .lyx file (or elsewhere) would I place the authdate.bst
 file you kindly supplied?
 
 You can put it anywhere you want, but the best place is the directory
 where your .lyx file is. You select the bst file by clicking 'BibTeX
 Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts
 
 If you still have questions don't hesitate to ask, but be specific,
 please.

Hope I was this time.

Thanks,
Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

I am using 2.0.6

That is the latest stable version. I thought you worked with older version
since there is no toolsoutputlatex Bibliography Processor menu
in lyx 2.0.6. Now I see you only left out 'Preferences' step.


### here I meant the 'et al' after more then 2 authors in a (one!)
reference:
author 1
author 1 and author 2
author 1 et all (3 authors or more)

I still don't get it. Could you please give some real example embedded
in text? Anyway the et al. is handled automatically by bibtex.
If there is only one author the output is: (author year)
2 authors, output: (author1 and author2 year)
3 author, output: (author1 et al. year).

You find more examples in the natbib manual, Section 2.3 Basic
Citation Commands.

I suggest that you create a new file and insert only short text in it with
different citations and look at the output. Experience with it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts

I always keep the specific style along with the document.
I keep different documents in separate directories with the necessary
files (images, bibtex database and style file etc.).

So if I want to transfer/copy the document to another computer I transfer
the whole document directory. 

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 I am using 2.0.6
 
 That is the latest stable version. I thought you worked with older
 version since there is no toolsoutputlatex Bibliography Processor
 menu in lyx 2.0.6. Now I see you only left out 'Preferences' step.

Thanks again for your help, Csikos.

I tried for quite some time this morning to get the Lyx2.1beta installed by 
using LinuxMint Debian 15, but without success. I used 
http://ppa.launchpad.net/lyx-
devel/daily/ubuntu/dists/debian/main/source/Sources
so I gave up and used my lyx 2.0.6
(error: it could not find the lyx2.1 package
 
 ### here I meant the 'et al' after more then 2 authors in a (one!)
 reference:
 author 1
 author 1 and author 2
 author 1 et all (3 authors or more)
 
 I still don't get it. Could you please give some real example embedded
 in text? Anyway the et al. is handled automatically by bibtex.
 If there is only one author the output is: (author year)
 2 authors, output: (author1 and author2 year)
 3 author, output: (author1 et al. year).

For clarification I include a small lyx file and bib file with which I tried 
out your authdate.bst file you had sent, but it did not work (?? instead of 
citations, no references, no error message.
Instead I tried the authordate1, 2, 3 and 4 bst files from within lyx
and found authordate1 useful, but not adequate. 
So I have to fiddle around with it (I tried many other bst files from the 
dropdown menu, but none was as I need it). 

 
 You find more examples in the natbib manual, Section 2.3 Basic
 Citation Commands.

will read that and try to set up a correct one for my needs via makebst or 
something alike.
 
 I suggest that you create a new file and insert only short text in it
 with different citations and look at the output. Experience with it.
 
 ### I guess there is a 'normal' place? I have it now in .lyx/layouts
 
 I always keep the specific style along with the document.
 I keep different documents in separate directories with the necessary
 files (images, bibtex database and style file etc.).

So did I, except the style files. 

 
 So if I want to transfer/copy the document to another computer I
 transfer the whole document directory.

Yes.

Thanks for your patience.
I was hoping to get some help from the publisher (sv), but nothing so far.

Wolfgang
 
 bcsikos
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Bruce1972,
  author = {Bruce, V. G.},
  title = {Mutants of the biological clock in \emph{{C}hlamydomonas reinhardi}},
  journal = {Genetics},
  year = {1972},
  volume = {70},
  pages = {537--548},
  abstract = {A genetic analysis of the biological clock in Chlamydomonas reinhardi
	has been initiated. Of six wild-type strains tested (3 mt(+) and
	3 mt(-)), five had periods close to 24 hr whereas one had a 21-hr
	period. Mutants with altered clock period have been isolated. The
	periods of 3 of these variant strains are temperature compensated.
	Genetic crosses involving a long-period mutant suggest that a single
	gene confers the long-period character, and in general clock-period
	length seems to be a useful phenotypic measure of alterations in
	the clock due to genetic differences. One phase mutant was found
	but its behavior was variable and the phase of the rhythm, relative
	to a light-dark transition which initiates the rhythm, does not seem
	to be reliable as a parameter of clock differences. No markers have
	yet been mapped.},
  keywords = {Biological Clocks; Cell Movement; Chlamydomonas; Chlorophyta; Circadian
	Rhythm; Crosses, Genetic; Genotype; Methods; Mutation, drug effects;
	Nitrosoguanidines, pharmacology; Phenotype; Photic Stimulation; Temperature;
	Time Factors},
  language = {eng},
  medline-pst = {ppublish},
  owner = {wolfgang},
  pmid = {5034771},
  timestamp = {2012.03.02}
}

@ARTICLE{Gaskill2010,
  author = {Christa Gaskill and Jennifer Forbes-Stovall and Bruce Kessler and
	Mike Young and Claire A Rinehart and Sigrid Jacobshagen},
  title = {Improved automated monitoring and new analysis algorithm for circadian
	phototaxis rhythms in \emph{{C}hlamydomonas}},
  journal = {Plant Physiol Bioch},
  year = {2010},
  volume = {48},
  pages = {239--246},
  abstract = {Automated monitoring of circadian rhythms is an efficient way of gaining
	insight into oscillation parameters like period and phase for the
	underlying pacemaker of the circadian clock. 
	
	
	Measurement of the circadian rhythm of phototaxis (swimming towards
	light) exhibited by the green alga Chlamydomonas reinhardtii has
	been automated by directing a narrow and dim light beam through a
	culture at regular intervals and determining the decrease in light
	transmittance due to the accumulation of cells in the beam. 
	
	
	In this study, the monitoring process was optimized by constructing
	a new computer-controlled measuring machine that limits the test
	beam to wavelengths reported to be specific for 

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:

Hi, 

I think all my problems are solved. One of the authors of the chapters of 
the book insisted to send in a latex file to Springer publisher, and this 
was accepted. So he probably has the correct bst style file which I could 
use. And I don't need to convert to rtf or whatever. Heureka. One should be 
more courages in respect to the publishers (and editors). 

Thanks all for valuable help and making me learn quite a bit again.

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 20:46:14 schrieb Csikos Bela:
> >So I select under tools>output>latex> Bibliography Processor > bibtex
> >(or custom? or bibtex8?)
> 
> It seems you are using an older lyx version. It should work with it,
> still I suggest upgrading lyx to version 2.x.

###Thanks for your answer.
I am using 2.0.6
May be I should upgrade, but I am always afraid I do something wrong and 
can't work with it afterward. There is a deadline for a book chapter 
waiting...

> 
> Set bibliography processor to bibtex. bibtex8 might work as well, I
> never tried it. If you select bibtex, make sure those fields in the bib
> database file that will be in the output do have only ASCII or latin-1
> encoded characters. Special characters should be replaced by latex
> commands (eg. ö is \"{o} etc.).
> 
> >Since I have over 700 citations, I used Jabref for my bibliography and
> >clicked the references via the lyx-export of jabref to the
> >corresponding places of my document. If I use 
\setcitestyle{aysep={}}
> >instead of your proposed \setcitestyle{round,aysep={}}, and if I put
> >() around the citation, I get what I need.
> 
> Do not add manually '(' and ')' around citations. The opening and
> closing braces (rounded, square, or other) are part of the citation.
> And it is better to add the citations within lyx.
> 
> I don't know if jabref can handle the two different types of citations:
>  ' and 'text (Author year) text'. Can it make a
> difference? If you insert the citations within lyx you can select which
> type you want. If you look at the source you can see that the latex
> command for the two types are different, \citet and \citep.
> 
> Also, if you have several citations in a group, lyx can handle it.
> Can jabref handle that?
###I do it via lyx (add)
> 
> Unfortunately you have to go through all the citations and adjust them
> manually. Or you can work on the .lyx source file directly using a text
> editor and replacing all cite* command with citep. (Make a backup
> of the original file before editing!) After this open your edited file
> in lyx, find the few (I suppose) occasions of 'text Author (year) text'
> type citations and adjust them manually.
> 
> The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
> commands in the preamble have the same effect, as round is the
> default option in case of author-year citation. Removing or adding it
> does not make any difference.
> 
> >But what about eg: (Praschak-Rieder and Willeit 2012) and in case
> >of three authors and more (Crosthwait et al. 1997)?
> 
> I don't understand what your question is.

### here I meant the 'et al' after more then 2 authors in a (one!) 
reference:
author 1
author 1 and author 2
author 1 et all (3 authors or more)

> Unfortunately latex handles citations in goups. One group is all
> the citations selected and added at the same time. All these citations
> will be between the same pair of parentheses. If you add neighboring
> citations separately, they will be within different parentheses pairs.
> 
> The source also shows the difference. For example.
> 
> 3 citations in one group:
> 
> \citep{citation1,citation2,citaton3}
> 
> The output will be:
> 
> (author1 year1, author2 year2, author3 year3)
> 
> However if you add them separately, like this:
> 
> \citep{citation1} \citep{citation2} \cite{citaton3}
> 
> the output will be:
> 
> (author1 year1) (author2 year2) (author3 year3)
> 
> You can adjust the opening and closing braces and the seperators
> between authors etc using \setcitestyle.
> 
> Read the natbib manual (available at CTAN) section 2.9 Selecting
> citation punctuation.
> 
> >Where in the .lyx file (or elsewhere) would I place the authdate.bst
> >file you kindly supplied?
> 
> You can put it anywhere you want, but the best place is the directory
> where your .lyx file is. You select the bst file by clicking 'BibTeX
> Generated Bibliography' and browse for it.

### I guess there is a 'normal' place? I have it now in .lyx/layouts
> 
> If you still have questions don't hesitate to ask, but be specific,
> please.

Hope I was this time.

Thanks,
Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann  írta:

>I am using 2.0.6

That is the latest stable version. I thought you worked with older version
since there is no tools>output>latex> Bibliography Processor menu
in lyx 2.0.6. Now I see you only left out 'Preferences' step.


>### here I meant the 'et al' after more then 2 authors in a (one!)
>reference:
>author 1
>author 1 and author 2
>author 1 et all (3 authors or more)

I still don't get it. Could you please give some real example embedded
in text? Anyway the et al. is handled automatically by bibtex.
If there is only one author the output is: (author year)
2 authors, output: (author1 and author2 year)
3 author, output: (author1 et al. year).

You find more examples in the natbib manual, Section 2.3 Basic
Citation Commands.

I suggest that you create a new file and insert only short text in it with
different citations and look at the output. Experience with it.

>### I guess there is a 'normal' place? I have it now in .lyx/layouts

I always keep the specific style along with the document.
I keep different documents in separate directories with the necessary
files (images, bibtex database and style file etc.).

So if I want to transfer/copy the document to another computer I transfer
the whole document directory. 

bcsikos

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:
> Wolfgang Engelmann  írta:
> >I am using 2.0.6
> 
> That is the latest stable version. I thought you worked with older
> version since there is no tools>output>latex> Bibliography Processor
> menu in lyx 2.0.6. Now I see you only left out 'Preferences' step.

Thanks again for your help, Csikos.

I tried for quite some time this morning to get the Lyx2.1beta installed by 
using LinuxMint Debian 15, but without success. I used 
http://ppa.launchpad.net/lyx-
devel/daily/ubuntu/dists/debian/main/source/Sources
so I gave up and used my lyx 2.0.6
(error: it could not find the lyx2.1 package
> 
> >### here I meant the 'et al' after more then 2 authors in a (one!)
> >reference:
> >author 1
> >author 1 and author 2
> >author 1 et all (3 authors or more)
> 
> I still don't get it. Could you please give some real example embedded
> in text? Anyway the et al. is handled automatically by bibtex.
> If there is only one author the output is: (author year)
> 2 authors, output: (author1 and author2 year)
> 3 author, output: (author1 et al. year).

For clarification I include a small lyx file and bib file with which I tried 
out your authdate.bst file you had sent, but it did not work (?? instead of 
citations, no references, no error message.
Instead I tried the authordate1, 2, 3 and 4 bst files from within lyx
and found authordate1 useful, but not adequate. 
So I have to fiddle around with it (I tried many other bst files from the 
dropdown menu, but none was as I need it). 

> 
> You find more examples in the natbib manual, Section 2.3 Basic
> Citation Commands.

will read that and try to set up a correct one for my needs via makebst or 
something alike.
> 
> I suggest that you create a new file and insert only short text in it
> with different citations and look at the output. Experience with it.
> 
> >### I guess there is a 'normal' place? I have it now in .lyx/layouts
> 
> I always keep the specific style along with the document.
> I keep different documents in separate directories with the necessary
> files (images, bibtex database and style file etc.).

So did I, except the style files. 

> 
> So if I want to transfer/copy the document to another computer I
> transfer the whole document directory.

Yes.

Thanks for your patience.
I was hoping to get some help from the publisher (sv), but nothing so far.

Wolfgang
> 
> bcsikos
% This file was created with JabRef 2.7b.
% Encoding: ISO8859_1

@ARTICLE{Bruce1972,
  author = {Bruce, V. G.},
  title = {Mutants of the biological clock in \emph{{C}hlamydomonas reinhardi}},
  journal = {Genetics},
  year = {1972},
  volume = {70},
  pages = {537--548},
  abstract = {A genetic analysis of the biological clock in Chlamydomonas reinhardi
	has been initiated. Of six wild-type strains tested (3 mt(+) and
	3 mt(-)), five had periods close to 24 hr whereas one had a 21-hr
	period. Mutants with altered clock period have been isolated. The
	periods of 3 of these variant strains are temperature compensated.
	Genetic crosses involving a long-period mutant suggest that a single
	gene confers the long-period character, and in general clock-period
	length seems to be a useful phenotypic measure of alterations in
	the clock due to genetic differences. One phase mutant was found
	but its behavior was variable and the phase of the rhythm, relative
	to a light-dark transition which initiates the rhythm, does not seem
	to be reliable as a parameter of clock differences. No markers have
	yet been mapped.},
  keywords = {Biological Clocks; Cell Movement; Chlamydomonas; Chlorophyta; Circadian
	Rhythm; Crosses, Genetic; Genotype; Methods; Mutation, drug effects;
	Nitrosoguanidines, pharmacology; Phenotype; Photic Stimulation; Temperature;
	Time Factors},
  language = {eng},
  medline-pst = {ppublish},
  owner = {wolfgang},
  pmid = {5034771},
  timestamp = {2012.03.02}
}

@ARTICLE{Gaskill2010,
  author = {Christa Gaskill and Jennifer Forbes-Stovall and Bruce Kessler and
	Mike Young and Claire A Rinehart and Sigrid Jacobshagen},
  title = {Improved automated monitoring and new analysis algorithm for circadian
	phototaxis rhythms in \emph{{C}hlamydomonas}},
  journal = {Plant Physiol Bioch},
  year = {2010},
  volume = {48},
  pages = {239--246},
  abstract = {Automated monitoring of circadian rhythms is an efficient way of gaining
	insight into oscillation parameters like period and phase for the
	underlying pacemaker of the circadian clock. 
	
	
	Measurement of the circadian rhythm of phototaxis (swimming towards
	light) exhibited by the green alga Chlamydomonas reinhardtii has
	been automated by directing a narrow and dim light beam through a
	culture at regular intervals and determining the decrease in light
	transmittance due to the accumulation of cells in the beam. 
	
	
	In this study, the monitoring process was optimized by constructing
	a new computer-controlled measuring machine that limits the test
	

Re: Citation and reference style

[Wolfgang Engelmann]

Am Friday, 23. August 2013, 11:21:26 schrieb Csikos Bela:

Hi, 

I think all my problems are solved. One of the authors of the chapters of 
the book insisted to send in a latex file to Springer publisher, and this 
was accepted. So he probably has the correct bst style file which I could 
use. And I don't need to convert to rtf or whatever. Heureka. One should be 
more courages in respect to the publishers (and editors). 

Thanks all for valuable help and making me learn quite a bit again.

Wolfgang

Citation and reference style

[Wolfgang Engelmann]

Dear List

I need the following formating in the references:
Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
Weitzman, E. D. (1982)
Mathematical model of the human circadian system with two interacting 
oscillators. Am. J. Physiol. 242, 3–17.

I use under Debian squeeze in Lyx
document class book (KOMA script) 
class options: authoryear
in Bibliography Citation Style: natbib style: author-year

and get the following:
R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
Weitzman. Mathematical model of the human circadian system with two 
interacting oscillators. AmPhysiol, 242:3–17, 1982.

Note: The abbreviation of the Journal name is not important

Furthermore, I need the following formating of citations in the document 
Menaker et al. (1997) says ..
and
as mentioned (Lamprey et al. 1997).

what I get is
Menaker et al. [1997] 
and
as mentioned Lamprey et al. [1997]

The main question is, where in the net could I find examples for it to figure 
out myself.
The most urgent question is, how could I fix it. 

Should it be done in the 
document class and class options
and/or in Bibliography Citation Style
or in the preamble?
Do I have to use makebst, or can I avoid it?

How difficult is it nowadays to use biblatex. I tried before but failed.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

Dear List

I need the following formating in the references:

Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
Weitzman, E. D.
(1982) Mathematical model of the human circadian system with two interacting
oscillators. Am. J. Physiol. 242, 3–17.

I use under Debian squeeze in Lyx document class book (KOMA script)
class options: authoryear
in Bibliography Citation style: natbib style: author-year

and get the following:
R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
Weitzman.
Mathematical model of the human circadian system with two interacting 
oscillators.
AmPhysiol, 242:3–17, 1982.

Note: The abbreviation of the Journal name is not important

Furthermore, I need the following formating of citations in the document
Menaker et al. (1997) says ..
and
as mentioned (Lamprey et al. 1997).
what I get is
Menaker et al. [1997]
and
as mentioned Lamprey et al. [1997]

The main question is, where in the net could I find examples for it to figure 
out myself.
The most urgent question is, how could I fix it.
Should it be done in the document class and class options and/or in 
Bibliography Citation
style or in the preamble? Do I have to use makebst, or can I avoid it?
How difficult is it nowadays to use biblatex. I tried before but failed.

Wolfgang


Hello:

1. I can't help you regarding biblatex as I don't have experience with it.
I like to tweak bibliography styles according to my like/need, and I found that 
it is more
difficult in biblatex than in bibtex with natbib.

2. Using bibtex, the natbib package can do what you want.
The look/style of bibliography and citations mostly will depend on 3 things:
  a. The bibliography style (.bst file).
  b. The citation command for a given citation.
  c. The content of the bibtex database (.bib file).

3. Let's go through it how to get the styles you want.

In LyX go to Document-Settings. Do not apply the class option 'authoryear'
you mentioned. Go to 'Bibliography' and select 'Natbib' and 'Natbib-style:
Author-Year. This loads natbib package automatically. Click OK or Apply.

In the document where you want to insert your reference list, do:
Insert-List/TOC-BibTeX bibliography. Select a style file (e.g. plainnat) and
your bibtex database (.bib) file. Click OK.

Next insert a citation into your document by Insert-Citation or clicking the
insert citation icon. Select the citations, click 'Add'. Look at the 
'Formatting:
Citation style' pulldown menu in the window. Here you can select the style of
the citation; 'Menaker et al. (1997)' or '(Lamprey et al. 1997)'.

By default you will get [ ] limiters, but you need ( ) instead.
Write in your document preamble (Document-Settings-LaTeX Preamble):

\setcitestyle{round,aysep={}}

The aysep={} defines the separator between author and name in the citations.

Now you have to adjust the references style according to your needs.
You can try to find a .bst style file on the net and use it.
You can also try the different style files which come with latex
installations (plainnat, authordate, harvard etc.).
Or you can make your own customized style by using custom-bib
or bib-it. See this message:

http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html

I attach a .bst file (authdate.bst) that might fit your needs.

bcsikos



authdate.bst
Description: Binary data

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 Dear List
 
 I need the following formating in the references:
 
 Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and
 Weitzman, E. D. (1982) Mathematical model of the human circadian
 system with two interacting oscillators. Am. J. Physiol. 242, 3–17.
 
 I use under Debian squeeze in Lyx document class book (KOMA script)
 class options: authoryear
 in Bibliography Citation style: natbib style: author-year
 
 and get the following:
 R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E.
 D. Weitzman. Mathematical model of the human circadian system with two
 interacting oscillators. AmPhysiol, 242:3–17, 1982.
 
 Note: The abbreviation of the Journal name is not important
 
 Furthermore, I need the following formating of citations in the
 document Menaker et al. (1997) says ..
 and
 as mentioned (Lamprey et al. 1997).
 what I get is
 Menaker et al. [1997]
 and
 as mentioned Lamprey et al. [1997]
 
 The main question is, where in the net could I find examples for it to
 figure out myself. The most urgent question is, how could I fix it.
 Should it be done in the document class and class options and/or in
 Bibliography Citation style or in the preamble? Do I have to use
 makebst, or can I avoid it? How difficult is it nowadays to use
 biblatex. I tried before but failed.
 
 Wolfgang

Thanks, Csikos
for your comprehensive explanation. Unfortunately, I have still questions.
 
 Hello:
 
 1. I can't help you regarding biblatex as I don't have experience with
 it. I like to tweak bibliography styles according to my like/need, and
 I found that it is more difficult in biblatex than in bibtex with
 natbib.

So I select under toolsoutputlatex Bibliography Processor  bibtex 
(or custom? or bibtex8?)
 
 2. Using bibtex, the natbib package can do what you want.
 The look/style of bibliography and citations mostly will depend on 3
 things: a. The bibliography style (.bst file).
   b. The citation command for a given citation.
   c. The content of the bibtex database (.bib file).
 
 3. Let's go through it how to get the styles you want.
 
 In LyX go to Document-Settings. Do not apply the class option
 'authoryear' you mentioned. Go to 'Bibliography' and select 'Natbib'
 and 'Natbib-style: Author-Year. This loads natbib package
 automatically. Click OK or Apply.

done

 
 In the document where you want to insert your reference list, do:
 Insert-List/TOC-BibTeX bibliography. Select a style file (e.g.
 plainnat) and your bibtex database (.bib) file. Click OK.
 
 Next insert a citation into your document by Insert-Citation or
 clicking the insert citation icon. Select the citations, click 'Add'.

ok

 Look at the 'Formatting: Citation style' pulldown menu in the window.
 Here you can select the style of the citation; 'Menaker et al. (1997)'
 or '(Lamprey et al. 1997)'.

Since I have over 700 citations, I used Jabref for my bibliography and 
clicked the references via the lyx-export of jabref to the corresponding 
places of my document. If I use \setcitestyle{aysep={}} instead of your 
proposed \setcitestyle{round,aysep={}}, and if I put () around the 
citation, I get what I need. But what about eg: 
(Praschak-Rieder and Willeit 2012)
and in case of three authors and more 
(Crosthwait et al. 1997)?
 
 By default you will get [ ] limiters, but you need ( ) instead.
 Write in your document preamble (Document-Settings-LaTeX Preamble):
 
 \setcitestyle{round,aysep={}}

 
 The aysep={} defines the separator between author and name in the
 citations.
 
 Now you have to adjust the references style according to your needs.
 You can try to find a .bst style file on the net and use it.
 You can also try the different style files which come with latex
 installations (plainnat, authordate, harvard etc.).
 Or you can make your own customized style by using custom-bib
 or bib-it. See this message:
 
 http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
 
 I attach a .bst file (authdate.bst) that might fit your needs.
 
 bcsikos

will try your style, thanks a lot

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:

snip
 Now you have to adjust the references style according to your needs.
 You can try to find a .bst style file on the net and use it.
 You can also try the different style files which come with latex
 installations (plainnat, authordate, harvard etc.).
 Or you can make your own customized style by using custom-bib
 or bib-it. See this message:
 
 http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
 
 I attach a .bst file (authdate.bst) that might fit your needs.
 
 bcsikos

Where in the .lyx file (or elsewhere) would I place the authdate.bst file you 
kindly supplied?
Under layouts? Which is empty so far.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

So I select under toolsoutputlatex Bibliography Processor  bibtex
(or custom? or bibtex8?)

It seems you are using an older lyx version. It should work with it, still I 
suggest
upgrading lyx to version 2.x.

Set bibliography processor to bibtex. bibtex8 might work as well, I never tried 
it.
If you select bibtex, make sure those fields in the bib database file that will 
be in
the output do have only ASCII or latin-1 encoded characters. Special characters
should be replaced by latex commands (eg. ö is \{o} etc.).

Since I have over 700 citations, I used Jabref for my bibliography and
clicked the references via the lyx-export of jabref to the corresponding
places of my document. If I use \setcitestyle{aysep={}} instead of your
proposed \setcitestyle{round,aysep={}}, and if I put () around the
citation, I get what I need.

Do not add manually '(' and ')' around citations. The opening and closing
braces (rounded, square, or other) are part of the citation.
And it is better to add the citations within lyx.

I don't know if jabref can handle the two different types of citations:
 ' and 'text (Author year) text'. Can it make a
difference? If you insert the citations within lyx you can select which
type you want. If you look at the source you can see that the latex
command for the two types are different, \citet and \citep.

Also, if you have several citations in a group, lyx can handle it.
Can jabref handle that?

Unfortunately you have to go through all the citations and adjust them
manually. Or you can work on the .lyx source file directly using a text
editor and replacing all cite* command with citep. (Make a backup
of the original file before editing!) After this open your edited file
in lyx, find the few (I suppose) occasions of 'text Author (year) text'
type citations and adjust them manually.

The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
commands in the preamble have the same effect, as round is the
default option in case of author-year citation. Removing or adding it
does not make any difference.

But what about eg: (Praschak-Rieder and Willeit 2012) and in case
of three authors and more (Crosthwait et al. 1997)?

I don't understand what your question is.
Unfortunately latex handles citations in goups. One group is all
the citations selected and added at the same time. All these citations
will be between the same pair of parentheses. If you add neighboring
citations separately, they will be within different parentheses pairs.

The source also shows the difference. For example.

3 citations in one group:

\citep{citation1,citation2,citaton3}

The output will be:

(author1 year1, author2 year2, author3 year3)

However if you add them separately, like this:

\citep{citation1} \citep{citation2} \cite{citaton3}

the output will be:

(author1 year1) (author2 year2) (author3 year3)

You can adjust the opening and closing braces and the seperators
between authors etc using \setcitestyle.

Read the natbib manual (available at CTAN) section 2.9 Selecting
citation punctuation.

Where in the .lyx file (or elsewhere) would I place the authdate.bst
file you kindly supplied?

You can put it anywhere you want, but the best place is the directory
where your .lyx file is. You select the bst file by clicking 'BibTeX Generated
Bibliography' and browse for it.

If you still have questions don't hesitate to ask, but be specific, please.

bcsikos

Citation and reference style

[Wolfgang Engelmann]

Dear List

I need the following formating in the references:
Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
Weitzman, E. D. (1982)
Mathematical model of the human circadian system with two interacting 
oscillators. Am. J. Physiol. 242, 3–17.

I use under Debian squeeze in Lyx
document class book (KOMA script) 
class options: authoryear
in Bibliography Citation Style: natbib style: author-year

and get the following:
R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
Weitzman. Mathematical model of the human circadian system with two 
interacting oscillators. AmPhysiol, 242:3–17, 1982.

Note: The abbreviation of the Journal name is not important

Furthermore, I need the following formating of citations in the document 
Menaker et al. (1997) says ..
and
as mentioned (Lamprey et al. 1997).

what I get is
Menaker et al. [1997] 
and
as mentioned Lamprey et al. [1997]

The main question is, where in the net could I find examples for it to figure 
out myself.
The most urgent question is, how could I fix it. 

Should it be done in the 
document class and class options
and/or in Bibliography Citation Style
or in the preamble?
Do I have to use makebst, or can I avoid it?

How difficult is it nowadays to use biblatex. I tried before but failed.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann engelm...@uni-tuebingen.de írta:

Dear List

I need the following formating in the references:

Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
Weitzman, E. D.
(1982) Mathematical model of the human circadian system with two interacting
oscillators. Am. J. Physiol. 242, 3–17.

I use under Debian squeeze in Lyx document class book (KOMA script)
class options: authoryear
in Bibliography Citation style: natbib style: author-year

and get the following:
R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
Weitzman.
Mathematical model of the human circadian system with two interacting 
oscillators.
AmPhysiol, 242:3–17, 1982.

Note: The abbreviation of the Journal name is not important

Furthermore, I need the following formating of citations in the document
Menaker et al. (1997) says ..
and
as mentioned (Lamprey et al. 1997).
what I get is
Menaker et al. [1997]
and
as mentioned Lamprey et al. [1997]

The main question is, where in the net could I find examples for it to figure 
out myself.
The most urgent question is, how could I fix it.
Should it be done in the document class and class options and/or in 
Bibliography Citation
style or in the preamble? Do I have to use makebst, or can I avoid it?
How difficult is it nowadays to use biblatex. I tried before but failed.

Wolfgang


Hello:

1. I can't help you regarding biblatex as I don't have experience with it.
I like to tweak bibliography styles according to my like/need, and I found that 
it is more
difficult in biblatex than in bibtex with natbib.

2. Using bibtex, the natbib package can do what you want.
The look/style of bibliography and citations mostly will depend on 3 things:
  a. The bibliography style (.bst file).
  b. The citation command for a given citation.
  c. The content of the bibtex database (.bib file).

3. Let's go through it how to get the styles you want.

In LyX go to Document-Settings. Do not apply the class option 'authoryear'
you mentioned. Go to 'Bibliography' and select 'Natbib' and 'Natbib-style:
Author-Year. This loads natbib package automatically. Click OK or Apply.

In the document where you want to insert your reference list, do:
Insert-List/TOC-BibTeX bibliography. Select a style file (e.g. plainnat) and
your bibtex database (.bib) file. Click OK.

Next insert a citation into your document by Insert-Citation or clicking the
insert citation icon. Select the citations, click 'Add'. Look at the 
'Formatting:
Citation style' pulldown menu in the window. Here you can select the style of
the citation; 'Menaker et al. (1997)' or '(Lamprey et al. 1997)'.

By default you will get [ ] limiters, but you need ( ) instead.
Write in your document preamble (Document-Settings-LaTeX Preamble):

\setcitestyle{round,aysep={}}

The aysep={} defines the separator between author and name in the citations.

Now you have to adjust the references style according to your needs.
You can try to find a .bst style file on the net and use it.
You can also try the different style files which come with latex
installations (plainnat, authordate, harvard etc.).
Or you can make your own customized style by using custom-bib
or bib-it. See this message:

http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html

I attach a .bst file (authdate.bst) that might fit your needs.

bcsikos



authdate.bst
Description: Binary data

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:
 Wolfgang Engelmann engelm...@uni-tuebingen.de írta:
 Dear List
 
 I need the following formating in the references:
 
 Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and
 Weitzman, E. D. (1982) Mathematical model of the human circadian
 system with two interacting oscillators. Am. J. Physiol. 242, 3–17.
 
 I use under Debian squeeze in Lyx document class book (KOMA script)
 class options: authoryear
 in Bibliography Citation style: natbib style: author-year
 
 and get the following:
 R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E.
 D. Weitzman. Mathematical model of the human circadian system with two
 interacting oscillators. AmPhysiol, 242:3–17, 1982.
 
 Note: The abbreviation of the Journal name is not important
 
 Furthermore, I need the following formating of citations in the
 document Menaker et al. (1997) says ..
 and
 as mentioned (Lamprey et al. 1997).
 what I get is
 Menaker et al. [1997]
 and
 as mentioned Lamprey et al. [1997]
 
 The main question is, where in the net could I find examples for it to
 figure out myself. The most urgent question is, how could I fix it.
 Should it be done in the document class and class options and/or in
 Bibliography Citation style or in the preamble? Do I have to use
 makebst, or can I avoid it? How difficult is it nowadays to use
 biblatex. I tried before but failed.
 
 Wolfgang

Thanks, Csikos
for your comprehensive explanation. Unfortunately, I have still questions.
 
 Hello:
 
 1. I can't help you regarding biblatex as I don't have experience with
 it. I like to tweak bibliography styles according to my like/need, and
 I found that it is more difficult in biblatex than in bibtex with
 natbib.

So I select under toolsoutputlatex Bibliography Processor  bibtex 
(or custom? or bibtex8?)
 
 2. Using bibtex, the natbib package can do what you want.
 The look/style of bibliography and citations mostly will depend on 3
 things: a. The bibliography style (.bst file).
   b. The citation command for a given citation.
   c. The content of the bibtex database (.bib file).
 
 3. Let's go through it how to get the styles you want.
 
 In LyX go to Document-Settings. Do not apply the class option
 'authoryear' you mentioned. Go to 'Bibliography' and select 'Natbib'
 and 'Natbib-style: Author-Year. This loads natbib package
 automatically. Click OK or Apply.

done

 
 In the document where you want to insert your reference list, do:
 Insert-List/TOC-BibTeX bibliography. Select a style file (e.g.
 plainnat) and your bibtex database (.bib) file. Click OK.
 
 Next insert a citation into your document by Insert-Citation or
 clicking the insert citation icon. Select the citations, click 'Add'.

ok

 Look at the 'Formatting: Citation style' pulldown menu in the window.
 Here you can select the style of the citation; 'Menaker et al. (1997)'
 or '(Lamprey et al. 1997)'.

Since I have over 700 citations, I used Jabref for my bibliography and 
clicked the references via the lyx-export of jabref to the corresponding 
places of my document. If I use \setcitestyle{aysep={}} instead of your 
proposed \setcitestyle{round,aysep={}}, and if I put () around the 
citation, I get what I need. But what about eg: 
(Praschak-Rieder and Willeit 2012)
and in case of three authors and more 
(Crosthwait et al. 1997)?
 
 By default you will get [ ] limiters, but you need ( ) instead.
 Write in your document preamble (Document-Settings-LaTeX Preamble):
 
 \setcitestyle{round,aysep={}}

 
 The aysep={} defines the separator between author and name in the
 citations.
 
 Now you have to adjust the references style according to your needs.
 You can try to find a .bst style file on the net and use it.
 You can also try the different style files which come with latex
 installations (plainnat, authordate, harvard etc.).
 Or you can make your own customized style by using custom-bib
 or bib-it. See this message:
 
 http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
 
 I attach a .bst file (authdate.bst) that might fit your needs.
 
 bcsikos

will try your style, thanks a lot

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:

snip
 Now you have to adjust the references style according to your needs.
 You can try to find a .bst style file on the net and use it.
 You can also try the different style files which come with latex
 installations (plainnat, authordate, harvard etc.).
 Or you can make your own customized style by using custom-bib
 or bib-it. See this message:
 
 http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
 
 I attach a .bst file (authdate.bst) that might fit your needs.
 
 bcsikos

Where in the .lyx file (or elsewhere) would I place the authdate.bst file you 
kindly supplied?
Under layouts? Which is empty so far.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

So I select under toolsoutputlatex Bibliography Processor  bibtex
(or custom? or bibtex8?)

It seems you are using an older lyx version. It should work with it, still I 
suggest
upgrading lyx to version 2.x.

Set bibliography processor to bibtex. bibtex8 might work as well, I never tried 
it.
If you select bibtex, make sure those fields in the bib database file that will 
be in
the output do have only ASCII or latin-1 encoded characters. Special characters
should be replaced by latex commands (eg. ö is \{o} etc.).

Since I have over 700 citations, I used Jabref for my bibliography and
clicked the references via the lyx-export of jabref to the corresponding
places of my document. If I use \setcitestyle{aysep={}} instead of your
proposed \setcitestyle{round,aysep={}}, and if I put () around the
citation, I get what I need.

Do not add manually '(' and ')' around citations. The opening and closing
braces (rounded, square, or other) are part of the citation.
And it is better to add the citations within lyx.

I don't know if jabref can handle the two different types of citations:
 ' and 'text (Author year) text'. Can it make a
difference? If you insert the citations within lyx you can select which
type you want. If you look at the source you can see that the latex
command for the two types are different, \citet and \citep.

Also, if you have several citations in a group, lyx can handle it.
Can jabref handle that?

Unfortunately you have to go through all the citations and adjust them
manually. Or you can work on the .lyx source file directly using a text
editor and replacing all cite* command with citep. (Make a backup
of the original file before editing!) After this open your edited file
in lyx, find the few (I suppose) occasions of 'text Author (year) text'
type citations and adjust them manually.

The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
commands in the preamble have the same effect, as round is the
default option in case of author-year citation. Removing or adding it
does not make any difference.

But what about eg: (Praschak-Rieder and Willeit 2012) and in case
of three authors and more (Crosthwait et al. 1997)?

I don't understand what your question is.
Unfortunately latex handles citations in goups. One group is all
the citations selected and added at the same time. All these citations
will be between the same pair of parentheses. If you add neighboring
citations separately, they will be within different parentheses pairs.

The source also shows the difference. For example.

3 citations in one group:

\citep{citation1,citation2,citaton3}

The output will be:

(author1 year1, author2 year2, author3 year3)

However if you add them separately, like this:

\citep{citation1} \citep{citation2} \cite{citaton3}

the output will be:

(author1 year1) (author2 year2) (author3 year3)

You can adjust the opening and closing braces and the seperators
between authors etc using \setcitestyle.

Read the natbib manual (available at CTAN) section 2.9 Selecting
citation punctuation.

Where in the .lyx file (or elsewhere) would I place the authdate.bst
file you kindly supplied?

You can put it anywhere you want, but the best place is the directory
where your .lyx file is. You select the bst file by clicking 'BibTeX Generated
Bibliography' and browse for it.

If you still have questions don't hesitate to ask, but be specific, please.

bcsikos

Citation and reference style

[Wolfgang Engelmann]

Dear List

I need the following formating in the references:
Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
Weitzman, E. D. (1982)
Mathematical model of the human circadian system with two interacting 
oscillators. Am. J. Physiol. 242, 3–17.

I use under Debian squeeze in Lyx
document class> book (KOMA script) 
class options: authoryear
in Bibliography Citation Style: natbib style: author-year

and get the following:
R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
Weitzman. Mathematical model of the human circadian system with two 
interacting oscillators. AmPhysiol, 242:3–17, 1982.

Note: The abbreviation of the Journal name is not important

Furthermore, I need the following formating of citations in the document 
Menaker et al. (1997) says ..
and
as mentioned (Lamprey et al. 1997).

what I get is
Menaker et al. [1997] 
and
as mentioned Lamprey et al. [1997]

The main question is, where in the net could I find examples for it to figure 
out myself.
The most urgent question is, how could I fix it. 

Should it be done in the 
document class and class options
and/or in Bibliography Citation Style
or in the preamble?
Do I have to use makebst, or can I avoid it?

How difficult is it nowadays to use biblatex. I tried before but failed.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

Wolfgang Engelmann  írta:
>
>Dear List
>
>I need the following formating in the references:
>
>Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and 
>Weitzman, E. D.
>(1982) Mathematical model of the human circadian system with two interacting
>oscillators. Am. J. Physiol. 242, 3–17.
>
>I use under Debian squeeze in Lyx document class> book (KOMA script)
>class options: authoryear
>in Bibliography Citation style: natbib style: author-year
>
>and get the following:
>R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E. D. 
>Weitzman.
>Mathematical model of the human circadian system with two interacting 
>oscillators.
>AmPhysiol, 242:3–17, 1982.
>
>Note: The abbreviation of the Journal name is not important
>
>Furthermore, I need the following formating of citations in the document
>Menaker et al. (1997) says ..
>and
>as mentioned (Lamprey et al. 1997).
>what I get is
>Menaker et al. [1997]
>and
>as mentioned Lamprey et al. [1997]
>
>The main question is, where in the net could I find examples for it to figure 
>out myself.
>The most urgent question is, how could I fix it.
>Should it be done in the document class and class options and/or in 
>Bibliography Citation
>style or in the preamble? Do I have to use makebst, or can I avoid it?
>How difficult is it nowadays to use biblatex. I tried before but failed.
>
>Wolfgang


Hello:

1. I can't help you regarding biblatex as I don't have experience with it.
I like to tweak bibliography styles according to my like/need, and I found that 
it is more
difficult in biblatex than in bibtex with natbib.

2. Using bibtex, the natbib package can do what you want.
The look/style of bibliography and citations mostly will depend on 3 things:
  a. The bibliography style (.bst file).
  b. The citation command for a given citation.
  c. The content of the bibtex database (.bib file).

3. Let's go through it how to get the styles you want.

In LyX go to Document->Settings. Do not apply the class option 'authoryear'
you mentioned. Go to 'Bibliography' and select 'Natbib' and 'Natbib-style:
Author-Year". This loads natbib package automatically. Click OK or Apply.

In the document where you want to insert your reference list, do:
Insert->List/TOC->BibTeX bibliography. Select a style file (e.g. plainnat) and
your bibtex database (.bib) file. Click OK.

Next insert a citation into your document by Insert->Citation or clicking the
insert citation icon. Select the citations, click 'Add'. Look at the 
'Formatting:
Citation style' pulldown menu in the window. Here you can select the style of
the citation; 'Menaker et al. (1997)' or '(Lamprey et al. 1997)'.

By default you will get [ ] limiters, but you need ( ) instead.
Write in your document preamble (Document->Settings->LaTeX Preamble):

\setcitestyle{round,aysep={}}

The aysep={} defines the separator between author and name in the citations.

Now you have to adjust the references style according to your needs.
You can try to find a .bst style file on the net and use it.
You can also try the different style files which come with latex
installations (plainnat, authordate, harvard etc.).
Or you can make your own customized style by using custom-bib
or bib-it. See this message:

http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html

I attach a .bst file (authdate.bst) that might fit your needs.

bcsikos



authdate.bst
Description: Binary data

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:
> Wolfgang Engelmann  írta:
> >Dear List
> >
> >I need the following formating in the references:
> >
> >Kronauer, R. E., Czeisler, C. A., Pilato, S. F., Moore-Ede, M. C. and
> >Weitzman, E. D. (1982) Mathematical model of the human circadian
> >system with two interacting oscillators. Am. J. Physiol. 242, 3–17.
> >
> >I use under Debian squeeze in Lyx document class> book (KOMA script)
> >class options: authoryear
> >in Bibliography Citation style: natbib style: author-year
> >
> >and get the following:
> >R. E. Kronauer, C. A. Czeisler, S. F. Pilato, M. C. Moore-Ede, and E.
> >D. Weitzman. Mathematical model of the human circadian system with two
> >interacting oscillators. AmPhysiol, 242:3–17, 1982.
> >
> >Note: The abbreviation of the Journal name is not important
> >
> >Furthermore, I need the following formating of citations in the
> >document Menaker et al. (1997) says ..
> >and
> >as mentioned (Lamprey et al. 1997).
> >what I get is
> >Menaker et al. [1997]
> >and
> >as mentioned Lamprey et al. [1997]
> >
> >The main question is, where in the net could I find examples for it to
> >figure out myself. The most urgent question is, how could I fix it.
> >Should it be done in the document class and class options and/or in
> >Bibliography Citation style or in the preamble? Do I have to use
> >makebst, or can I avoid it? How difficult is it nowadays to use
> >biblatex. I tried before but failed.
> >
> >Wolfgang

Thanks, Csikos
for your comprehensive explanation. Unfortunately, I have still questions.
> 
> Hello:
> 
> 1. I can't help you regarding biblatex as I don't have experience with
> it. I like to tweak bibliography styles according to my like/need, and
> I found that it is more difficult in biblatex than in bibtex with
> natbib.

So I select under tools>output>latex> Bibliography Processor > bibtex 
(or custom? or bibtex8?)
> 
> 2. Using bibtex, the natbib package can do what you want.
> The look/style of bibliography and citations mostly will depend on 3
> things: a. The bibliography style (.bst file).
>   b. The citation command for a given citation.
>   c. The content of the bibtex database (.bib file).
> 
> 3. Let's go through it how to get the styles you want.
> 
> In LyX go to Document->Settings. Do not apply the class option
> 'authoryear' you mentioned. Go to 'Bibliography' and select 'Natbib'
> and 'Natbib-style: Author-Year". This loads natbib package
> automatically. Click OK or Apply.

done

> 
> In the document where you want to insert your reference list, do:
> Insert->List/TOC->BibTeX bibliography. Select a style file (e.g.
> plainnat) and your bibtex database (.bib) file. Click OK.
> 
> Next insert a citation into your document by Insert->Citation or
> clicking the insert citation icon. Select the citations, click 'Add'.

ok

> Look at the 'Formatting: Citation style' pulldown menu in the window.
> Here you can select the style of the citation; 'Menaker et al. (1997)'
> or '(Lamprey et al. 1997)'.

Since I have over 700 citations, I used Jabref for my bibliography and 
clicked the references via the lyx-export of jabref to the corresponding 
places of my document. If I use \setcitestyle{aysep={}} instead of your 
proposed \setcitestyle{round,aysep={}}, and if I put () around the 
citation, I get what I need. But what about eg: 
(Praschak-Rieder and Willeit 2012)
and in case of three authors and more 
(Crosthwait et al. 1997)?
> 
> By default you will get [ ] limiters, but you need ( ) instead.
> Write in your document preamble (Document->Settings->LaTeX Preamble):
> 
> \setcitestyle{round,aysep={}}

> 
> The aysep={} defines the separator between author and name in the
> citations.
> 
> Now you have to adjust the references style according to your needs.
> You can try to find a .bst style file on the net and use it.
> You can also try the different style files which come with latex
> installations (plainnat, authordate, harvard etc.).
> Or you can make your own customized style by using custom-bib
> or bib-it. See this message:
> 
> http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
> 
> I attach a .bst file (authdate.bst) that might fit your needs.
> 
> bcsikos

will try your style, thanks a lot

Wolfgang

Re: Citation and reference style

[Wolfgang Engelmann]

Am Thursday, 22. August 2013, 13:34:33 schrieb Csikos Bela:

snip
> Now you have to adjust the references style according to your needs.
> You can try to find a .bst style file on the net and use it.
> You can also try the different style files which come with latex
> installations (plainnat, authordate, harvard etc.).
> Or you can make your own customized style by using custom-bib
> or bib-it. See this message:
> 
> http://www.mail-archive.com/lyx-users@lists.lyx.org/msg96191.html
> 
> I attach a .bst file (authdate.bst) that might fit your needs.
> 
> bcsikos

Where in the .lyx file (or elsewhere) would I place the authdate.bst file you 
kindly supplied?
Under layouts? Which is empty so far.

Wolfgang

Re: Citation and reference style

[Csikos Bela]

>So I select under tools>output>latex> Bibliography Processor > bibtex
>(or custom? or bibtex8?)

It seems you are using an older lyx version. It should work with it, still I 
suggest
upgrading lyx to version 2.x.

Set bibliography processor to bibtex. bibtex8 might work as well, I never tried 
it.
If you select bibtex, make sure those fields in the bib database file that will 
be in
the output do have only ASCII or latin-1 encoded characters. Special characters
should be replaced by latex commands (eg. ö is \"{o} etc.).

>Since I have over 700 citations, I used Jabref for my bibliography and
>clicked the references via the lyx-export of jabref to the corresponding
>places of my document. If I use \setcitestyle{aysep={}} instead of your
>proposed \setcitestyle{round,aysep={}}, and if I put () around the
>citation, I get what I need.

Do not add manually '(' and ')' around citations. The opening and closing
braces (rounded, square, or other) are part of the citation.
And it is better to add the citations within lyx.

I don't know if jabref can handle the two different types of citations:
 ' and 'text (Author year) text'. Can it make a
difference? If you insert the citations within lyx you can select which
type you want. If you look at the source you can see that the latex
command for the two types are different, \citet and \citep.

Also, if you have several citations in a group, lyx can handle it.
Can jabref handle that?

Unfortunately you have to go through all the citations and adjust them
manually. Or you can work on the .lyx source file directly using a text
editor and replacing all cite* command with citep. (Make a backup
of the original file before editing!) After this open your edited file
in lyx, find the few (I suppose) occasions of 'text Author (year) text'
type citations and adjust them manually.

The  \setcitestyle{round,aysep={}} and  \setcitestyle{aysep={}}
commands in the preamble have the same effect, as round is the
default option in case of author-year citation. Removing or adding it
does not make any difference.

>But what about eg: (Praschak-Rieder and Willeit 2012) and in case
>of three authors and more (Crosthwait et al. 1997)?

I don't understand what your question is.
Unfortunately latex handles citations in goups. One group is all
the citations selected and added at the same time. All these citations
will be between the same pair of parentheses. If you add neighboring
citations separately, they will be within different parentheses pairs.

The source also shows the difference. For example.

3 citations in one group:

\citep{citation1,citation2,citaton3}

The output will be:

(author1 year1, author2 year2, author3 year3)

However if you add them separately, like this:

\citep{citation1} \citep{citation2} \cite{citaton3}

the output will be:

(author1 year1) (author2 year2) (author3 year3)

You can adjust the opening and closing braces and the seperators
between authors etc using \setcitestyle.

Read the natbib manual (available at CTAN) section 2.9 Selecting
citation punctuation.

>Where in the .lyx file (or elsewhere) would I place the authdate.bst
>file you kindly supplied?

You can put it anywhere you want, but the best place is the directory
where your .lyx file is. You select the bst file by clicking 'BibTeX Generated
Bibliography' and browse for it.

If you still have questions don't hesitate to ask, but be specific, please.

bcsikos