[GenABEL-dev] [Genabel-commits] r1429 - pkg/GenABEL/man

[Maksim Struchalin]

Thanks you Lennart

So, I guess 80 lines should be a limit for PGC.Rd.

Two suggestions to the document:
1) I would add a recommendation to leave comments to the C/R code. 
Sometimes it is just impossible to understand what is some code for.
2) Add description at the head of to each file with code like.

For example, in every file with code I ever wrote I have a small 
description on the top like:

//#=====================================================================================
//#
//#       Filename:  gtps_container.h
//#
//#    Description:  Set of functions for merging two snp.data class objects.
//#
//#        Version:  1.0
//#        Created:  18-March-2008
//#       Revision:  none
//#
//#
//#         Author:  Maksim V. Struchalin, Yurii S. Aulchenko
//#        Company:  ErasmusMC, Epidemiology & Biostatistics Department, The Netherlands.
//#          Email:  m.struchalin@@erasmusmc.nl, i.aoultchenko at erasmusmc.nl
//#
//#=====================================================================================


from which it is clear who wrote the file (person's name and contacts), 
when and for whom. This is convinient for other developers who is gonna 
edit this file in the future to address their quiestions directly to the 
person who wrote the original code.

best,
Maksim


On 29/11/2013 16:25, L.C. Karssen wrote:
> Dear Maksim, Yakov, others,
>
> About coding style, please see the document on GenABEL coding standards
> (work in progress) we created some time ago:
> http://genabel.r-forge.r-project.org/codingstyle.html
>
> It would be great to have uniform coding in all of the GenABEL suite.
>
> By the way, suggestions for additions/corrections of the document are
> welcome!
>
>
> Lennart.
>
>
>
> On 11/29/2013 10:20 AM, Maksim Struchalin wrote:
>> Hi Yakov,
>>
>> I made this change because when I run "R CMD check --as-cran ", I got a
>> message:
>> ______________________________________________
>> * checking Rd line widths ... NOTE
>> Rd file
>> '/home/maksim/work/GenABEL_project/genabel/pkg/GenABEL.Rcheck/00_pkg_src/GenABEL/man/PGC.Rd':
>>
>> \examples lines wider than 100 characters:
>> #result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1, pol.d=2,
>> plot=TRUE, start.corr=FALSE,n_quiantile=3)
>> ______________________________________________
>>
>> Here are guidlines how to write .Rd files
>> (http://developer.r-project.org/Rds.html).
>> If I were you, I would replace "result=PGC(d..." by "result<-PGC(d..."
>> because using <- instead of = is common R rule for assignments.
>>
>> It recommends to keep the line length in .Rd file not more then 65
>> characters but I guess this an old rule and now the limit is 100
>> characters.
>>
>> best,
>> Maksim
>>
>> On 28/11/2013 16:38, Yury Aulchenko wrote:
>>> Yakov,
>>>
>>> please pay attention to this commit (I know that you were changing the
>>> code of the GC procedures recently)
>>>
>>> YA
>>>
>>> On Nov 28, 2013, at 05:38 AM, noreply at r-forge.r-project.org wrote:
>>>
>>>> Author: maksim
>>>> Date: 2013-11-28 05:38:54 +0100 (Thu, 28 Nov 2013)
>>>> New Revision: 1429
>>>>
>>>> Modified:
>>>>     pkg/GenABEL/man/PGC.Rd
>>>> Log:
>>>> Deleteted comments because R CMD check --as-cran said that these
>>>> lines are wider than 100 characters and they will be truncated in the
>>>> PDF manual. This should not have any influence on the code generated
>>>> from it.
>>>>
>>>> Modified: pkg/GenABEL/man/PGC.Rd
>>>> ===================================================================
>>>> --- pkg/GenABEL/man/PGC.Rd    2013-11-28 04:21:29 UTC (rev 1428)
>>>> +++ pkg/GenABEL/man/PGC.Rd    2013-11-28 04:38:54 UTC (rev 1429)
>>>> @@ -63,8 +63,6 @@
>>>> s <- summary(ge03d2)
>>>> freq <- s$Q.2
>>>> result=PGC(data=chi2.1df,method="median",p=freq,df=1, pol.d=2,
>>>> plot=TRUE, lmax=1.1,start.corr=FALSE)
>>>> -#"group_regress" is better to use when we have more than 50K SNPs
>>>> -#result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1,
>>>> pol.d=2, plot=TRUE, start.corr=FALSE,n_quiantile=3)
>>>> }
>>>> \author{
>>>>     Yakov Tsepilov
>>>>
>>>> _______________________________________________
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>>>>
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