[Bioc-devel] downloads number status shields for packages

[Wolfgang Huber]

Hervé

Thank you, looks great. Regarding files like https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats: woudln’t it be good to 
- provide column headers
- give the file a reasonable extension reminding of its format
- format it such that it can be read with default parameters e.g. by read.csv or readr::read_csv?
- include package name and year among the columns, to allow easy rbind-ing of several of such files
- also useful might be such a file with just all the packages and years in it.

Best wishes
	Wolfgang

> On May 5, 2016, at 21:03 GMT+2, Hervé Pagès <hpages at fredhutch.org> wrote:
> 
> Hi,
> 
> The download report is actually about to change. See:
> 
>  https://bioconductor.org/packages/new-stats/bioc/Biobase/
> 
> for how the new stats are going to look. This is work in progress (ETA
> is next week) but an important change is that you'll be able to get the
> numbers from tabulated files (e.g. the Biobase_<year>_stats files in the
> case of Biobase) so parsing HTML won't be necessary.
> 
> Cheers,
> H.
> 
> On 05/05/2016 11:51 AM, Lori Shepherd wrote:
>> Hi Marcin,
>> 
>> Here is a link to how Bioconductor creates it's badges:
>> https://github.com/Bioconductor/bioconductor.org/blob/master/Rakefile#L648
>> 
>> If you would like to create a badge for raw counts the following might
>> be of use to you. Please also see help on XML Path Language:
>> https://www.w3.org/TR/xpath/#path-abbrev
>> 
>> 
>> 
>> library(xml2)
>> url = "http://bioconductor.org/packages/stats/bioc/RTCGA.html"
>> doc = read_html(url)
>> rtcga = xml_find_all(doc, "//table[@class='stats']/tr/td[2]/text()")
>> %>% as.character %>% as.integer
>> 
>> url2 = "http://bioconductor.org/packages/stats/index.html"
>> doc2 = read_html(url2)
>> all = xml_find_all(doc2, "//table[@class='stats']/tr/td[2]/text()")
>> %>% as.character %>% as.integer
>> 
>> 
>> 
>> On Wed, May 4, 2016 at 3:43 PM, Marcin Kosiński <m.p.kosinski at gmail.com> wrote:
>>> Hi Robert,
>>> 
>>> Thanks for reply.
>>> 
>>> What if I am interested in both showing raw counts and percentiles?
>>> If this is not created and no one is willing to create sush shields, then I
>>> can volounteer for that.
>>> It'll be great to have some examples on how the percentile badges were
>>> created.
>>> 
>>> Best,
>>> Marcin
>>> 
>>> 
>>> 2016-05-04 17:22 GMT+02:00 Dan Tenenbaum <dtenenba at fredhutch.org>:
>>> 
>>>> That's correct.
>>>> Dan
>>>> 
>>>> 
>>>> ----- Original Message -----
>>>>> From: "Andrzej Oleś" <andrzej.oles at gmail.com>
>>>>> To: "Robert M. Flight" <rflight79 at gmail.com>
>>>>> Cc: "Marcin Kosiński" <m.p.kosinski at gmail.com>, "bioc-devel" <
>>>> bioc-devel at r-project.org>, "Dan Tenenbaum"
>>>>> <dtenenba at fredhutch.org>
>>>>> Sent: Wednesday, May 4, 2016 8:15:36 AM
>>>>> Subject: Re: [Bioc-devel] downloads number status shields for packages
>>>> 
>>>>> Hi Marcin, Robert,
>>>>> 
>>>>> I think one problem with raw counts is that these reflect only downloads
>>>>> from BioC servers and not from the mirrors - is that correct @Dan?
>>>>> 
>>>>> Cheers,
>>>>> Andrzej
>>>>> 
>>>>> On Wed, May 4, 2016 at 5:11 PM, Robert M. Flight <rflight79 at gmail.com>
>>>>> wrote:
>>>>> 
>>>>>> Those numbers are used to calculate the percentile download stat that is
>>>>>> already on a given bioconductor package landing page. See
>>>>>> http://bioconductor.org/packages/release/bioc/html/RTCGA.html
>>>>>> 
>>>>>> I believe this was the way the Bioc admins went instead of just raw
>>>>>> downloads.
>>>>>> 
>>>>>> -Robert
>>>>>> 
>>>>>> On Wed, May 4, 2016 at 10:58 AM Marcin Kosiński <m.p.kosinski at gmail.com
>>>>> 
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi all,
>>>>>>> 
>>>>>>> Have anyone considered creating shields (http://shields.io/) with the
>>>>>>> status of total downloads number for packages held on bioc? This
>>>> already
>>>>>>> works for CRAN packages http://cranlogs.r-pkg.org/
>>>>>>> 
>>>>>>> It could take total `Nb of downloads` from the right table like here
>>>>>>> http://bioconductor.org/packages/stats/bioc/RTCGA.html
>>>>>>> 
>>>>>>> Best,
>>>>>>> Marcin
>>>>>>> 
>>>>>>>         [[alternative HTML version deleted]]
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>> 
>>>>>> 
>>>>>>         [[alternative HTML version deleted]]
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> 
>>> 
>>>         [[alternative HTML version deleted]]
>>> 
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>> 
>> _______________________________________________
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>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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> 
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Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de
http://www.huber.embl.de