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 <hpa...@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.kosin...@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 <dtene...@fredhutch.org>:
>>>
>>>> That's correct.
>>>> Dan
>>>>
>>>>
>>>> ----- Original Message -----
>>>>> From: "Andrzej Oleś" <andrzej.o...@gmail.com>
>>>>> To: "Robert M. Flight" <rfligh...@gmail.com>
>>>>> Cc: "Marcin Kosiński" <m.p.kosin...@gmail.com>, "bioc-devel" <
>>>> bioc-devel@r-project.org>, "Dan Tenenbaum"
>>>>> <dtene...@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 <rfligh...@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.kosin...@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@r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Wolfgang
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
http://www.huber.embl.de
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