[Bioc-devel] downloads number status shields for packages

Herv?

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, Herv? Pag?s <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 Kosi?ski <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 Ole?" <andrzej.oles at gmail.com>
To: "Robert M. Flight" <rflight79 at gmail.com>
Cc: "Marcin Kosi?ski" <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 Kosi?ski <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

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--
Herv? Pag?s

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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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