ropensci-archive/alm

:no_entry: ARCHIVED :no_entry: R Client for the Lagotto Altmetrics Platform

alm's Issues

Readme xhtml

From kurt hornik

These have README.md files which when converted to (X)HTML using a
current version of pandoc show problems when validated using W3C Markup
Validator, see below.

Most of these problems are caused by using images without giving a name
(so the required alt attribute for <img> is not provided), or using <br>
instead of <br/>.

Pls fix these problems in your README.md files for your next release: in
all cases I inspected, the fixes were obvious and confirmation using
pandoc and W3C markup validator seemed unnecessary.

Please also visit your package check web page at http://cran.r-project.org/web/checks/check_results_PACKAGENAME.html to see if other problems need to be addressed as well.

Parse new events sources

• datacite
• [] copernicus Don't see any events data for this source, prob only relavant for folks getting data from copernicus installation
• articlecoverage
• articlecoveragecurated

Put DESCRIPTION field in DESCRIPTION file for rCharts

From Kurt Hornik

These seem to include packages not in the mainstream repositories in
their Suggests or Enhances. For such cases, the CRAN Repository Policy
now says

Packages on which a CRAN package depends should be available from a
mainstream repository: if any mentioned in Suggests or Enhances fields
are not from such a repository, where to obtain them should be
mentioned in the Description field of the DESCRIPTION file.

Pls check that your package meets this requirement, and if not provide
the necessary updates.

$alm ([email protected])
[1] "rCharts"

Add egs for DataCite installation

ALM API v5 coming

Changes:

• JSON only (no more XML)
• no more days, months, year parameter
• we include the group name with sources
• signposts are renamed to group names: viewed, cited, saved, discussed, recommended
• pagination (50 per page)
• results are in data object, there is an error object with every response

e.g, call with new format:

http://almhack.crowdometer.org/api/v5/articles?api_key=cBYJpjzC5fNwmvVJPJeE&source=mendeley&order=mendeley

rbuildignore figure/ folder in vignettes/

see https://cran.rstudio.com/web/checks/check_results_alm.html

Make visualization function for output of signposts fxn

ggplot2 new version fix

ggplot2 now imports and exports unit() and arrow() from grid, and
alpha() from scales. Many packages seem to have unused unqualified import
statements which now generates a warning on package install. (You could argue
that this is a false positive since the conflicting names both point to the
same object.). This affects:

Import all non-base R fxns

see https://cran.rstudio.com/web/checks/check_results_alm.html

Write parser for detailed events for PMC Europe Citations, PMC Europe Database Links, Reddit, WordPress.com, and OpenEdition

• PMC europe - appears to be no events data to parse for this source
• PMC europe data
• REddit
• Wordpress
• Openedition seems its' been removed

Submit new version to CRAN ignoring tests

readme fixes

These packages contain README.md files with invalid HTML output created
by pandoc 1.12.4.2 according to W3C-validator.

I attach the HTML errors and warnings found below, and will put copies
of the corresponding HTML files up at
http://www.r-project.org/nosvn/pandoc.

Please investigate the problems and fix as needed.

Afaics, many of the problems are caused by adding "raw" HTML elements in
the README.md files and not realizing that the default output format
"html" is XHTML 1 (and not HTML 5). E.g., a raw
results in an

end tag for "br" omitted, but OMITTAG NO was specified

error.

Best
-k

---

alm.html:
  Valid: FALSE (errors: 1, warnings: 0)
  Errors:
    line  col  message
     430   98  required attribute "alt" not specified

Mendeley events parser is broken

For alm_events() need to label each element with the appropriate identifier

Because the order of elements input to the query are not preserved in the returned response. This could lead to huge problems if users assume that the order is the same.

alm_signposts fxn

There's no longer a signposts slot in data output from Lagotto applicatino, update fxn

modularize alm fxn so it's not so fing big

Add info about authentication to api_requests man file

From http://alm.plos.org/api#!/api_requests/Api_V5_ApiRequests_index_get_0

Write parser for F1000 and Figshare sources

Right now they just return the raw data as a list.

Updates for ALM v.2.7

• added signpost numbers (aggregate metrics) that are also part of the info=summary response: views, shares, bookmarks, citations. Helpful for writing ALM widgets
• added by day (first 30 days), by month and by year metrics to info=detail and info=history for those sources that have date information (e.g. CrossRef only for year)

alm_events() fxn is giving back incorrect data

Fix it

Breaking change on source parameter

Now source only takes one type as an input.

Change docs and throw warning for this

remove rcharts from egs, description, etc.

These have Suggests or Enhances in non-mainstream repositories as listed
below. The CRAN Policy has

Packages on which a CRAN package depends should be available from a
mainstream repository: if any mentioned in ‘Suggests’ or ‘Enhances’
fields are not from such a repository, where to obtain them at a
repository should be specified in an ‘Additional_repositories’ field
of the DESCRIPTION file (as a comma-separated list of repository URLs)
or for other means of access, described in the ‘Description’ field.

(where in any case, the packages mentioned should be available for
installation using the standard R package management tools).

Can you pls update your packages accordingly?

Ideally, all Suggests or Enhances in non-mainstream repositories would
be available from repositories in Additional_repositories fields. In
most cases, the mentioned packages seem to be available from either
R-Forge or Omegahat, so updating is straightforward.

Require httr v > 1

changes in v3.2

https://github.com/articlemetrics/alm/blob/master/docs/api.md

Incorporate visualization fxns from plosOpenR

Crossref ALM

Crossref seems to work out of the box: https://gist.github.com/sckott/9192541

Make sure things are all working as expected, Add some tests for crossref specifically, etc.

Add option to drop all sources with no data in `alm_events()`

Right now, alm_events() gives back lots of sources with no data potentially. Perhpas parameter to toggle giving back these empty sets or not. I guess with no data, just give back NA?

Vignettes now need to be in a vignettes directory

Directory 'vignettes' has been the preferred location for vignette sources since 2.14.0 (long before non-Sweave vignettes were supported) and will shortly become obligatory. They will not be recognized as having vignettes in future, so need to be updated now to use a 'vignettes' directory.

Replace any use of plyr::ddply/ldply calls to using data.table

need for speed 🚤

ALM API v.2.8 will require API keys (1st to do so)

...not sure when this is coming...

Param name changes

• source -> sourceid
• publisher -> publisherid

Summary statistics for each endpoint

Something like events on this page http://alm.plos.org/sources

Drop signposts

gone in v6

almevents throwing errors in tests on travis

and report from cran central...

fixign now.

alm status, do something with other sources, not just plos alm endpoint

...

v6 api update

martin says a new version is upcoming, to go live at least with plos service at end of april

api docs http://labs.lagotto.io/api

running on labs.lagotto.io and software.lagotto.io so far

Fix vignette

has wrong information about api keys

API key no longer needed

but only since Lagotto version 3.12.7, check for it being implemented in other instances, and make change once it's at least in crossref http://articlemetrics.github.io/status/

Add api_requests endpoint

base url http://alm.plos.org/api_requests

Add `alm_source` fxn to just search by a alm source

see also #22

Error on using mdid

alm(mdid="35791700-6d00-11df-a2b2-0026b95e3eb7")[,-c(6:8)]

Error : client error: (404) Not Found
NULL

Procedure for obtaining API keys has changed

API key generation has been integrated into the ALM application in release 2.8. For PLOS it means going to http://alm.plos.org, and signing in via your PLOS accounts.

Other installations of the ALM application might use Mozilla Persona or Github OAuth as signin options.

Reminder from Kurt Hornik to fix readme

/data/Repositories/CRAN/web/packages/alm/README.html:
  Valid: FALSE (errors: 1, warnings: 0)
  Errors:
    line  col  message
     431   98  required attribute "alt" not specified

cran folks want change on rcharts stuff

Passes its tests for me as well, but I see

Suggests or Enhances not in mainstream repositories:
  rCharts

and

* checking R code for possible problems ... NOTE
plot_signposts: no visible global function definition for ‘nPlot’

Can you pls fix the latter as necessary.  For the former, the Policy has

 Packages on which a CRAN package depends should be available from a
  mainstream repository: if any mentioned in Suggests or Enhances fields
  are not from such a repository, where to obtain them should be
  specified in the Additional_repositories field of the DESCRIPTION file
  as a comma-separated list of repository URLs.

So pls fix accordingly.

Fix alm_ids() so that it returns the sum_metrics data outputs

Seems not to return that right now, weird

parsing in alm_events not working in some cases

fix, send fix to CRAN next week

Submit to CRAN when stable

Add alm_status fxn

For the ../status endpoint

Merge dev to master soon

Add paging parameters

Add rows parameter, call it per_page. And add page parameter, called page.

Only used i think when only source parameter used so that the user is essentially querying ALM data based on the type of source alm data, in which case paging takes effect (50 max), and then per_page param comes in.

May want to create a separate fxn for this, hmmm