Review Request : J. Stachelek #11

jsta · 2015-11-03T03:42:44Z

AUTHOR

Dear @ReScience/editors,

I request a review for the replication of the following paper:

Least-cost modelling on irregular landscape graphs, T.R. Etherington. Landscape
ecology, 27.7, 2012.

I believe the original results have been faithfully replicated
as explained in the accompanying article.

The repository lives at https://github.com/jsta/ReScience-submission/tree/STACHELEK

git clone https://github.com/jsta/ReScience-submission.git
cd ReScience-submission
git checkout STACHELEK
Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'
make all

EDITOR

Editor acknowledgment
Review 1 started (@dmcglinn) Nov 17, 2015
Review 2 started (@tpoisot) Nov 18, 2015
Review 1 decision [accept/reject] Feb 22, 2016
Review 2 decision [accept/reject] Feb 22, 2016
Editor decision [accept/reject] March 2, 2016

jsta · 2015-11-03T03:55:58Z

AUTHOR

My quick search for possible reviewers on Github turned up @Martin-Jung

rougier · 2015-11-03T06:53:17Z

EDITOR-IN-CHIEF

Thank you very much for the submission (as well as the suggested name of the reviewer).
An editor should soon acknowledge the submission to start the review. Don't hesitate to remind us if it was not the case in the next few days.

jsta · 2015-11-06T15:27:57Z

AUTHOR

Another potential reviewer might be @whalend

FedericoV · 2015-11-06T15:39:21Z

EXTERN

A colleague of mine, Duccio Rocchini (http://gis.cri.fmach.it/rocchini/) is quite experience in Python programming and geography and said he'd like to review. @rougier is it ok to invite him as a reviewer for this?

rougier · 2015-11-06T19:48:01Z

EDITOR-IN-CHIEF

Great, I will invite both to register to the board. In the meantime, we found an editor that should soon take over this review. @FedericoV Do you have the GitHub name for Duccio ?

karthik · 2015-11-09T19:14:03Z

EDITOR

Hi all,
I just wanted to chime in and say that I'll take over as editor of this submission. I'll follow up with reviewer recommendations shortly.

karthik · 2015-11-16T19:57:58Z

EDITOR

Just updating the thread that we'll finalize reviewers in a day or two. Sorry for the delay.

karthik · 2015-11-17T20:31:47Z

EDITOR

Reviewer 1, Dan McGlinn @dmcglinn has accepted.

tpoisot · 2015-11-18T17:00:10Z

REVIEWER 2

In Makefile, the update_code target is rsync'ing local files (from /home/jose/...).

tpoisot · 2015-11-18T17:01:41Z

REVIEWER 2

code/README.md still has a placeholder text.

jsta · 2015-11-18T21:27:35Z

AUTHOR

Thanks @tpoisot. Both of the issues arise because of my uncertainty with how to integrate my existing R package into the submission repo. I left the call to rsync in Makefile for my own benefit (note it is not called by the all target) but this could be removed or replaced by git clone or curl or something else.

I left the code/README.md file in the repo purely because it appears in the code repo of the first article. They place all of their code files at top level of the code folder whereas I follow the R package subfolder conventions. I would prefer simply to remove code/README.md in favor of code/irlgraph/README.md but I defer to the @ReScience/editors.

This also brings up the issue of devtools::install_github() versus R CMD INSTALL. Should I be treating the code associated with the article as static (R CMD INSTALL) or dynamic (devtools::install_github())?

tpoisot · 2015-11-18T21:41:01Z

REVIEWER 2

For the last point -- I think you can use install_github to point to a particular commit using its hash, so you would keep the benefit of using this but still treat the code as essentially static.

jsta · 2016-01-15T16:12:18Z

AUTHOR

@karthik @tpoisot @dmcglinn I implemented a Docker pdf build in c03fe28

karthik · 2016-01-18T21:53:52Z

EDITOR

@dmcglinn @tpoisot Can you two do a pull from the current PR and build? It works fine for me. If you are also able to replicate, we can close this up before the end of January. Thanks very much.

PS: It finishes in under a minute.

tpoisot · 2016-02-01T19:03:18Z

REVIEWER 2

Sorry for taking my sweet little time about testing.

Issue 1

Here is what I got:

▶ ReScience-submission on STACHELEK is clean $ make all
Rscript -e 'rmarkdown::render("code/irlgraph/vignettes/irlgraph.Rmd")'
Error in loadNamespace(name) : 
  aucun package nommé ‘rmarkdown’ n'est trouvé
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Exécution arrêtée
Makefile:6 : la recette pour la cible « code/irlgraph/vignettes/irlgraph.pdf » a échouée
make: *** [code/irlgraph/vignettes/irlgraph.pdf] Erreur 1

I solved this by installing rmarkdown.

Issue 2

Here is the relevant line

pandoc --standalone --filter /home/tpoisot/.cabal/bin/pandoc-crossref --template=rescience-template.tex --latex-engine=xelatex --biblatex --bibliography=article.bib -M "crossrefYaml=crossref.yaml" --output article.tex article.md
pandoc: Filter /home/tpoisot/.cabal/bin/pandoc-crossref not found

On my system, the filter is called pandoc-citeproc, and pandoc-citeproc is in the path (and is at /usr/bin/pandoc-citeproc).

This one can be solved with the right variables passed to the different makefiles.

jsta · 2016-02-01T19:38:14Z

AUTHOR

@tpoisot
Have you seen the build instructions in README.md? They include installation of rmarkdown.

Are you able to build the article in the master branch (not STACHELEK)? The master branch article/README.md says to use pandoc-crossref not pandoc-citeproc...
I hope this is not related to the version problem discussed at #13

jsta · 2016-02-12T20:28:52Z

AUTHOR

@tpoisot @dmcglinn: According to @rougier in #13, you do not need to actually compile the pdf as reviewers. In order to build only the figures substitute the make all line in README.md with make panel-resize_images. The figure images can then be found in the article folder.

Also, you would not need the Haskell/cabal/pandoc-crossref dependencies.

tpoisot · 2016-02-12T20:59:41Z

REVIEWER 2
@karthik Working, no more comments/requests.

rougier · 2016-02-13T06:09:57Z

EDITOR-IN-CHIEF

@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !

dmcglinn · 2016-02-13T11:31:50Z

REVIEWER 1

@karthik this is working for me too. I also apologize for the long delays. No more comments.

On Feb 13, 2016, at 1:10 AM, Nicolas P. Rougier [email protected] wrote:

EDITOR-IN-CHIEF

@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !

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karthik · 2016-02-14T22:45:42Z

EDITOR

Thank you @tpoisot and @dmcglinn
I'll look this over shortly and update the thread.

karthik · 2016-03-03T03:50:29Z

EDITOR

@jsta Apologies for all the delays. But I have also reviewed the submission and the original landscape ecology paper by Etherington and am happy that the original code and figures have been reproduced. I'm happy to accept the submission.

jsta · 2016-03-04T00:15:50Z

AUTHOR

Thanks @karthik , please let me know if I can do anything else to prep the PR for import.

rougier · 2016-03-04T08:25:57Z

EDITOR-IN-CHIEF

@jsta Until actual import (soon), please do not commit to the repo.
@karthik I can take care of the final publication if you want.

rougier · 2016-03-07T10:24:10Z

EDITOR-IN-CHIEF

@karthik I will take care of the publication.
@jsta You need to have all the output images either in your code repository (or in the article repository) such that I can build the PDF without running the code. Does that make sense ?

jsta · 2016-03-07T13:06:09Z

@rougier I have added many images to the repo. You should be able to build
the PDF now.
On Mar 7, 2016 5:24 AM, "Nicolas P. Rougier" [email protected]
wrote:

@karthik https://github.com/karthik I will make the publication.
@jsta https://github.com/jsta You need to have all the output images
either in your code repository (or in the article repository) such that I
can build the PDF without running the code. Does that make sense ?

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#11 (comment)
.

rougier · 2016-03-07T13:09:41Z

@jsta Thanks.

rougier · 2016-03-07T18:05:10Z

@jsta Could you also give 2/3 keywords ? (We need to add a keyword fields in the template)

rougier · 2016-03-07T18:31:12Z

This submission has been accepted for publication, and has been published and will soon appear at https://github.com/ReScience/ReScience/wiki/Current-Issue

karthik · 2016-03-08T09:28:09Z

Thanks @rougier!

jsta added 10 commits October 17, 2015 18:31

fill-in yaml front matter, rename files

e145496

first draft of intro and methods

2593052

first draft of results and conclusions

1d10d26

reflow text, we work figure alignment/size

10a67af

add fig files

62f43fb

add more detail about geoCorrection

248f51c

copy irlgraph code

41d79ca

rename directional bias figure

c07c780

implement Makefile building

c82f0cd

fix fig caption ending

32c3e27

rougier added Physical Science 01 - Request labels Nov 3, 2015

jsta added 4 commits November 3, 2015 09:01

fix low res figures

a0f57d3

correct typos, change personal pronouns to reflect single author

25a510b

add fig number links

05453c4

fix remaining collective personal pronoun

45732fd

rougier assigned karthik Nov 9, 2015

rougier added the 02 - Review label Nov 19, 2015

jsta added 4 commits December 30, 2015 10:37

lint code, fix incomplete parameter and fxn documentation

1e25312

fix bad quotes in README

29981b2

cleanup Makefiles

8bc6cb5

implement Docker pdf build

c03fe28

jsta added 2 commits February 13, 2016 11:24

point Makefile default to figure build not pdf build, update README

5b087c0

fix rmarkdown dependencies

b9b2b8e

rougier added the 03 - Accepted label Mar 3, 2016

add all images to repo

347cd55

rougier added the 04 - Published label Mar 7, 2016

rougier closed this Mar 7, 2016

ReScience locked and limited conversation to collaborators Mar 7, 2016

rougier added the R label Jul 3, 2016

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Review Request : J. Stachelek #11

Review Request : J. Stachelek #11

jsta commented Nov 3, 2015

jsta commented Nov 3, 2015

rougier commented Nov 3, 2015

jsta commented Nov 6, 2015

FedericoV commented Nov 6, 2015

rougier commented Nov 6, 2015

karthik commented Nov 9, 2015

karthik commented Nov 16, 2015

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tpoisot commented Nov 18, 2015

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jsta commented Nov 18, 2015

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tpoisot commented Feb 1, 2016

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jsta commented Mar 4, 2016

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karthik commented Mar 8, 2016

Review Request : J. Stachelek #11

Review Request : J. Stachelek #11

Conversation

jsta commented Nov 3, 2015

jsta commented Nov 3, 2015

rougier commented Nov 3, 2015

jsta commented Nov 6, 2015

FedericoV commented Nov 6, 2015

rougier commented Nov 6, 2015

karthik commented Nov 9, 2015

karthik commented Nov 16, 2015

karthik commented Nov 17, 2015

tpoisot commented Nov 18, 2015

tpoisot commented Nov 18, 2015

jsta commented Nov 18, 2015

tpoisot commented Nov 18, 2015

jsta commented Jan 15, 2016

karthik commented Jan 18, 2016

tpoisot commented Feb 1, 2016

Issue 1

Issue 2

jsta commented Feb 1, 2016

jsta commented Feb 12, 2016

tpoisot commented Feb 12, 2016

rougier commented Feb 13, 2016

dmcglinn commented Feb 13, 2016

karthik commented Feb 14, 2016

karthik commented Mar 3, 2016

jsta commented Mar 4, 2016

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