Closed whedon closed 5 years ago
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Attempting PDF compilation. Reticulating splines etc...
Sorry, I'm at a conference this week. Will complete this next week!
@nuest @benmarwick - friendly reminder to complete your reviews when you get a chance :grin:
Thanks, working on it!
Hey guys!
Do not forget me
This is a kind reminder :)
@nuest @benmarwick - friendly reminder to complete your reviews when you get a chance 😁
Yes, please take a look at this when you get a chance please!
Sincere apologies for the delay, too many GH emails and this one fell through the cracks. I started my review and have some first comments that can be addressed rightaway, see issues linked above. I'll start the functional evaluation next.
I gave the paper.md
a first read, some comments/questions:
sample.tiff
is missing, probably must be dmsp.tiff
areaSource
differs on my machine compared to what the paper has, starting at the fourth decimal place... is this relevant or expected?> CO_emissions <- emission(TOTAL,"CO",list(SP = SP, MG = MG),grid,mm=28, plot = T)
[1] "calculating emissions for CO using molar mass = 28 ..."
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) :
'from' must be a finite number
In addition: Warning messages:
1: In asMethod(object) :
complete map seems to be NA's -- no selection was made
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
In my opinion the submission needs some work. I am also not a domain expert, so I cannot say anything about the validity of the method included in the package.
@benmarwick Are you familiar with the methodology and kind of analysis the package performs?
Yes, to start with, I'd love to see another attempt at a clear statement of what problems the software is designed to solve and who the target audience is? Who are the users likely to be? I've just done a tiny bit work helping students in atmospheric chemistry, so the methods here are not familiar to me.
I can run the example code until here:
TOTAL <- totalEmission(veiculos,EF,pol = c("CO"),verbose = T)
Error: $ operator is invalid for atomic vectors
5.
as.character.units(structure(1127549.32468524, units = structure(list(
numerator = "t", denominator = "year"), .Names = c("numerator",
"denominator"), class = "symbolic_units"), class = "units"))
4.
as.character(structure(1127549.32468524, units = structure(list(
numerator = "t", denominator = "year"), .Names = c("numerator",
"denominator"), class = "symbolic_units"), class = "units"))
3.
paste("Total of", pol[i], ":", sum(total_t_y), units::deparse_unit(total_t_y))
2.
print(paste("Total of", pol[i], ":", sum(total_t_y), units::deparse_unit(total_t_y))) at totalEmission.R#62
1.
totalEmission(veiculos, EF, pol = c("CO"), verbose = T)
I've noted this at the repo here: https://github.com/atmoschem/EmissV/issues/16
Update: seems I was missing some Linux libraries. I'll continue testing on Windows.
Thank @nuest and @benmarwick
I'm working on the text (and the code). Soon I will update the package and write here some detailed explanations
Hi @nuest and @benmarwick, thanks for the suggestions, some corrections have already been made to the package and the suggestions in the article have already been incorporated.
@nuest I make some changes in the paper (and in the repository)
sample.tiff
was changed for dmsp.tiff
, this is a smaller file (for CRAN submission).g/d
on each image pixel
.emission
function with plot = T
, the reason is that output is a matrix with can be written in model input files (with the cited packages) and is not georeferencedrasterSource
was updated (to always deal with NAs
)eixport
has specific functions for write in wrf input files@benmarwick the main problem is the need of input data for air quality models, depending on the region there is no information about the temporal or spatial distribution of the vehicular emissions or in some cases, the information is at a national level and not updated for decades. The audience is students and researchers who are interesting in using numerical air quality models but don't have a good inventory or wants an alternative inventory.
The function vehicles
have more detailed description and the number of vehicles is integer now.
I'm Working on the package remain Issues!
Hi @nuest , @benmarwick and @arfon
I have some news: EmissV was accepted on CRAN.
The paper was revised:
When you have time, take a look.
thank you
PS: We are planning the use of EmissV in some Argentine cities in the next months.
I have some news: EmissV was accepted on CRAN.
Great! Thanks for the update @Schuch666.
@nuest, @benmarwick - could you come and take another look at this sometime in the next couple of weeks?
Ping @nuest, @benmarwick :smile: please come any take another look at this package sometime soon.
Hey guys @nuest @benmarwick
Please come any take another look at this package
This is a kindly reminder
hi @arfon, I'm co-author of this paper and package. Is it possible to speed up the review process? Thanks! Sergio
Friendly reminder to come back to this review sometime soon please @nuest & @benmarwick
@Schuch666 Thanks for taking the time to work on our suggestions, and for your understanding that this takes longer than it should. Congrats for getting the package on CRAN!
@whedon generate pdf
Ok, so PDF re-generation does not seem to work... @arfon did I miss something here?
paper.md
without any issues - good!> TOTAL <- totalEmission(fleet,EF,pol = c("CO"),verbose = T)
Total of CO : 1128297.0993334 t year-1
@arfon Does the author have to make a new release on GitHub? Not sure how to answer the "matches" checklist item. Thanks!
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
Ok, so PDF re-generation does not seem to work... @arfon did I miss something here?
☝️ try @whedon generate pdf
@arfon Does the author have to make a new release on GitHub? Not sure how to answer the "matches" checklist item. Thanks!
Basically this is a question about the version number you see here (0.664.3
) and what you find on GitHub.
Hi @benmarwick - do you know when you will be able to complete your review by?
I see a few minor questions and some need for rephrasing, as described in https://github.com/openjournals/joss-reviews/issues/662#issuecomment-411080315, other than that I'm done.
Hey @nuest , thanks for the suggestions.
The reason itself of emission being the "scapegoat" is that a difficult and highly multidisciplinary task. In the case of the anthropogenic emissions, the main difficulty is to create an updated inventory (sometimes there is no inventory available) with the available information (sometimes there is a very low amount of information available). I think one reason can be that the responsibility for the emissions is not of the model user in many cases.
I added some text to the Introduction:
'The anthropogenic emissions, especially vehicular emissions, are highly dependent on human activity and constantly changing due to various factors ranging from economic (such as the state of conservation of the fleet, renewal of the fleet and the price of fuel) to legal aspects (such as the vehicle routing).'
Atmospheric models are continuously developed by research institutions. As well as ways to assimilate a wide variety of data (atmospheric, terrestrial, vegetation, etc.) as satellite images, classifications and parameterizations. The EmissV allow the user to create the emissions with data like tables, shapefiles and images this give the user some power to use available information and more responsibility.
A statement of need of the package use has added next to this:
'The EmissV is an R package that estimates vehicular emissions by a top-down approach, the emissions are calculated using the statistical description of the fleet at available level (National, State, City, etc). The following steps show an example of the workflow for calculating vehicular emissions, this emissions are initially temporally and spatially disaggregated, and then distributed spatially and temporally to be used as input in numeric air quality models such WRF-Chem [@Grelletal2005].'
The values slightly different results in some outputs had updated, the reason it can be that the function vehicles operate on integer numbers only now (that make more sense to me).
If any point can be improved let me know
PS: I changed the 'veiculos' for fleet
Hi, @benmarwick , are you still with us?
@Schuch666 Please double check the documentation to mention that output values might differ slightly. If users run your algorithms and compare outcomes (e.g. in a reproducible research set-up, a reviewer runs an article manuscript) they should be aware that small differences can occur and why.
That's all from me then: LGTM 👍
@Schuch666 Please double check the documentation to mention that output values might differ slightly. If users run your algorithms and compare outcomes (e.g. in a reproducible research set-up, a reviewer runs an article manuscript) they should be aware that small differences can occur and why.
Once you've addressed this comment @Schuch666 I think we're good to accept here.
thank you @arfon
I put a note in the text talking about these differences that can appear in the calculated values and in the figures due to changes between versions of the package (in the code or in the sample files) and also of the version of its dependencies.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@Schuch666 - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.
Hi @arfon
I upload to Zenodo with the following DOI: 10.5281/zenodo.1451027
best regards
@whedon set 10.5281/zenodo.1451027 as archive
OK. 10.5281/zenodo.1451027 is the archive.
@nuest - many thanks for your review here ✨
@Schuch666 - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00662 :zap: :rocket: :boom:
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Submitting author: @Schuch666 (Daniel Schuch) Repository: https://github.com/atmoschem/EmissV Version: 0.664.3 Editor: @arfon Reviewer: @nuest, @benmarwick Archive: 10.5281/zenodo.1451027
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paper.md
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