cran-task-views / hydrology Goto Github PK

Looks like in particular the Modeling section has some duplication.

From Achim:

Currently, the <info> section is collapsed into a single line. This
makes it very hard for me to edit it. I typically do this when packages on
CRAN get archived so that I omit them from the .ctv. When you do the next
update on GitHub you need to reflect this as well...and it also gives you
the chance to review whether plain ommission is really the best strategy.
Sometimes packages re-appear or are still on GitHub or there are
replacement packages etc.

Add https://CRAN.R-project.org/package=rmweather likely in the modelling section

From Achim:

Similarly, it would be convenient if <packagelist> were ordered alphabetically.

Hello,

I am the maintainer of the package baseflow, which is now on CRAN. Source code is available here. Could you consider adding it to the list ?

It is a hydrograph analysis package that implements a hydrograph separation method detailed in an article, which is under review in HESS : Pelletier, A. and Andréassian, V.: Hydrograph separation: an impartial parametrization for an imperfect method, Hydrol. Earth Syst. Sci. Discuss., https://doi.org/10.5194/hess-2019-503, in review, 2019.

Thank you in advance.

From Achim:

Please use <view>...</view> to link to other CRAN task views. The
non-CRAN "views" should be regular <a href="...">...</a> tags. I would
strongly encourage not to call these "task views" to avoid confusion among
readers.

Package newly added to CRAN

package name: nhdR
repository: https://github.com/jsta/nhdR
development URL: https://github.com/jsta/nhdR
description/detail: Tools for working with the National Hydrography Dataset, with functions for querying, downloading, and networking both the NHD https://www.usgs.gov/core-science-systems/ngp/national-hydrography and NHDPlus http://www.horizon-systems.com/nhdplus datasets.

From Achim:

You should include the .ctv in the SVN on R-Forge and then I can easily
release it on CRAN.

Archived on: 2019-09-03

https://cran.r-project.org/web/packages/WaterML/index.html

The fasstr package listed under 'Data Analysis' is now a CRAN package (https://CRAN.R-project.org/package=fasstr). As fasstr functions complete more than just data tidying (various flow statistics, trends and other analyses are included), I would recommend placing it in the 'Hydrograph analysis' section. Thanks!

From Achim:

You currently haven't selected any "core" packages, i.e., those package
that you most people would need to do hydrology in R. (As currently there
is none, the .ctv as an empty: <pkg priority="core"></pkg>.)

Please consider adding this very useful FedData package.

This is the information provided on its GitHub page

Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources. The package enables extraction from seven datasets:

• The National Elevation Dataset (NED) digital elevation models (1 and 1/3 arc-second; USGS)
• The National Hydrography Dataset (NHD) (USGS)
• The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA
• The Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA
• The Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC)
• The International Tree Ring Data Bank (ITRDB), coordinated by National Climatic Data Center at NOAA
• The National Land Cover Database (NLCD) from 2011, 2006, and 2001

add: CDECRetrieve
CRAN: https://cran.r-project.org/package=CDECRetrieve
Github: https://github.com/FlowWest/CDECRetrieve
Description: CDEC maintains a set of web services at http://cdec.water.ca.gov/queryTools.html. In order to better interact and analyze the data this R packages allows users to quickly and easily retrieve data.

@samzipper @ilapros

What do you think the best approach to deal with packages that were previously on CRAN but then have been removed for policy violations. For example: https://cran.r-project.org/web/packages/sbtools/index.html

My suggestion is to leave them in the hydrology task view for six months. They show up in the check_ctv_packages step in our process. If after six months the problem still hasn't been resolved, we remove them from the task view. Thoughts?

Figure this out:

diff:
	git pull
	svn checkout svn://svn.r-forge.r-project.org/svnroot/ctv/pkg/inst/ctv
	cp ./ctv/Hydrology.ctv Hydrology.ctv
	git diff Hydrology.ctv > cran.diff
	git checkout -- Hydrology.ctv
	rm -r ./ctv

svn:
	svn checkout svn+ssh://[email protected]/svnroot/ctv/
	cp Hydrology.ctv ./ctv/pkg/inst/ctv/
	cd ./ctv
	svn status

release:
	cd ./ctv
	svn commit --message "update Hydrology"
	cd ../
	rm -r ./ctv

Package name: smapr: Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
CRAN: https://cran.r-project.org/web/packages/smapr/index.html
Repository: https://github.com/ropensci/smapr
Description/detail: Facilitates programmatic access to NASA Soil Moisture Active Passive (SMAP) data with R. It includes functions to search for, acquire, and extract SMAP data.

Package to add: somspace
CRAN: https://cran.r-project.org/package=somspace
Github: https://github.com/imarkonis/somspace
Vignette: https://imarkonis.github.io/somspace/
Description: Application of the Self-Organizing Maps technique for spatial classification of time series. The package uses spatial data, point or gridded, to create clusters with similar characteristics. The clusters can be further refined to a smaller number of regions by hierarchical clustering and their spatial dependencies can be presented as complex networks. Thus, meaningful maps can be created, representing the regional heterogeneity of a single variable. In the vignette, spatial classification of European Palmer Drought Severity index is presented.

From Achim:

Collapsing all the <info> into a single might not be ideal for
maintenance of the .ctv file. Note that I will regularly edit the .ctv
when packages on CRAN get archived (and less often also wehn packages get
un-archived). I've pointed out the same problem to the WebTechnologies
maintainers.

I don't think I understand what he means here, probably because I don't really understand the CTV file generation process. @boshek , does this make sense to you?

https://cran.r-project.org/web/packages/CoSMoS/index.html

Need to make it clearer that it is only the hydrology.md is the only file that is edited.

From Achim:

The <info> text highlights links to various useful resources on the web
(e.g., Riccardo Rigon's page, ROpenSci MapTools Listing, RHydro project,
etc.). It would be useful to also include these in the <links> section.

From Achim:

The current version of the task view does not distinguish very clearly
between CRAN and GitHub packages. So users might be confused that
available.views() and install.views() etc. do not get them all packages.
Other task views address this by adding a note such as "on GitHub" or so
when non-CRAN packages are listed in the <info> section.

Stumbled upon this blogpost which could be referenced (and it probably would be worth checking whether any of the packages mentioned in there is missing in the TaskView)
https://waterprogramming.wordpress.com/2019/07/08/packages-for-hydrological-data-retrieval-and-statistical-analysis/?utm_source=dlvr.it&utm_medium=twitter

https://CRAN.R-project.org/package=kiwisR

Options are:
-Hydrology and meteorology
-Water (or water science)
-Hydroscience

I think my final vote is 'water science', as it encompasses hydrology, meteorology, and ecology - all of which are represented in the packages we include - but is also not so specific so if a meteorology task view gets spun off later, we wouldn't have to rename.

@ilapros @boshek - final votes?

A package I've been working on the last little bit: rforecastca. We might consider adding it to the "Meterological data" section.

Package Description:
Allows users to retrieve weather forecasts from Environment Canada’s Datamart service in tabular format.

Currently the package supports retrieving the following forecasts:

• CityPage Weather
• North American Ensemble Forecast System

I will be continuing to chip away at adding new forecasts. Currently just have these two because they're available in easily parse-able XML files (many of the others are in spatial formats that require some more thought/effort).

As far as I know, this is only R package currently in development which allows querying Environment Canada forecasts from Datamart.

From Achim:

Instead of "Open Data TaskView" I would recommend "rOpenSci Task View:
Open Data" to clarify that it is an rOpenSci resource and not on CRAN.

Make this more informative: https://github.com/ropensci/Hydrology/runs/317898879#step:14:13

When I was working on adding prism, the makefile would not work for me initially.

The error related to the quotes used in the call to R, e.g., install.packages("ctv", repos = "http://cran.rstudio.com/").

I was able to fix this by replacing all of the calls to R with calls to Rscript.

I think this is a windows issue, but maybe my quick research didn't quite fully explain the issue.

If you are not using windows, could you confirm that it will work for you with Rscript, and if it does, consider switching to it? Or maybe there are other reasons to stick with R over Rscript?

Hello,

Please consider adding the openair package too.

This is the information provided on its GitHub page:

openair is an R package developed for the purpose of analysing air
quality data — or more generally atmospheric composition data.

This package continues to develop and input from other developers would
be welcome. A summary of some of the features are:

• Access to data from several hundred UK air pollution monitoring
  sites through the importAURN and importKCL functions.
• Utility functions such as timeAverage and selectByDate to
  make it easier to manipulate atmospheric composition data.
• Flexible wind and pollution roses through windRose and
  pollutionRose.
• Flexible plot conditioning to easily plot data by hour or the day,
  day of the week, season etc. through the openair type option
  available in most functions.
• More sophisticated bivariate polar plots and conditional
  probability functions to help characterise different sources of
  pollution. A paper on the latter is available
  here.
• Access to NOAA Hysplit
  pre-calculated annual 96-hour back trajectories and many
  plotting and analysis functions e.g. trajectory frequencies,
  Potential Source Contribution Function and trajectory clustering.
• Many functions for air quality model evaluation using the
  flexible methods described above e.g. the type option to easily
  evaluate models by season, hour of the day etc. These include key
  model statistics, Taylor Diagram, Conditional Quantile plots.

First of all, thank you for promoting hydrology related packages through this Task View! This will be a great resource for hydrologists starting with R to do their analysis. In this respect, I am wondering whether the urban hydrology field is also covered? For example, I am working a lot with the well known Stormwater Management Model SWMM by the US EPA, for which I created the R package {swmmr} to interface with model results and the model itself. Do you think this fits to the hydrology CTV?

@szipper @ilapros

What do you think about this approach? Keep the badges here on github but remove them for CRAN?

Following this post: https://blog.r-hub.io/2019/11/26/pkgsearch/

Goal is just the essence of each package

To add: whitebox

CRAN: https://cran.r-project.org/web/packages/whitebox/index.html
GitHub: https://github.com/giswqs/whiteboxR

Description: R frontend of the 'WhiteboxTools' geospatial data analysis platform. Includes functions for common tasks in GIS, remote sensing and image processing, spatial hydrological analysis, terrain analysis, and LiDAR data processing.

From Achim:

Omit the GitHub-specific comment about "this README...". It's fine to
link to the issues on GitHub but the text needs to work on CRAN.

Archived on 2019-05-13
https://cran.r-project.org/web/packages/sbtools/index.html

https://cran.r-project.org/web/packages/VICmodel/index.html

Thanks.

For some packages the github tag is used, although they exist on CRAN. I imagine we should link the CRAN version of the package, which is supposedly not in development and which can be installed without devtools.
Noticed for EGRET, EGRETci - others seem OK but worth double checking

https://CRAN.R-project.org/package=clifro

Into meteorological data

https://cran.r-project.org/web/packages/prism/index.html

Likely in the Met section

From Achim:

Currently all of your items use a format such as:
dataRetrieval Collection of functions to ...
This not grammatically correct. Other task address this by either adding a
colon "dataRetrieval: Collection of ..." or turning it into a proper
phrase "dataRetrieval provides a collection of ..." etc. In your case it's
probably easier to go for the former solution and just add colons.

Some list items in the <info> section lack a period at the end.

From Achim:

The task views in the <links> section are currently included with a <a>
tag linking to the CRAN master site. Instead you should simply use
<view>Environmetrics</view> etc. This will generate a suitable <a> linking
to the local task view on the respective mirror.

I'm wondering if nasapower isn't a good fit for this CTV as well for the daily meteorology it provides?

package name: nasapower
repository: https://github.com/ropensci/nasapower
description/detail from DESCRIPTION:

Client for 'NASA' 'POWER' global meteorology, surface solar
energy and climatology data 'API'.  'POWER' (Prediction Of Worldwide Energy
Resource) data are freely available global meteorology and surface solar
energy climatology data for download with a resolution of 1/2 by 1/2 arc
degree longitude and latitude and are funded through the 'NASA' Earth
Science Directorate Applied Science Program.  For more on the data
themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.

As in maptools TaskView: https://github.com/ropensci/maptools

Note to self... Probably useful to mention in the text/links to related resources: https://github.com/raoulcollenteur/Python-Hydrology-Tools

These tags are causing problems with the MakeFile for me: https://github.com/ropensci/hydrometeorology/blame/master/hydrometeo.md#L38

These seem like really good info. Perhaps we can incorporate them directly into each package description?

@ilapros Can I ask where you thought these would eventually be displayed?

https://cran.r-project.org/web/packages/lfstat/index.html
https://cran.r-project.org/web/packages/Evapotranspiration/index.html

To whom it may concern,

As an R user working with hydrology, I am really interested in the topic and this repo. I would like to express my appreciation to the developer and maintainers for their time and effort.

I understand the developer and maintainers were trying to test and implement some new features in this package. However, at your convenience, would you please check the reason why many notifications with little information were pushed via email? Around 12 emails with the topic of trying to automate with gh-actions (#57) .

Thank you again for your excellent work.

Best,
Wenlong