agrdatasci / climatrends Goto Github PK

Per JOSS review checklist, the software papers need to present the state of the field by providing a brief overview of other commonly-used software/packages and describe how this software compares to them. Please consider adding such a short paragraph to the text.

JOSS review checklist also requires the package documentation to include a "Statement of need" text. The summary section of the documentation briefly touches upon it but please consider including more distinct text that clearly states what problems the software is designed to solve and who the target audience is both in the manuscript and the documentation.

Point to the paper review issue on JOSS openjournals/joss-reviews#4199

Now both rainfall() and temperature() returns single point time observations for the required time series. Allow the functions to return these indices in time series intervals, like chirps::precip_indices().

JOSS papers should be between 250-1000 words whereas the current article is 3153 words which is significantly longer than the upper (1000 words) limit.

While this is more of an editorial thing, I thought I would comment on this because by JOSS guidelines you may be asked to reduce the length of your paper and it could be nice to be on the same page about how this will happen in practice.

Add integration with package chirps to compute the rainfall indices using CHIRPS data

Check the feasibility in implementing new indices based on these papers

https://doi.org/10.1016/j.agrformet.2011.06.012

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-018-0375-7

https://www.mdpi.com/2073-4395/9/9/566

I was trying the cbean example in the JOSS paper starting on line 148:

library(climatrends)
library(PlackettLuce)
library(tidyverse)

# number of days required to accumulate gdd from planting date to maturity
gdd <- GDD(modis,
           day.one = cbean$planting_date,
           degree.days = 900,
           return.as = 'ndays')

which assumes the cbean dataset is loaded to the environment.

The dataset is linked on line 130, but I'm not sure this is a proper/preferred way. Maybe this dataset could be included in the package like the other example datasets (i.e. load by data("cbean", package = "climatrends")), or it could be deposited to some repository and linked/loaded that way.

I get an error when I run this code from the vignette:

library(climatrends)
    lonlat <- data.frame(lon = 129.19,
                         lat = 36.39)
    
    GDD(lonlat, 
        day.one = "2019-04-01",
        last.day = "2019-10-01",
        degree.days = 150, 
        return.as = "ndays")
#> Getting climate data from NASA POWER
#> Error in get_power(community = "ag", lonlat = c(129, 36, 132, 39), pars = c("T2M_MAX", : could not find function "get_power"

^{Created on 2022-08-16 by the reprex package (v2.0.1)}

Hi, I was trying out the example code snippet in the JOSS paper:

library(climatrends)
library(sf)
library(nasapower)
# create a polygon within the coordinates 7, 17, 59, 63
e <- matrix(c(7, 59, 17, 59, 17, 63,
              7, 63, 7, 59),
            nrow = 5, ncol = 2, byrow = TRUE)

e <- st_polygon(list(e))
# sample 100 points in the hexagonal type
p <- st_sample(e, 100, type = 'hexagonal')
p <- st_as_sf(p, crs = 4326)
# compute the temperature indices using the random points
temp <- temperature(p, day.one = '2000-01-01', last.day = '2019-12-31',
                    timeseries = TRUE, intervals = 365)

But I'm getting the following error:

Getting climate data from NASA POWER 

Fetching data for 22 regions with 5 x 5 arc-degree 

Error: HTTP (422) - The request was well-formed but was unable to be followed due to semantic errors (WebDAV; RFC 4918)
  Please do not request a time period greater than 366 days.

When I set last.day = '2000-12-31' it works fine, could you address this error or revise the text in the paper?

Implement data gathering from large geographic areas.

library("climatrends")

lonlat <- data.frame(lon = c(-4.96, 11.09),
                     lat = c(37.82, 60.80))

# random dates within 2018-05-15 and 2018-05-2
set.seed(321)
dates <- as.integer(runif(2, 17666, 17670))
dates <- as.Date(dates, origin = "1970-01-01")

# get temperature indices for 40 days after day.one
temperature(lonlat,
            day.one = dates,
            span = 40)

Error: 
Please provide correct bounding box values. The bounding box
can only enclose a max of 10 x 10 region of 0.5 degree values
or a 5 x 5 region of 1 degree values, (i.e. 100 points total). 

As part of JOSS requirements, I noticed that two package contributors listed in the package DESCRIPTION file (Solberg and van Etten) are neither co-authors nor mentioned in the acknowledgements. If contributions don’t warrant authorship, please identify and acknowledge their contributions. openjournals/joss-reviews#4405,

When following the installation in the README

Installing from CRAN works.

However, installing the development version fails - on both Windows and Ubuntu:

remotes::install_github("agrdatasci/climatrends")

I get the following errors:

Downloading GitHub repo agrdatasci/climatrends@HEAD
✓ checking for file ‘/tmp/RtmpPZhckZ/remotes192662211476/AgrDataSci-climatrends-cddf697/DESCRIPTION’ (372ms)
─ preparing ‘climatrends’:
✓ checking DESCRIPTION meta-information ...
─ installing the package to process help pages
-----------------------------------
─ installing source package ‘climatrends’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in library("nasapower") : there is no package called ‘nasapower’
Error: unable to load R code in package ‘climatrends’
Execution halted
ERROR: lazy loading failed for package ‘climatrends’
─ removing ‘/tmp/RtmpyuDRgM/Rinst197f6af92b2/climatrends’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'climatrends' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> *** moving datasets to lazyload DB
E> ** inst
E> ** byte-compile and prepare package for lazy loading
E> Error in library("nasapower") : there is no package called ‘nasapower’
E> Error: unable to load R code in package ‘climatrends’
E> Execution halted
E> ERROR: lazy loading failed for package ‘climatrends’
E> * removing ‘/tmp/RtmpyuDRgM/Rinst197f6af92b2/climatrends’
E> -----------------------------------
E> ERROR: package installation failed

Dear contributors of the climatrends R package and authors of the JOSS paper,

I'm Istem Fer, I'm one of the reviewers of your paper. I thought I would start with this issue regarding the lack of "Statement of need" section (to be followed by some other format issues). I'll try to keep issues focused and compact so that you can close them one by one as we go. Here we go:

JOSS articles are required to have A Statement of need section (titled as such) that clearly illustrates the research purpose of the software and places it in the context of related work. Please add this section to your pdf accordingly.

going through openjournals/joss-reviews#4405 and to pass JOSS requirement "License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?"

I see that the license is stated in the DESCRIPTION file, but this would help comply with JOSS requirements. For an existing convention to follow, it appears tidyverse packages have a file named LICENSE, like yours, as well as a LICENSE.md file with the license text, and this convention appears to be generated by the usethis::use_mit_license() function