cshs-cwra/cshshydrology

Main package

CSHShydRology

Installing this package

The package may be downloaded directly from CRAN with:

install.packages("CSHShydRology")

Previous versions of the package and manuals can be found by clicking on releases. The latest version of the package may also be installed directly from this repository. The procedure is

1. Install the package "devtools" - you only have to do this once. Note that this will also install several dependancies
2. Load the devtools library
3. Install the package.

The commands are:

if (!require(devtools)) install.packages("devtools")
library(devtools)
install_github("CSHS-CWRA/CSHShydRology")

What is CSHS Hydrology?

This is an R package of functions used by Canadian hydrologists. The name is in recognition of the support provided by the Canadian Association Society for Hydrological Sciences (CSHS) which is an affiliated society of the Canadian Water Resources Association (CWRA). The CSHS website is https://cwra.org/en/affiliates-programs/cshs/.

Themes

This package contains functions which are grouped into themes. Currently the themes include:

• Statistical hydrology (trend detection, data screening, frequency analysis, regionalization),
• Basic data manipulations (input/conversion/adapter functions, missing data infilling),
• Visualization (data visualization, standardized plotting functions),
• Spatial hydrology (basin delineation, landscape data analysis, working with GIS),
• Streamflow measurement analysis (rating curve analysis, velocity profiles, naturalization).

Other themes, such as Network design/analysis (homogeneity assessment), and Ecohydrology (fisheries and ecological analysis) will also be added if there is interest.

Coding standards

General standards

The general coding standards are as specified in the Google R coding guide at https://google.github.io/styleguide/Rguide.xml.

External packages

To reduce errors, it is a good idea to reduce reliance on other packages as much as is possible. Please check through the functions already referenced in the DESCRIPTION file before adding additional functions. When it is necessary to add a reference to an additional package, please do the following: Make the package suggested, rather than required. Make a note in the function’s Roxygen documentation that the function uses the package. Make sure that the version number of the package is referenced properly. When more than one function requires a given package, it can be made a required packages.

Devtools

To make package development easier, we will use the package devtools, which provides several tools. This package is explained at https://github.com/hadley/devtools.

Checking

The devtools check function will be used check each function for errors in syntax and style. Each function must pass the checks with zero warnings, errors or notes. Note that once you have loaded devtools, the check function can be accessed from a menu or from the build tab in Rstudio. It is also a good idea to manually run the check function from the command line, i.e.

R CMD check

as this can catch other problems.

Documentation

All functions need to be documented using the Roxygen package, which allows you to create the help files and documentation using comments in your function. The package is explained at https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html. Rstudio has a very nice quick reference for Roxygen which you can access with Help|Roxygen Quick Reference. Each function must include the name of the authors(s). Please include your email address, and any publications that you want to reference. Note that the package itself also has a function. This contains documentation about the package as a whole, as well as settings which are used to create the package NAMESPACE file. Note that this means that the NAMESPACE file should never be edited directly by anyone. When the package is compiled and tested, Roxygen will create a .Rd file for each function, the package, and for the included data files. These files should never be edited manually. If you want to check how your .Rd file will look, you can load it into Rstudio, which can render it.

Vignettes

Vignettes are long form documentation which can be included in R packages. They can include long descriptions and worked examples, and are very useful to thoroughly explain functions to the users. The creation process is explained at http://r-pkgs.had.co.nz/vignettes.html. Even if you don’t write code, you can contribute to writing vignettes for functions.

Testing

The testthat package allows unit tests to be created for each function. The function is executed, using specified data, and the results are compared to specified values. Unit tests should be used whenever possible, as they will identify problems caused by changes in upstream packages. The testthat package is explained in detail in http://r-pkgs.had.co.nz/tests.html.

Test data

Each function is required to have an example, which should be executable code. The only exception should be for code which is intended to access data which may not be available, such as data downloaded from a server. The example, vignettes, and unit tests will all require test data sets. The data are stored in the /data folder of the package, and should be stored as .Rdata (binary) files, unless reading in data from another format is the point of the function. CRAN has a maximum limit of 1 MB for test data, so we will need to minimise the datasets we include. We should minimise the size of each test dataset and re-use the same data in as many functions as possible. If a function requires data output by another function, both functions can be included in the example. Each dataset needs to be documented in the same way as a function. The creation of datasets and their documentation is explained at http://r-pkgs.had.co.nz/data.html.

Working with GitHub

There is a lot of information available on using git and GitHub in R. The best starting point is https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN which shows how to integrate git and GitHub with RStudio.

Citation

The package citation may be generated with the following command in R.

citation("CSHShydRology")

cshshydrology's Issues

Example run times

Several examples are being flagged in the check --as-cran as taking excessively long to execute

Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ch_flow_raster_trend 9.152  0.428   9.584
ch_regime_plot       8.354  0.375   8.730
ch_polar_plot        8.150  0.371   8.528

We should probably try using them with smaller data sets.

Session Info

CRAN issue #3 examples for unexported functions

You have examples for unexported functions.
ch_decades_plot() in:
ch_decades_plot.Rd
Please either omit these examples or export the functions

Session Info

CRAN issue #5 writing information to console that cannot be suppressed

You write information messages to the console that cannot be easily
suppressed.
It is more R like to generate objects that can be used to extract the
information a user is interested in, and then print() that object.
Instead of print()/cat() rather use message()/warning() or
if(verbose)cat(..) (or maybe stop()) if you really have to write text to
the console.
(except for print, summary, interactive functions

Session Info

ch_wbt_catchment_onestep - catchment.shp export is actually the channel.shp

Love this function, but the catchment.shp export at the end is actually the channel data. Thankfully the catchment.tif is correct so I've been converting that to .shp.

My reproducible example is the help example (one day I"ll learn to make reprex).

Cheers

library(raster)
test_raster <- ch_volcano_raster()
dem_raster_file <- tempfile(fileext = c(".tif"))
writeRaster(test_raster, dem_raster_file, format = "GTiff")
wd <- tempdir()
pourpoint_file <- tempfile("volcano_pourpoints", fileext = ".shp")
pourpoints <- ch_volcano_pourpoints(pourpoint_file)
catchment <- ch_wbt_catchment_onestep(wd = wd, in_dem = dem_raster_file,
pp_sf = pourpoints, sink_method = "fill", threshold = 1, snap_dist = 10)

> devtools::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_Canada.utf8
 ctype    English_Canada.utf8
 tz       America/Los_Angeles
 date     2023-03-02
 rstudio  2022.12.0+353 Elsbeth Geranium (desktop)
 pandoc   2.12 @ C:\\Users\\jmorris\\ANACON~1\\Scripts\\pandoc.exe

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package       * version  date (UTC) lib source
 assertthat      0.2.1    2019-03-21 [1] CRAN (R 4.2.0)
 boot            1.3-28   2021-05-03 [2] CRAN (R 4.2.0)
 cachem          1.0.6    2021-08-19 [1] CRAN (R 4.2.0)
 callr           3.7.3    2022-11-02 [1] CRAN (R 4.2.2)
 circular        0.4-95   2022-04-26 [1] CRAN (R 4.2.2)
 class           7.3-20   2022-01-16 [2] CRAN (R 4.2.0)
 classInt        0.4-8    2022-09-29 [1] CRAN (R 4.2.2)
 cli             3.4.1    2022-09-23 [1] CRAN (R 4.2.1)
 codetools       0.2-18   2020-11-04 [2] CRAN (R 4.2.0)
 colorspace      2.0-3    2022-02-21 [1] CRAN (R 4.2.0)
 crayon          1.5.2    2022-09-29 [1] CRAN (R 4.2.2)
 CSHShydRology * 1.3.0    2022-11-16 [1] CRAN (R 4.2.0)
 DBI             1.1.3    2022-06-18 [1] CRAN (R 4.2.2)
 devtools        2.4.5    2022-10-11 [1] CRAN (R 4.2.2)
 digest          0.6.30   2022-10-18 [1] CRAN (R 4.2.2)
 dotCall64       1.0-2    2022-10-03 [1] CRAN (R 4.2.2)
 dplyr           1.0.10   2022-09-01 [1] CRAN (R 4.2.2)
 e1071           1.7-12   2022-10-24 [1] CRAN (R 4.2.2)
 ellipsis        0.3.2    2021-04-29 [1] CRAN (R 4.2.0)
 fansi           1.0.3    2022-03-24 [1] CRAN (R 4.2.0)
 farver          2.1.1    2022-07-06 [1] CRAN (R 4.2.2)
 fastmap         1.1.0    2021-01-25 [1] CRAN (R 4.2.0)
 fields          14.1     2022-08-12 [1] CRAN (R 4.2.2)
 fs              1.5.2    2021-12-08 [1] CRAN (R 4.2.0)
 generics        0.1.3    2022-07-05 [1] CRAN (R 4.2.2)
 ggplot2         3.4.0    2022-11-04 [1] CRAN (R 4.2.2)
 ggspatial       1.1.6    2022-07-08 [1] CRAN (R 4.2.2)
 glue            1.6.2    2022-02-24 [1] CRAN (R 4.2.0)
 gridExtra       2.3      2017-09-09 [1] CRAN (R 4.2.0)
 gtable          0.3.1    2022-09-01 [1] CRAN (R 4.2.2)
 here          * 1.0.1    2020-12-13 [1] CRAN (R 4.2.0)
 htmltools       0.5.3    2022-07-18 [1] CRAN (R 4.2.2)
 htmlwidgets     1.5.4    2021-09-08 [1] CRAN (R 4.2.0)
 httpuv          1.6.6    2022-09-08 [1] CRAN (R 4.2.2)
 httr            1.4.4    2022-08-17 [1] CRAN (R 4.2.2)
 Kendall         2.2.1    2022-03-20 [1] CRAN (R 4.2.0)
 KernSmooth      2.23-20  2021-05-03 [2] CRAN (R 4.2.0)
 later           1.3.0    2021-08-18 [1] CRAN (R 4.2.0)
 lattice         0.20-45  2021-09-22 [2] CRAN (R 4.2.0)
 lifecycle       1.0.3    2022-10-07 [1] CRAN (R 4.2.1)
 lubridate       1.9.0    2022-11-06 [1] CRAN (R 4.2.2)
 magrittr        2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
 maps            3.4.1    2022-10-30 [1] CRAN (R 4.2.2)
 memoise         2.0.1    2021-11-26 [1] CRAN (R 4.2.0)
 mime            0.12     2021-09-28 [1] CRAN (R 4.2.0)
 miniUI          0.1.1.1  2018-05-18 [1] CRAN (R 4.2.0)
 munsell         0.5.0    2018-06-12 [1] CRAN (R 4.2.0)
 mvtnorm         1.1-3    2021-10-08 [1] CRAN (R 4.2.0)
 pillar          1.8.1    2022-08-19 [1] CRAN (R 4.2.2)
 pkgbuild        1.3.1    2021-12-20 [1] CRAN (R 4.2.0)
 pkgconfig       2.0.3    2019-09-22 [1] CRAN (R 4.2.0)
 pkgload         1.3.2    2022-11-16 [1] CRAN (R 4.2.0)
 plotrix         3.8-2    2021-09-08 [1] CRAN (R 4.2.0)
 prettyunits     1.1.1    2020-01-24 [1] CRAN (R 4.2.0)
 processx        3.8.0    2022-10-26 [1] CRAN (R 4.2.2)
 profvis         0.3.7    2020-11-02 [1] CRAN (R 4.2.2)
 promises        1.2.0.1  2021-02-11 [1] CRAN (R 4.2.0)
 proxy           0.4-27   2022-06-09 [1] CRAN (R 4.2.2)
 ps              1.7.2    2022-10-26 [1] CRAN (R 4.2.2)
 purrr           0.3.5    2022-10-06 [1] CRAN (R 4.2.2)
 R6              2.5.1    2021-08-19 [1] CRAN (R 4.2.0)
 raster          3.6-3    2022-09-18 [1] CRAN (R 4.2.2)
 Rcpp            1.0.9    2022-07-08 [1] CRAN (R 4.2.2)
 remotes         2.4.2    2021-11-30 [1] CRAN (R 4.2.1)
 rgdal           1.6-2    2022-11-09 [1] CRAN (R 4.2.2)
 rlang           1.0.6    2022-09-24 [1] CRAN (R 4.2.1)
 rprojroot       2.0.3    2022-04-02 [1] CRAN (R 4.2.0)
 rstudioapi      0.14     2022-08-22 [1] CRAN (R 4.2.2)
 scales          1.2.1    2022-08-20 [1] CRAN (R 4.2.2)
 sessioninfo     1.2.2    2021-12-06 [1] CRAN (R 4.2.0)
 sf              1.0-9    2022-11-08 [1] CRAN (R 4.2.2)
 shiny           1.7.3    2022-10-25 [1] CRAN (R 4.2.2)
 sp              1.5-1    2022-11-07 [1] CRAN (R 4.2.2)
 spam            2.9-1    2022-08-07 [1] CRAN (R 4.2.2)
 stringi         1.7.8    2022-07-11 [1] CRAN (R 4.2.1)
 stringr         1.4.1    2022-08-20 [1] CRAN (R 4.2.2)
 terra           1.6-17   2022-09-10 [1] CRAN (R 4.2.1)
 tibble          3.1.8    2022-07-22 [1] CRAN (R 4.2.2)
 tidyhydat       0.5.7    2022-10-16 [1] CRAN (R 4.2.2)
 tidyselect      1.2.0    2022-10-10 [1] CRAN (R 4.2.1)
 timechange      0.1.1    2022-11-04 [1] CRAN (R 4.2.2)
 timeDate        4021.106 2022-09-30 [1] CRAN (R 4.2.1)
 units           0.8-0    2022-02-05 [1] CRAN (R 4.2.0)
 urlchecker      1.0.1    2021-11-30 [1] CRAN (R 4.2.2)
 usethis         2.1.6    2022-05-25 [1] CRAN (R 4.2.2)
 utf8            1.2.2    2021-07-24 [1] CRAN (R 4.2.0)
 vctrs           0.5.1    2022-11-16 [1] CRAN (R 4.2.2)
 viridis         0.6.2    2021-10-13 [1] CRAN (R 4.2.0)
 viridisLite     0.4.1    2022-08-22 [1] CRAN (R 4.2.2)
 whitebox        2.2.0    2022-10-27 [1] CRAN (R 4.2.2)
 withr           2.5.0    2022-03-03 [1] CRAN (R 4.2.0)
 xtable          1.8-4    2019-04-21 [1] CRAN (R 4.2.0)

 [1] C:/Users/jmorris/AppData/Local/R/win-library/4.2
 [2] C:/Program Files/R/R-4.2.0/library

CRAN Issue #1 use TRUE and FALSE instead of T and F

Please write TRUE and FALSE instead of T and F. (Please don't use 'T' or
'F' as vector names.), e.g.:
man/ch_hydrograph_plot.Rd

Session Info

Can't set the y-axis label in hydrograph_plot

Session Info

Session info --------------------------------------------------------------------------------------------------------------------------
 setting  value                   

    
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.423)           
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Regina              
 date     2018-05-23                  

Packages ------------------------------------------------------------------------------------------------------------------------------
 package       * version date       source        
 backports       1.1.2   2017-12-13 cran (@1.1.2) 
 base          * 3.4.4   2018-03-16 local         
 compiler        3.4.4   2018-03-16 local         
 CSHShydRology * 0.0.1   2018-05-23 local         
 datasets      * 3.4.4   2018-03-16 local         
 devtools        1.13.5  2018-02-18 CRAN (R 3.4.3)
 digest          0.6.15  2018-01-28 CRAN (R 3.4.3)
 evaluate        0.10.1  2017-06-24 CRAN (R 3.4.1)
 graphics      * 3.4.4   2018-03-16 local         
 grDevices     * 3.4.4   2018-03-16 local         
 htmltools       0.3.6   2017-04-28 CRAN (R 3.4.1)
 knitr           1.20    2018-02-20 CRAN (R 3.4.3)
 lubridate       1.7.3   2018-02-27 CRAN (R 3.4.3)
 magrittr        1.5     2014-11-22 CRAN (R 3.4.1)
 memoise         1.1.0   2017-04-21 CRAN (R 3.4.1)
 methods       * 3.4.4   2018-03-16 local         
 Rcpp            0.12.16 2018-03-13 CRAN (R 3.4.4)
 rmarkdown       1.9     2018-03-01 CRAN (R 3.4.3)
 rprojroot       1.3-2   2018-01-03 cran (@1.3-2) 
 rsconnect       0.8.8   2018-03-09 CRAN (R 3.4.3)
 stats         * 3.4.4   2018-03-16 local         
 stringi         1.1.7   2018-03-12 CRAN (R 3.4.4)
 stringr         1.3.0   2018-02-19 CRAN (R 3.4.3)
 tools           3.4.4   2018-03-16 local         
 utils         * 3.4.4   2018-03-16 local         
 withr           2.1.2   2018-03-15 CRAN (R 3.4.4)
 yaml            2.1.18  2018-03-08 CRAN (R 3.4.3)

When I try to change the y-axis title, it fails. The last chunk in the attached pdf shows the issue

hydrograph_plot.pdf

Dead URL in README

Found this dead link while taking a look through the package to find areas I can clean up/contribute.

The link to the CSHS page at the end of the "What is CSHS Hydrology?" section of the README 404s.

Link is currently http://www.cwra.org/en/branches/affiliates/cshs-a

Would submit a PR but not sure where this link should actually point.

Link location in README:

Resulting 404:

Additional functions in the package

I will appreciate if the following routine tasks performed by most hydrologists are added to the package:
-Time series gap infilling
-Flow naturalization
-Streamflow data extension
-Flow transfer to an ungauged site
-Annual and seasonal autocorrelations and cross-correlations
-ARIMA models for stochastic time series recreation, or at least AR models, both univariate and multivariate. It must have a -module for data analysis, a module for fitting a model and a module for generate series using the fitted model. ( I am sure this tools already exist in R, but the idea would be to included them in the CWRA package and linked with the Canada dataset.)
-Spatial and temporal disaggregation methods….including flow disaggregation methods
-Statistics related to storage, drought and surplus
-Scaling and standardization

Issues in hydrograph.plot

Session Info

 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.453)           
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Regina              
 date     2018-06-12                  

Packages -------------------------------------------------------------------------------------------------------------------------------
 package   * version date       source        
 base      * 3.4.4   2018-03-16 local         
 compiler    3.4.4   2018-03-16 local         
 datasets  * 3.4.4   2018-03-16 local         
 devtools    1.13.5  2018-02-18 CRAN (R 3.4.3)
 digest      0.6.15  2018-01-28 CRAN (R 3.4.3)
 graphics  * 3.4.4   2018-03-16 local         
 grDevices * 3.4.4   2018-03-16 local         
 memoise     1.1.0   2017-04-21 CRAN (R 3.4.1)
 methods   * 3.4.4   2018-03-16 local         
 stats     * 3.4.4   2018-03-16 local         
 tools       3.4.4   2018-03-16 local         
 utils     * 3.4.4   2018-03-16 local         
 withr       2.1.2   2018-03-15 CRAN (R 3.4.4)
 yaml        2.1.18  2018-03-08 CRAN (R 3.4.3)

There are a couple of issues:

1. The function name i(hydrograph.plot) is delimited by a period. This is not what the Google style guide recommends https://google.github.io/styleguide/Rguide.xml#identifiers:
   function names have initial capital letters and no dots
   Currently all of our function names begin with lower-case letters, but using the dot as a delimiter can cause problems on Windows systems as the second word can be confused with the file extension.
2. I get these warnings when I run check()

hydrograph.plot: no visible global function definition for ‘par’
hydrograph.plot: no visible global function definition for ‘plot’
hydrograph.plot: no visible global function definition for ‘grid’
hydrograph.plot: no visible global function definition for ‘polygon’
hydrograph.plot: no visible global function definition for ‘lines’
hydrograph.plot: no visible global function definition for ‘axis’
hydrograph.plot: no visible global function definition for ‘mtext’
hydrograph.plot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis grid legend lines mtext par plot polygon
Consider adding
  importFrom("graphics", "axis", "grid", "legend", "lines", "mtext",
             "par", "plot", "polygon")
to your NAMESPACE file.

You can add the functions to NAMESPACE, by adding statements to hydrology-package.R, i.e.

#' @import (timeDate)
#' @import (raster)
#' @import (Kendall)
#' @import (fields)

The functions called from other packages all need to be specified using the :: notation, specifying the name of the package, as in graphics::axis() etc.

CRAN issue #7 deleting user's objects

Please do not modify the user's global environment or the user's home
filespace in your examples or vignettes by deleting objects
rm(list = ls())

Session Info

Whitfield branch

The function names in the Whitfield branch all begin with a lower-case letter, which is contradicted by the Google code standards at https://google.github.io/styleguide/Rguide.xml#identifiers:

I got the following errors when running check()

checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘Graphics’ ‘Kendall’ ‘fields’ ‘raster’ ‘timeDate’
...
ocumented arguments not in \usage in documentation object 'HYDAT_list':
  ‘stnID’ ‘stn’

Undocumented arguments in documentation object 'doys'
  ‘Date’
Documented arguments not in \usage in documentation object 'doys':
  ‘{Date}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

Issues with Dan Moore's vignette

1. There is a local path in the camp_creek_test vignette:

wd <- "C:/cshshydrology/spatial_functions/working"

Also there is a commented out one in ShannonFalls_spatialhydrology vignette
# dem <- raster::raster("c:/Research/Shannon Falls/Map/cdem_dem_151108_134502_tif/cdem_dem_151108_134502.tif")

2. We get a lot of warnings when using the library() function in the Vignettes, because of all of the raster functions, e.g.

There were 15 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘CSHShydRology’
2: replacing previous import ‘lubridate::origin’ by ‘raster::origin’ when loading ‘CSHShydRology’
3: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘CSHShydRology’
4: replacing previous import ‘raster::density’ by ‘stats::density’ when loading ‘CSHShydRology’
5: replacing previous import ‘raster::weighted.mean’ by ‘stats::weighted.mean’ when loading ‘CSHShydRology’
6: replacing previous import ‘raster::predict’ by ‘stats::predict’ when loading ‘CSHShydRology’
7: replacing previous import ‘raster::aggregate’ by ‘stats::aggregate’ when loading ‘CSHShydRology’
8: replacing previous import ‘raster::quantile’ by ‘stats::quantile’ when loading ‘CSHShydRology’
9: replacing previous import ‘raster::update’ by ‘stats::update’ when loading ‘CSHShydRology’
10: replacing previous import ‘raster::tail’ by ‘utils::tail’ when loading ‘CSHShydRology’
11: replacing previous import ‘raster::stack’ by ‘utils::stack’ when loading ‘CSHShydRology’
12: replacing previous import ‘raster::unstack’ by ‘utils::unstack’ when loading ‘CSHShydRology’
13: replacing previous import ‘raster::head’ by ‘utils::head’ when loading ‘CSHShydRology’
14: replacing previous import ‘raster::image’ by ‘graphics::image’ when loading ‘CSHShydRology’
15: replacing previous import ‘raster::plot’ by ‘graphics::plot’ when loading ‘CSHShydRology’

There are a couple of ways of getting around this.
The best way is to avoid the conflicts
The library() function has some options, including:

exclude,include.only	character vector of names of objects to exclude or include in the attached frame. Only one of these arguments may be used in a call to library or require

We can use this to only include the functions that we need.

Alternatively (and this is definitely poorer style), the library() function also has the option

warn.conflicts	logical. If TRUE, warnings are printed about conflicts from attaching the new package. A conflict is a function masking a function, or a non-function masking a non-function. The default is TRUE unless specified as FALSE in the conflicts.policy option.

If we have to, we could set this to FALSE, but that's not my preference

CRAN issue #4 use of \dontrun instead of \donttest

\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by
the user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user.
Does not seem necessary in all cases.

Please unwrap the examples if they are executable in < 5 sec, or replace
\dontrun{} with \donttest{}.

Please put functions which download data in \donttest{}.

Session Info

CRAN issue #8 - AGPL licence

License components with restrictions and base license permitting such:
AGPL-3 | file LICENSE

The license file is only needed in case of attribution requirements or
other possible restrictions.
Hence please omit it.

Session Info

Feature request - deriving precipitation events from precipitation time series

A function to basically isolate rainfall events from precipitation data would be helpful, and has been requested for usage in groundwater event modelling in particular.

First cut of this could use some first order derivative criteria to detect a rate of change in precip to capture rise and fall in precip intensity (?). Would likely require hourly or higher resolution data

CRAN issue #6 changing user's options

Please make sure that you do not change the user's options, par or
working directory. If you really have to do so within functions, please
ensure with an immediate call of on.exit() that the settings are reset
when the function is exited. e.g.:
...
oldpar <- par(no.readonly = TRUE) # code line i
on.exit(par(oldpar)) # code line i + 1
...
par(mfrow=c(2,2)) # somewhere after
...

...
old <- options() # code line i
on.exit(options(old)) # code line i+1
...
options(scipen = 999)
...
e.g.:
If you're not familiar with the function, please check ?on.exit. This
function makes it possible to restore options before exiting a function
even if the function breaks. Therefore it needs to be called immediately
after the option change within a function.

Please always make sure to reset to user's options(), working directory
or par() after you changed it in examples and vignettes and demos.
e.g.: inst/doc/hydrograph_plot.R
oldpar <- par(mgp = c(2.5, 1, 0))
...
par(oldpar)

Session Info

CRAN issue #2 missing return value for function

Please add \value to .Rd files regarding exported methods and explain
the functions results in the documentation. Please write about the
structure of the output (class) and also what the output means. (If a
function does not return a value, please document that too, e.g.
\value{No return value, called for side effects} or similar)
Missing Rd-tags:
ch_axis_doy.Rd: \value

Session Info

Dan_Moore_spatial branch

Session Info

Lots of errors found by check().

• there are many undocumented function arguments
• many of the functions don't have examples
• functions don't have import statements
  I have fixed ch_saga_catchment() as an example of how it can be done,
  but many the other functions need to be fixed.

Enhancement - transparent colour utility

RC to do

• add transparent colour function to package as a useful utility function for base plots (requested by Paul)