ccviR: NatureServe Climate Change Vulnerability Index

[see24]

Submitting Author !--author1-->@see24<!--end-author1-- Reviewers: Editor: Language Code Submitting Author: Sarah Endicott (@see24)
Repository: https://github.com/LandSciTech/ccviR Submission type: Pre-submission

---

• Paste the full DESCRIPTION file inside a code block below:

Package: ccviR
Title: NatureServe CCVI in R
Version: 0.0.0.9003
Authors@R: person(given = "Sarah",
  family = "Endicott",
  role = c("aut", "cre"),
  email = "sarah.endicott@canada.ca",
  comment = c(ORCID = "0000-0001-9644-5343"))
Description: The [NatureServe Climate change vulnerability index (CCVI)](https://www.natureserve.org/conservation-tools/climate-change-vulnerability-index) 
is currently distributed as an excel spreadsheet and is used to calculate a relative climate 
change vulnerability index for any North American species. Some of the factors in the spreadsheet require
geospatial computations and the user is expected to do these externally in GIS software. 
The ccviR package performs the spatial analysis and index calculation in R making it 
reproducible and also provides a Shiny app interface for calculating the index. 
License: TBD
Encoding: UTF-8
LazyData: true
Imports: 
    dplyr,
    raster,
    sf,
    purrr,
    tidyr,
    shiny,
    stringr,
    units,
    exactextractr,
    shinyFiles,
    shinyjs,
    tmap,
    ggplot2,
    shinycssloaders,
    R.utils,
    fs,
    plotly,
    shinyFeedback,
    rgdal,
    methods,
    stats,
    utils
Suggests: 
    gdalUtils,
    testthat (>= 2.1.0),
    knitr,
    rmarkdown,
    shinytest
RoxygenNote: 7.1.1
VignetteBuilder: knitr

Scope

• Please indicate which category or categories from our package fit policies or statistical package categories this package falls under. (Please check an appropriate box below):

  Data Lifecycle Packages

  • [ ] data retrieval

  • [ ] data extraction

  • [ ] database access

  • [ ] data munging

  • [ ] data deposition

  • [ ] workflow automation

  • [ ] version control

  • [ ] citation management and bibliometrics

  • [x] scientific software wrappers

  • [ ] database software bindings

  • [ ] geospatial data

  • [ ] text data

    Statistical Packages

  • [ ] Bayesian and Monte Carlo Routines

  • [ ] Dimensionality Reduction, Clustering, and Unsupervised Learning

  • [ ] Machine Learning

  • [ ] Regression and Supervised Learning

  • [ ] Exploratory Data Analysis (EDA) and Summary Statistics

  • [ ] Spatial Analyses

  • [ ] Time Series Analyses

• Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of: If you consider an excel spreadsheet programmed with an algorithm to be software then this package makes the NatureServe CCVI software accessible from R. I am not sure if this counts or if the "software" being wrapped here is broad enough for ROpenSci

• If submitting a statistical package, have you already incorporated documentation of standards into your code via the srr package?

• Who is the target audience and what are scientific applications of this package?
  The NatureServe CCVI has been used in many situations eg (Young, 2015) this package would make it possible to do it in R and the Shiny app makes it more user friendly to biologists or conservation planners without the technical skills to do the GIS analysis. The package also makes it more reproducible since there are no calculations being transferred from GIS to the spreadsheet by hand.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? Not that I know of.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research? NA

• Any other questions or issues we should be aware of?: The package is still in development so the repo is currently private because of my employers approach to OSS but it will be open source once completed. The developer of the NatureServe CCVI has approved of the package informally but we haven't gone further than that yet. It is not quite ready for submission but I was curious if it would fit the criteria.

[ropensci-review-bot]

Missing values: author1, repourl, language

[ldecicco-USGS]

I think there is some potential for this to be considered "scientific software wrappers". Until the repo can be made public however, I don't think we can make any further considerations.

[see24]

@ldecicco-USGS The repo is public now so I would be interested to know if you have further thoughts or suggestions.

Here is the missing info: author1: Sarah Endicott repourl: https://github.com/LandSciTech/ccviR language: EN

[ldecicco-USGS]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Error: Issue template has no 'repourl'

:wave:

[ldecicco-USGS]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

The following problems were found in your submission template:

• 'author1' variable must be GitHub hanle only ('@myhandle')
• submission type must be one of [Standard, Estandar, Stats]
• HTML variable [reviewers-list] is missing
• HTML variable [due-dates-list] is missing Editors: Please ensure these problems with the submission template are rectified. Package checks have been started regardless.

:wave:

[ropensci-review-bot]

Note: The following R packages were unable to be installed/upgraded on our system: [lwgeom, stars, tmaptools, tmap]; some checks may be unreliable.

[ropensci-review-bot]

Checks for ccviR (v0.0.1.9000)

git hash: cf8ebefe

• :heavy_check_mark: Package name is available
• :heavy_multiplication_x: does not have a 'codemeta.json' file.
• :heavy_multiplication_x: does not have a 'contributing' file.
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_check_mark: All functions have examples.
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_multiplication_x: Package coverage failed
• :heavy_multiplication_x: R CMD check process failed with message: 'Build process failed'.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL (>= 3)

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate. |type |package | ncalls| |:----------|:---------------|------:| |internal |base | 357| |internal |ccviR | 63| |internal |graphics | 47| |internal |grDevices | 5| |internal |methods | 2| |imports |raster | 40| |imports |stats | 37| |imports |ggplot2 | 34| |imports |plotly | 18| |imports |purrr | 13| |imports |tidyr | 11| |imports |stringr | 9| |imports |fs | 9| |imports |tmap | 7| |imports |utils | 7| |imports |exactextractr | 5| |imports |units | 4| |imports |sf | 3| |imports |shinyjs | 3| |imports |shinyFiles | 1| |imports |shinycssloaders | 1| |imports |R.utils | 1| |imports |shinyvalidate | 1| |imports |dplyr | NA| |imports |shiny | NA| |imports |rgdal | NA| |imports |scales | NA| |imports |pkgload | NA| |suggests |testthat | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |shinytest | NA| |suggests |future | NA| |suggests |furrr | NA| |suggests |readxl | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

c (86), list (48), data.frame (29), F (20), ncol (12), matrix (11), col (10), names (9), as.vector (8), paste0 (8), rev (8), t (8), range (6), round (6), setdiff (5), all (4), as.data.frame (4), system.file (4), vapply (4), as.list (3), by (3), is.na (3), labels (3), levels (3), nrow (3), options (3), rep (3), seq (3), sum (3), T (3), expand.grid (2), file (2), file.path (2), grep (2), list.files (2), paste (2), Vectorize (2), warning (2), all.equal (1), as.numeric (1), conditionMessage (1), factor (1), for (1), ifelse (1), isTRUE (1), length (1), LETTERS (1), max (1), min (1), missing (1), mode (1), prod (1), split (1), system (1), unlist (1), url (1)

ccviR

bivar_map (7), calc_prop_raster (4), calc_vulnerability (3), calc_ind_monte (2), check_clim (2), check_polys (2), colmat (2), data_prep_server (2), getMultValues (2), ind_from_vuln (2), labelMandatory (2), load_clim (2), analyze_spatial (1), calc_gain_loss (1), calc_min_max_raster (1), calc_overlap_poly (1), ccvi_app (1), check_comment_ui (1), check_crs (1), check_trim (1), data_prep_app (1), data_prep_ui (1), get_clim_vars (1), get_file_ui (1), guideB (1), guideCNonSpatial (1), guideCSpatial (1), guideDNonSpatial (1), guideDSpatial (1), guideExposure (1), index_res_text (1), indexOutServer (1), indexOutUI (1), load_bookmark_server (1), load_bookmark_ui (1), make_map (1), make_pat (1), make_vuln_df (1), mig_exp_text (1), num_not_na (1), perc_not_overlap (1), plot_conf_score (1), ui (1)

graphics

text (18), title (13), box (8), legend (6), axis (2)

raster

reclassify (10), plot (8), cellStats (4), mask (3), extend (2), filename (2), freq (2), rasterToContour (2), sampleRegular (2), area (1), crop (1), raster (1), res (1), xres (1)

stats

poly (17), filter (9), df (5), setNames (3), dist (1), IQR (1), median (1)

ggplot2

aes (9), geom_raster (3), ggplot (3), element_text (2), facet_wrap (2), geom_point (2), theme (2), coord_cartesian (1), coord_flip (1), element_blank (1), expansion (1), geom_col (1), geom_linerange (1), labs (1), scale_fill_manual (1), scale_x_discrete (1), scale_y_continuous (1), theme_classic (1)

plotly

layout (8), plot_ly (4), add_annotations (3), config (2), ggplotly (1)

purrr

map (3), set_names (3), map_lgl (2), keep (1), map_df (1), map_dfr (1), map2 (1), pmap (1)

tidyr

pivot_longer (5), pivot_wider (4), unite (2)

fs

path (3), dir_copy (2), path_home (2), dir_create (1), path_file (1)

stringr

str_detect (3), str_subset (3), str_remove (2), str_replace_all (1)

tmap

tm_raster (3), tm_shape (2), tm_facets (1), tmap_options (1)

utils

data (3), getFromNamespace (2), read.csv (2)

exactextractr

exact_extract (5)

grDevices

palette (3), colorRampPalette (2)

units

set_units (3), drop_units (1)

sf

read_sf (1), st_buffer (1), st_crs (1)

shinyjs

toggleState (3)

methods

is (2)

R.utils

withTimeout (1)

shinycssloaders

withSpinner (1)

shinyFiles

shinyDirChoose (1)

shinyvalidate

InputValidator$new (1)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has: - code in R (100% in 30 files) and - 1 authors - 3 vignettes - no internal data file - 23 imported packages - 10 exported functions (median 17 lines of code) - 107 non-exported functions in R (median 20 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 30| 89.3| | |files_vignettes | 3| 92.4| | |files_tests | 15| 94.4| | |loc_R | 4581| 94.7| | |loc_vignettes | 262| 59.2| | |loc_tests | 661| 80.2| | |num_vignettes | 3| 94.2| | |n_fns_r | 117| 80.1| | |n_fns_r_exported | 10| 45.3| | |n_fns_r_not_exported | 107| 85.0| | |n_fns_per_file_r | 2| 39.5| | |num_params_per_fn | 4| 54.6| | |loc_per_fn_r | 20| 59.8| | |loc_per_fn_r_exp | 18| 42.0| | |loc_per_fn_r_not_exp | 20| 63.0| | |rel_whitespace_R | 14| 92.2| | |rel_whitespace_vignettes | 52| 74.6| | |rel_whitespace_tests | 32| 85.8| | |doclines_per_fn_exp | 42| 52.8| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 144| 84.7| | ---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [](https://github.com/see24/ccviR/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 2741909150|pages build and deployment |success |cba341 | 9|2022-07-26 | | 2741873086|pkgdown |success |cf8ebe | 28|2022-07-26 | | 2741873082|R-CMD-check |success |cf8ebe | 5|2022-07-26 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following error: 1. Error in proc$get_built_file() : Build process failed R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) ERROR: Test Coverage Failed #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) Error : Build failed, unknown error, standard output: * checking for file ‘ccviR/DESCRIPTION’ ... OK * preparing ‘ccviR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes ----------------------------------- ERROR: dependency ‘tmap’ is not available for package ‘ccviR’ * removing ‘/tmp/Rtmp01BEvr/Rinst221c768c443/ccviR’ ----------------------------------- ERROR: package installation failed #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 523 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 3 Avoid 1:ncol(...) expressions, use seq_len. | 1 Avoid 1:nrow(...) expressions, use seq_len. | 2 Avoid library() and require() calls in packages | 13 Lines should not be more than 80 characters. | 488 Use <-, not =, for assignment. | 16

---

4. Other Checks

Details of other checks (click to open)

:heavy_check_mark: Package contains the following (potentially) obsolete packages: - rgdal See our [Recommended Scaffolding](https://devguide.ropensci.org/building.html?q=scaffol#recommended-scaffolding) for alternatives.

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Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.1.54 | |pkgcheck |0.1.0.24 |

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Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.