From a2031123c0f9599e236ad950a7c70e35e22f20a8 Mon Sep 17 00:00:00 2001 From: Rebecca Fisher Date: Wed, 20 May 2026 10:05:15 +0800 Subject: [PATCH 1/3] Add R script to build a dynamic pkgdown.yml and minro tweaks to ensure build and update pkgdown site --- DESCRIPTION | 8 +- README.md | 15 +- _pkgdown.yml | 87 ++++++++++- data-raw/build_pkgdown_yml.R | 271 +++++++++++++++++++++++++++++++++++ 4 files changed, 369 insertions(+), 12 deletions(-) create mode 100644 data-raw/build_pkgdown_yml.R diff --git a/DESCRIPTION b/DESCRIPTION index 154ff4a..ce1dc6a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ssddata Title: Species Sensitivity Distribution Data -Version: 1.0.0 +Version: 1.0.0.9000 Authors@R: c( person("Rebecca", "Fisher", , "R.Fisher@aims.gov.au", role = c("aut", "cre")), person("Joe", "Thorley", , "joe@poissonconsulting.ca", role = "aut", @@ -32,10 +32,12 @@ Suggests: knitr, readr, kableExtra, - testthat, here, tidyverse, - rprojroot + rprojroot, + covr, + pkgdown, + testthat (>= 3.0.0) VignetteBuilder: quarto RdMacros: Rdpack diff --git a/README.md b/README.md index 30cf14a..f6821a9 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![R-CMD-check](https://github.com/open-AIMS/ssddata/workflows/R-CMD-check/badge.svg)](https://github.com/open-AIMS/ssddata/actions) +[![R-CMD-check](https://github.com/open-AIMS/ssddata/workflows/R-CMD-check/badge.svg?branch=dev)](https://github.com/open-AIMS/ssddata/actions) [![CRAN status](https://www.r-pkg.org/badges/version/ssddata)](https://CRAN.R-project.org/package=ssddata) @@ -20,14 +20,17 @@ The package includes a range of data sets sourced from the Canadian Council of Ministers of the Environment (ccme), the Australian Institute of Marine Science (aims), the Commonwealth Scientific and Industrial Research Organisation (csiro), and the Australian and New Zealand water -water quality guideline website (angz), as well as anonymous datasets -supplied by various parties (anon). The source of each dataset are -indicated using a pre-fix in the data name (e.g. ccme, aims, etc), with -the actual chemical name following (e.g. ccme_boron). +water quality guideline website (angz, all datasets with a published +date later than 2000), as well as anonymous datasets supplied by various +parties (anon). The source of each dataset are indicated using a pre-fix +in the data name (e.g. ccme, aims, etc), with the actual chemical name +following (e.g. ccme_boron). The package also includes wqbench_data, a large data set from the US EPA ECOTOX database, cleaned and standardized by the -[`wqbench`](https://github.com/bcgov/wqbench/) package. +[`wqbench`](https://github.com/bcgov/wqbench/) package; and anztox_data, +a large data set from the Australian and New Zealand water quality +guideline website, cleaned and standardized by the current package. Please see the relevant [reference](https://open-aims.github.io/ssddata/reference/index.html) diff --git a/_pkgdown.yml b/_pkgdown.yml index d92b5ad..2137840 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,89 @@ +# Generated by data-raw/build_pkgdown_yml.R +# Do not edit by hand - re-run the script to regenerate. + url: https://open-aims.github.io/ssddata/ template: bootstrap: 5 - # end - - +development: + mode: auto + +authors: + Rebecca Fisher: + href: https://www.aims.gov.au/about/our-people/dr-rebecca-fisher + Joe Thorley: + href: https://github.com/joethorley + + Ayla Pearson: + href: https://github.com/aylapearson + +reference: +- title: Package overview + desc: Overview and introductory help for the ssddata package. +- contents: + - ssddata-package +- title: Individual SSD datasets + desc: Single-chemical species sensitivity datasets grouped by data source. +- subtitle: "Data from the Australian Institute of Marine Science" + contents: + - aims_aluminium_marine + - aims_gallium_marine + - aims_molybdenum_marine +- subtitle: "Data provided from anonymous sources" + contents: + - anon_a + - anon_b + - anon_c + - anon_d + - anon_e +- subtitle: "Data from the Australian and New Zealand guidelines" + contents: + - anzg_alpha_cypermethrin_fresh + - anzg_aluminium_marine + - anzg_ametryn_fresh + - anzg_ammonia_fresh + - anzg_bisphenol_a_fresh + - anzg_bisphenol_a_marine + - anzg_boron_fresh + - anzg_chromium_III_fresh + - anzg_metolachlor_fresh +- subtitle: "Data from the Canadian Council of Ministers of the Environment" + contents: + - ccme_boron + - ccme_cadmium + - ccme_chloride + - ccme_endosulfan + - ccme_glyphosate + - ccme_silver + - ccme_uranium +- subtitle: "Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia" + contents: + - csiro_chlorine_marine + - csiro_cobalt_marine + - csiro_lead_marine + - csiro_nickel_fresh +- title: Multi-chemical SSD datasets + desc: Combined datasets containing all chemicals from each source organisation individual dataset. +- contents: + - aims_data + - anon_data + - anzg_data + - ccme_data + - csiro_data +- title: Multi-chemical derived SSD datasets + desc: Datasets derived or aggregated from primary online sources. +- contents: + - anztox_data + - wqbench_data +- title: Fitted SSD results + desc: Pre-fitted species sensitivity distribution model results. +- contents: + - ssd_fits +- title: Package functions + desc: Utility functions exported by the ssddata package. +- contents: + - get_ssddata + - getdata + - gm_mean + - ssd_data_sets diff --git a/data-raw/build_pkgdown_yml.R b/data-raw/build_pkgdown_yml.R new file mode 100644 index 0000000..8d3e88a --- /dev/null +++ b/data-raw/build_pkgdown_yml.R @@ -0,0 +1,271 @@ +# data-raw/build_pkgdown_yml.R +# +# Generates _pkgdown.yml for the ssddata package. +# +# Run this script from the package root after calling devtools::document(), +# so that the man/ directory is up to date before the YAML is rebuilt. +# +# Usage (from package root in R console): +# source("data-raw/build_pkgdown_yml.R") +# +# The script writes _pkgdown.yml to the package root, overwriting any +# existing file. Commit the result alongside any dataset changes. + +# --------------------------------------------------------------------------- +# 0. Guard: must be run from the package root +# --------------------------------------------------------------------------- + +if (!file.exists("DESCRIPTION")) { + stop( + "This script must be sourced from the package root directory ", + "(the folder that contains DESCRIPTION)." + ) +} + +# --------------------------------------------------------------------------- +# 1. Discover all documented topics from man/ +# --------------------------------------------------------------------------- + +rd_files <- list.files("man", pattern = "\\.Rd$", full.names = FALSE) + +if (length(rd_files) == 0L) { + stop( + "No .Rd files found in man/. ", + "Run devtools::document() before sourcing this script." + ) +} + +all_topics <- tools::file_path_sans_ext(rd_files) +all_topics <- sort(all_topics) + +message("Found ", length(all_topics), " documented topics in man/") + +# --------------------------------------------------------------------------- +# 2. Define the known source prefixes and their full heading labels +# (ordered as specified in issue #19) +# --------------------------------------------------------------------------- + +source_prefixes <- c( + "aims" = "Data from the Australian Institute of Marine Science", + "anon" = "Data provided from anonymous sources", + "anzg" = "Data from the Australian and New Zealand guidelines", + "ccme" = "Data from the Canadian Council of Ministers of the Environment", + "csiro" = "Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia" +) + +# Aggregate (*_data) topic names for the known prefixes +aggregate_topics <- paste0(names(source_prefixes), "_data") + +# Hard-coded derived datasets (do not follow the prefix_data naming pattern). +# Update this vector if new derived datasets are added to the package. +derived_topics <- c("anztox_data", "wqbench_data") + +# Hard-coded fitted results dataset. +# Update this vector if additional fitted-results topics are added. +fitted_topics <- c("ssd_fits") + +# Hard-coded package-overview topic. +# roxygen2 always names this -package, so this rarely needs changing. +overview_topics <- c("ssddata-package") + +# --------------------------------------------------------------------------- +# 3. Classify topics +# --------------------------------------------------------------------------- + +# 3a. Individual datasets: match a known prefix, exclude the *_data aggregate +individual_by_prefix <- lapply(names(source_prefixes), function(pfx) { + pattern <- paste0("^", pfx, "_") + matched <- grep(pattern, all_topics, value = TRUE) + matched <- matched[matched != paste0(pfx, "_data")] + sort(matched) +}) +names(individual_by_prefix) <- names(source_prefixes) + +# 3b. Multi-chemical aggregate datasets: only include those that exist in man/ +multi_topics <- intersect(aggregate_topics, all_topics) +multi_topics <- aggregate_topics[aggregate_topics %in% multi_topics] # preserve order + +# 3c. Derived datasets: only include those that exist in man/ +derived_topics_present <- intersect(derived_topics, all_topics) + +# 3d. Fitted results: only include those that exist in man/ +fitted_topics_present <- intersect(fitted_topics, all_topics) + +# 3e. Package overview: only include if it exists in man/ +overview_topics_present <- intersect(overview_topics, all_topics) + +# 3f. Package functions: every remaining topic not matched by any category above. +# Sorted alphabetically. Updates automatically as functions are added/removed. +accounted_for <- c( + overview_topics_present, + unlist(individual_by_prefix, use.names = FALSE), + multi_topics, + derived_topics_present, + fitted_topics_present +) +function_topics <- sort(setdiff(all_topics, accounted_for)) + +if (length(function_topics) > 0L) { + message( + " Placed ", + length(function_topics), + " topic(s) in 'Package functions':\n ", + paste(function_topics, collapse = ", ") + ) +} + +# --------------------------------------------------------------------------- +# 4. Helper: append a line to a character vector +# --------------------------------------------------------------------------- + +emit <- function(lines, ...) { + c(lines, paste0(...)) +} + +# --------------------------------------------------------------------------- +# 5. Build the YAML lines +# +# pkgdown reference structure (title, subtitle, contents are SIBLINGS in the +# top-level reference list — subtitle is NOT nested inside contents): +# +# reference: +# - title: Section heading #

+# desc: Optional description +# - subtitle: Subheading #

— sibling of title, not child +# desc: Optional description +# contents: +# - topic_name +# - subtitle: Another subheading +# contents: +# - another_topic +# - title: Next section +# ... +# --------------------------------------------------------------------------- + +yml <- character(0) + +# -- File header ------------------------------------------------------------- +yml <- emit(yml, "# Generated by data-raw/build_pkgdown_yml.R") +yml <- emit(yml, "# Do not edit by hand - re-run the script to regenerate.") +yml <- emit(yml, "") +yml <- emit(yml, "url: https://open-aims.github.io/ssddata/") +yml <- emit(yml, "") +yml <- emit(yml, "template:") +yml <- emit(yml, " bootstrap: 5") +yml <- emit(yml, "") +yml <- emit(yml, "development:") +yml <- emit(yml, " mode: auto") +yml <- emit(yml, "") + +# -- Authors ---------------------------------------------------------------- +fisher_url <- "https://www.aims.gov.au/about/our-people/dr-rebecca-fisher" +yml <- emit(yml, "authors:") +yml <- emit(yml, " Rebecca Fisher:") +yml <- emit(yml, " href: ", fisher_url) +yml <- emit(yml, " Joe Thorley:") +yml <- emit(yml, " href: https://github.com/joethorley") +yml <- emit(yml, "") +yml <- emit(yml, " Ayla Pearson:") +yml <- emit(yml, " href: https://github.com/aylapearson") +yml <- emit(yml, "") + +# -- Reference section ------------------------------------------------------- +yml <- emit(yml, "reference:") + +# ---- Section 0: Package overview ------------------------------------------- +if (length(overview_topics_present) > 0L) { + yml <- emit(yml, "- title: Package overview") + yml <- emit( + yml, + " desc: Overview and introductory help for the ssddata package." + ) + yml <- emit(yml, "- contents:") + for (ov in overview_topics_present) { + yml <- emit(yml, " - ", ov) + } +} + +# ---- Section 1: Individual SSD datasets ------------------------------------ +# The title entry has no contents of its own; each source group is a subtitle +# sibling that carries its own contents block. +yml <- emit(yml, "- title: Individual SSD datasets") +yml <- emit( + yml, + " desc: Single-chemical species sensitivity datasets grouped by data source." +) + +for (pfx in names(source_prefixes)) { + heading <- source_prefixes[[pfx]] + datasets <- individual_by_prefix[[pfx]] + + if (length(datasets) == 0L) { + message(" Note: no individual datasets found for prefix '", pfx, "_'") + next + } + + yml <- emit(yml, "- subtitle: \"", heading, "\"") + yml <- emit(yml, " contents:") + for (ds in datasets) { + yml <- emit(yml, " - ", ds) + } +} + +# ---- Section 2: Multi-chemical SSD datasets -------------------------------- +yml <- emit(yml, "- title: Multi-chemical SSD datasets") +yml <- emit( + yml, + " desc: Combined datasets containing all chemicals from each source organisation individual dataset." +) +yml <- emit(yml, "- contents:") +for (ds in multi_topics) { + yml <- emit(yml, " - ", ds) +} + +# ---- Section 3: Derived SSD datasets --------------------------------------- +yml <- emit(yml, "- title: Multi-chemical derived SSD datasets") +yml <- emit( + yml, + " desc: Datasets derived or aggregated from primary online sources." +) +yml <- emit(yml, "- contents:") +for (ds in derived_topics_present) { + yml <- emit(yml, " - ", ds) +} + +# ---- Section 4: Fitted SSD results ----------------------------------------- +if (length(fitted_topics_present) > 0L) { + yml <- emit(yml, "- title: Fitted SSD results") + yml <- emit( + yml, + " desc: Pre-fitted species sensitivity distribution model results." + ) + yml <- emit(yml, "- contents:") + for (ft in fitted_topics_present) { + yml <- emit(yml, " - ", ft) + } +} + +# ---- Section 5: Package functions ------------------------------------------ +if (length(function_topics) > 0L) { + yml <- emit(yml, "- title: Package functions") + yml <- emit(yml, " desc: Utility functions exported by the ssddata package.") + yml <- emit(yml, "- contents:") + for (fn in function_topics) { + yml <- emit(yml, " - ", fn) + } +} + +# --------------------------------------------------------------------------- +# 6. Write the file +# --------------------------------------------------------------------------- + +out_path <- "_pkgdown.yml" +writeLines(yml, out_path) +message("Written: ", normalizePath(out_path)) +message( + "Next steps:\n", + " 1. Review _pkgdown.yml for correctness\n", + " 2. Run pkgdown::build_reference_index() to check the reference page only\n", + " 3. Run pkgdown::build_site() for the full site\n", + " 4. Commit _pkgdown.yml" +) From d712997e578e163f2b69eb6a733b3bddc701575e Mon Sep 17 00:00:00 2001 From: Rebecca Fisher Date: Wed, 20 May 2026 10:06:20 +0800 Subject: [PATCH 2/3] Add github copilot instructions --- .github/copilot-instructions.md | 121 ++++++++++++++++++++++++++++++++ 1 file changed, 121 insertions(+) create mode 100644 .github/copilot-instructions.md diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md new file mode 100644 index 0000000..8e48dde --- /dev/null +++ b/.github/copilot-instructions.md @@ -0,0 +1,121 @@ +# ssddata — Copilot Instructions + +## Project Overview +`ssddata` is a data-only R package providing Species Sensitivity Distribution (SSD) benchmark datasets for evaluating SSD software (`ssdtools`, `Burrlioz`). It packages chemical toxicity datasets from CCME, AIMS, CSIRO, ANZG, and the US EPA ECOTOX database. + +## Architecture +- `R/` — Roxygen2 documentation files only; no logic except three utility functions (`get_ssddata()`, `gm_mean()`, `ssd_data_sets()`) +- `data/` — Pre-built `.rda` files (one per dataset); loaded via `LazyData: true` +- `data-raw/` — Source CSVs by org + build scripts; **not part of package build**; maintainer-only +- `tests/testthat/` — testthat edition 3 tests +- `vignettes/` — Quarto-based vignettes +- `inst/REFERENCES.bib` — Rdpack bibliography for `\insertRef{}` citations in roxygen docs + +## Dataset Conventions +- Individual datasets: `{prefix}_{chemical}` (e.g., `ccme_boron`, `aims_ddt`) +- Combined datasets: `{prefix}_data` (e.g., `ccme_data`, `aims_data`) +- Prefixes: `aims`, `ccme`, `csiro`, `anzg`, `anon`, `wqbench` +- All datasets stored as `tbl_df` +- Individual dataset `.R` doc files end with `NULL`; aggregate `*_data.R` files end with `"dataset_name"` + +## Code Style +- **Pipe**: `%>%` (magrittr) in `data-raw/` scripts; no pipe in `R/` package code +- **Imports**: Only `chk`, `dplyr`, `Rdpack`, `utils` — keep imports minimal +- **Input validation**: Use `chk` package for all user-facing function arguments (e.g., `chk::chk_string()`, `chk::chk_flag()`) +- **Side-effects**: Use `message()` only — no `print()` or `cat()` in exported functions +- **Docs**: Roxygen2 with markdown; use `Rdpack::reprompt()` and `\insertRef{key}{ssddata}` for literature citations + +## Build and Test +```r +devtools::load_all() +devtools::document() # regenerates roxygen2 + Rdpack docs +devtools::test() # runs testthat suite +devtools::check() # full R CMD CHECK + +# Rebuild all datasets from source +source("data-raw/source_all.R") +``` +CI runs `R-CMD-check` and `pkgdown` via GitHub Actions. + +## Testing Conventions +- Use `chk::check_data()` to validate dataset structure and value ranges +- Assert `message()` side-effects with `expect_message()` +- Test files mirror `R/` structure: `tests/testthat/test-{function}.R` + +## Adding a New Dataset +1. Add source CSV(s) to `data-raw/{prefix}/` +2. Add build code to `data-raw/create_data.R` using `usethis::use_data(..., overwrite = TRUE)` +3. Create `R/{prefix}_{chemical}.R` with roxygen2 docs ending in `NULL` +4. Update the relevant `{prefix}_data` aggregate and its `.R` doc file +5. Run `source("data-raw/source_all.R")` then `devtools::document()` + +--- + +## envirotox Integration + +### Source Package +[`poissonconsulting/envirotox`](https://github.com/poissonconsulting/envirotox) (v0.0.0.9003) is a separate data-only R package providing SSD datasets derived from the **EnviroTox database 2.0.0** (Connors et al. 2019, doi:10.1002/etc.4382). Its data will be integrated into `ssddata` under the `envirotox` prefix. + +### envirotox Datasets +Three datasets are exported from the package: + +#### `envirotox_acute` — 14,949 rows × 6 columns +Acute toxicity records (EC50/LC50) aggregated to one geometric mean concentration per species per chemical. + +| Column | Type | Description | +|---|---|---| +| `Chemical` | chr | Chemical name (short name before first `;`) | +| `Conc` | dbl | Geometric mean concentration (µg/L) | +| `Species` | chr | Latin species name | +| `Group` | chr | Taxonomic group (sentence case): `Fish`, `Invertebrate`, `Algae`, `Amphibian`, `Plant`, etc. | +| `Yanagihara24` | lgl | Meets Yanagihara et al. (2024) criteria: ≥10 species, ≥3 trophic groups, bimodality coefficient ≤ 0.555 | +| `Iwasaki25` | lgl | Meets Iwasaki et al. (2025) criteria: >50 species, ≥3 trophic groups (excludes certain metals) | + +Key constraint: `chk::check_key(envirotox_acute, c("Chemical", "Species"))` — unique per chemical × species. + +#### `envirotox_chronic` — 1,721 rows × 5 columns +Chronic toxicity records (NOEC/NOEL) aggregated similarly. + +| Column | Type | Description | +|---|---|---| +| `Chemical` | chr | Chemical name | +| `Conc` | dbl | Geometric mean concentration (µg/L) | +| `Species` | chr | Latin species name | +| `Group` | chr | Taxonomic group (sentence case) | +| `Yanagihara24` | lgl | Meets Yanagihara et al. (2024) criteria | + +Key constraint: `chk::check_key(envirotox_chronic, c("Chemical", "Species"))`. + +#### `envirotox_chemical` — 744 rows × 2 columns +Chemical lookup table joining the two datasets above. + +| Column | Type | Description | +|---|---|---| +| `Chemical` | chr | Chemical name (primary key) | +| `OriginalCAS` | int | Original CAS Registry Number (also a key) | + +### Data Processing Pipeline (data-raw/envirotox.R) +The build script (modified from Yanagihara et al. 2024 code) processes `envirotox.xlsx` (three sheets: `test`, `substance`, `taxonomy`): + +1. **Filter** records: acute = EC50/LC50 with `Test.type == "A"`; chronic = NOEC/NOEL with `Test.type == "C"`; exclude records where `Effect.is.5X.above.water.solubility == "1"` +2. **Unit conversion**: mg/L → µg/L (× 1000) +3. **Geometric mean** per `original.CAS × Latin.name` using `EnvStats::geoMean()` +4. **Minimum species/group thresholds**: ≥6 species, ≥2 trophic groups per chemical +5. **Bimodality coefficient** (BC) via `mousetrap::bimodality_coefficient(log10(Conc))` — used for `Yanagihara24` flag +6. **Group normalisation**: `"Invert"` → `"Invertebrate"`, `"Amphib"` → `"Amphibian"`, all sentence case +7. **`OriginalCAS` dropped** from acute/chronic before saving; kept only in `envirotox_chemical` + +### Integration into ssddata +When adding envirotox data to `ssddata`: + +- **Prefix**: `envirotox` (e.g., `envirotox_acute`, `envirotox_chronic`, `envirotox_chemical`) +- **Column mapping**: `ssddata` uses `Conc` (µg/L), `Species`, `Group` — matches envirotox columns directly; no `Chemical` column in individual `ssddata` datasets (chemical is encoded in dataset name for per-chemical sets) +- **Aggregate datasets**: `envirotox_acute` and `envirotox_chronic` are already multi-chemical aggregates; treat like `ccme_data` / `aims_data` — doc files end with `"envirotox_acute"` / `"envirotox_chronic"` +- **Source file**: place `envirotox.xlsx` in `data-raw/envirotox/` and the build script at `data-raw/envirotox/create_envirotox.R` +- **References to add to `inst/REFERENCES.bib`**: + - `Connors2019` — EnviroTox database paper (doi:10.1002/etc.4382) + - `Yanagihara2024` — distribution comparison paper (doi:10.1016/j.ecoenv.2024.116379) + - `Iwasaki2025` — model-averaging paper (doi:10.1093/etojnl/vgae060) + +### Key Difference from Other ssddata Sources +Unlike CCME/AIMS/CSIRO datasets (one dataset per chemical), envirotox datasets are pre-aggregated multi-chemical tables with a `Chemical` column acting as the grouping variable. The `Yanagihara24` and `Iwasaki25` logical flags allow subsetting to published benchmark subsets without creating separate datasets. From 72ba3aea090509a3940e75d932e79d02444ba161 Mon Sep 17 00:00:00 2001 From: Rebecca Fisher Date: Wed, 20 May 2026 10:35:27 +0800 Subject: [PATCH 3/3] Changed documentation scripts to write markdown syntax --- R/aims_aluminium_marine.R | 6 +++--- R/aims_data.R | 4 ++-- R/aims_gallium_marine.R | 6 +++--- R/aims_molybdenum_marine.R | 6 +++--- R/anon_a.R | 4 ++-- R/anon_b.R | 4 ++-- R/anon_c.R | 4 ++-- R/anon_d.R | 4 ++-- R/anon_data.R | 4 ++-- R/anon_e.R | 4 ++-- R/anzg_alpha_cypermethrin_fresh.R | 10 +++++----- R/anzg_aluminium_marine.R | 10 +++++----- R/anzg_ametryn_fresh.R | 10 +++++----- R/anzg_ammonia_fresh.R | 10 +++++----- R/anzg_bisphenol_a_fresh.R | 10 +++++----- R/anzg_bisphenol_a_marine.R | 10 +++++----- R/anzg_boron_fresh.R | 10 +++++----- R/anzg_chromium_III_fresh.R | 10 +++++----- R/anzg_data.R | 8 ++++---- R/anzg_metolachlor_fresh.R | 10 +++++----- R/ccme_boron.R | 6 +++--- R/ccme_cadmium.R | 6 +++--- R/ccme_chloride.R | 6 +++--- R/ccme_data.R | 4 ++-- R/ccme_endosulfan.R | 6 +++--- R/ccme_glyphosate.R | 6 +++--- R/ccme_silver.R | 6 +++--- R/ccme_uranium.R | 6 +++--- R/csiro_chlorine_marine.R | 6 +++--- R/csiro_cobalt_marine.R | 6 +++--- R/csiro_data.R | 4 ++-- R/csiro_lead_marine.R | 6 +++--- R/csiro_nickel_fresh.R | 6 +++--- data-raw/source_all.R | 11 +++-------- man/aims_aluminium_marine.Rd | 2 +- man/aims_gallium_marine.Rd | 2 +- man/aims_molybdenum_marine.Rd | 2 +- man/anzg_alpha_cypermethrin_fresh.Rd | 2 +- man/anzg_aluminium_marine.Rd | 2 +- man/anzg_ametryn_fresh.Rd | 2 +- man/anzg_ammonia_fresh.Rd | 2 +- man/anzg_bisphenol_a_fresh.Rd | 2 +- man/anzg_bisphenol_a_marine.Rd | 2 +- man/anzg_boron_fresh.Rd | 2 +- man/anzg_chromium_III_fresh.Rd | 2 +- man/anzg_metolachlor_fresh.Rd | 2 +- man/ccme_boron.Rd | 2 +- man/ccme_cadmium.Rd | 2 +- man/ccme_chloride.Rd | 2 +- man/ccme_endosulfan.Rd | 2 +- man/ccme_glyphosate.Rd | 2 +- man/ccme_silver.Rd | 2 +- man/ccme_uranium.Rd | 2 +- man/csiro_chlorine_marine.Rd | 2 +- man/csiro_cobalt_marine.Rd | 2 +- man/csiro_lead_marine.Rd | 2 +- man/csiro_nickel_fresh.Rd | 2 +- scripts/build.R | 17 +++++++++++------ 58 files changed, 146 insertions(+), 146 deletions(-) diff --git a/R/aims_aluminium_marine.R b/R/aims_aluminium_marine.R index 29cb833..7f504e7 100644 --- a/R/aims_aluminium_marine.R +++ b/R/aims_aluminium_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for aluminium_marine #' #' Species Sensitivity Data provided by the Australian Institute of Marine -#' Science for ***aluminium*** in marine water. +#' Science for \strong{\emph{aluminium}} in marine water. #' #' These data were sourced from: #'\insertRef{VanDam2018}{ssddata} @@ -23,8 +23,8 @@ #' #' @name aims_aluminium_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 20 rows and 9 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 20 rows and 9 columns. #' @keywords datasets #' @examples #' diff --git a/R/aims_data.R b/R/aims_data.R index 675c525..d0417a5 100644 --- a/R/aims_data.R +++ b/R/aims_data.R @@ -31,8 +31,8 @@ #' #' @name aims_data #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 40 rows and 11 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 40 rows and 11 columns. #' @keywords datasets #' @examples #' diff --git a/R/aims_gallium_marine.R b/R/aims_gallium_marine.R index 2ef63d2..a79bc50 100644 --- a/R/aims_gallium_marine.R +++ b/R/aims_gallium_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for gallium_marine #' #' Species Sensitivity Data provided by the Australian Institute of Marine -#' Science for ***gallium*** in marine water. +#' Science for \strong{\emph{gallium}} in marine water. #' #' These data were sourced from: #'\insertRef{VanDam2018}{ssddata} @@ -23,8 +23,8 @@ #' #' @name aims_gallium_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 6 rows and 9 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 6 rows and 9 columns. #' @keywords datasets #' @examples #' diff --git a/R/aims_molybdenum_marine.R b/R/aims_molybdenum_marine.R index 2951f19..7d08f42 100644 --- a/R/aims_molybdenum_marine.R +++ b/R/aims_molybdenum_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for molybdenum_marine #' #' Species Sensitivity Data provided by the Australian Institute of Marine -#' Science for ***molybdenum*** in marine water. +#' Science for \strong{\emph{molybdenum}} in marine water. #' #' These data were sourced from: #'\insertRef{VanDam2018}{ssddata} @@ -23,8 +23,8 @@ #' #' @name aims_molybdenum_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 14 rows and 9 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 14 rows and 9 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_a.R b/R/anon_a.R index ce64fc5..5cdb209 100644 --- a/R/anon_a.R +++ b/R/anon_a.R @@ -17,8 +17,8 @@ #' #' @name anon_a #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 18 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 18 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_b.R b/R/anon_b.R index 199f42e..3113121 100644 --- a/R/anon_b.R +++ b/R/anon_b.R @@ -17,8 +17,8 @@ #' #' @name anon_b #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 10 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 10 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_c.R b/R/anon_c.R index 5459b4c..ba8cffd 100644 --- a/R/anon_c.R +++ b/R/anon_c.R @@ -17,8 +17,8 @@ #' #' @name anon_c #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 16 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 16 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_d.R b/R/anon_d.R index 856c7c5..12f0404 100644 --- a/R/anon_d.R +++ b/R/anon_d.R @@ -17,8 +17,8 @@ #' #' @name anon_d #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 12 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 12 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_data.R b/R/anon_data.R index 37ca7ae..2668b4a 100644 --- a/R/anon_data.R +++ b/R/anon_data.R @@ -16,8 +16,8 @@ #' #' @name anon_data #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 73 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 73 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anon_e.R b/R/anon_e.R index b8943bf..c4467e6 100644 --- a/R/anon_e.R +++ b/R/anon_e.R @@ -17,8 +17,8 @@ #' #' @name anon_e #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 17 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 17 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_alpha_cypermethrin_fresh.R b/R/anzg_alpha_cypermethrin_fresh.R index af10292..2b66ff0 100644 --- a/R/anzg_alpha_cypermethrin_fresh.R +++ b/R/anzg_alpha_cypermethrin_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***alpha cypermethrin*** in freshwater. +#' for \strong{\emph{alpha cypermethrin}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{Alpha-cypermethrin2023}{ssddata} @@ -33,8 +33,8 @@ #' #' @name anzg_alpha_cypermethrin_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 14 rows and 7 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 14 rows and 7 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_aluminium_marine.R b/R/anzg_aluminium_marine.R index a425d85..fe7f210 100644 --- a/R/anzg_aluminium_marine.R +++ b/R/anzg_aluminium_marine.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***aluminium*** in marine water. +#' for \strong{\emph{aluminium}} in marine water. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{aluminium-marine2025}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_aluminium_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 18 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 18 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_ametryn_fresh.R b/R/anzg_ametryn_fresh.R index f1bec88..977da29 100644 --- a/R/anzg_ametryn_fresh.R +++ b/R/anzg_ametryn_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***ametryn*** in freshwater. +#' for \strong{\emph{ametryn}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{ametryn-fresh2025}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_ametryn_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 8 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 8 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_ammonia_fresh.R b/R/anzg_ammonia_fresh.R index f90bb37..d997d4f 100644 --- a/R/anzg_ammonia_fresh.R +++ b/R/anzg_ammonia_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***ammonia*** in freshwater. +#' for \strong{\emph{ammonia}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{ammonia-fresh2026}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_ammonia_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 40 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 40 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_bisphenol_a_fresh.R b/R/anzg_bisphenol_a_fresh.R index 6b5ee25..3336941 100644 --- a/R/anzg_bisphenol_a_fresh.R +++ b/R/anzg_bisphenol_a_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***bisphenol a*** in freshwater. +#' for \strong{\emph{bisphenol a}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{bisphenol-a-fresh2023}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_bisphenol_a_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 19 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 19 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_bisphenol_a_marine.R b/R/anzg_bisphenol_a_marine.R index ce1f4d3..e53af10 100644 --- a/R/anzg_bisphenol_a_marine.R +++ b/R/anzg_bisphenol_a_marine.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***bisphenol a*** in marine water. +#' for \strong{\emph{bisphenol a}} in marine water. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{bisphenol-a-marine2023}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_bisphenol_a_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 8 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 8 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_boron_fresh.R b/R/anzg_boron_fresh.R index 88fe333..f7d17df 100644 --- a/R/anzg_boron_fresh.R +++ b/R/anzg_boron_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***boron*** in freshwater. +#' for \strong{\emph{boron}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{boron-fresh2021}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_boron_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 22 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 22 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_chromium_III_fresh.R b/R/anzg_chromium_III_fresh.R index 5ff2209..2ef2460 100644 --- a/R/anzg_chromium_III_fresh.R +++ b/R/anzg_chromium_III_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***chromium III*** in freshwater. +#' for \strong{\emph{chromium III}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{chromiumIII-fresh2026}{ssddata} @@ -32,8 +32,8 @@ #' #' @name anzg_chromium_III_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 13 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 13 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_data.R b/R/anzg_data.R index 2a1f9c0..f8c4dca 100644 --- a/R/anzg_data.R +++ b/R/anzg_data.R @@ -4,10 +4,10 @@ #' Water and the Environment, Australia. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ). +#' \url{https://creativecommons.org/licenses/by/4.0/}). #' #' Additional information is available from the Water Quality website at -#' . +#' \url{https://www.waterquality.gov.au/}. #' #' Additional information may be available from the primary source for each #' chemical: @@ -50,8 +50,8 @@ #' #' @name anzg_data #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 163 rows and 12 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 163 rows and 12 columns. #' @keywords datasets #' @examples #' diff --git a/R/anzg_metolachlor_fresh.R b/R/anzg_metolachlor_fresh.R index 9b2d464..479f525 100644 --- a/R/anzg_metolachlor_fresh.R +++ b/R/anzg_metolachlor_fresh.R @@ -2,12 +2,12 @@ #' #' Species Sensitivity Data provided by the Department of Agriculture Water and #' the Environment, Australia. This data underpins the ANZG default guideline -#' for ***metolachlor*** in freshwater. +#' for \strong{\emph{metolachlor}} in freshwater. #' #' These data are licensed under CC BY 4.0 (summary of terms provided here: -#' ) Additional information +#' \url{https://creativecommons.org/licenses/by/4.0/}) Additional information #' is available from the Water Quality website at -#' +#' \url{https://www.waterquality.gov.au/} #' #' Please cite these data as: #'\insertRef{anzg_toxicant_2020}{ssddata} @@ -36,8 +36,8 @@ #' #' @name anzg_metolachlor_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 21 rows and 10 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 21 rows and 10 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_boron.R b/R/ccme_boron.R index 483ee6c..1c86e2c 100644 --- a/R/ccme_boron.R +++ b/R/ccme_boron.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_boron #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***boron***. +#' Environment for \strong{\emph{boron}}. #' #' Additional information is available from #'\insertRef{Boron}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_boron #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 28 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 28 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_cadmium.R b/R/ccme_cadmium.R index 1383c72..86a1286 100644 --- a/R/ccme_cadmium.R +++ b/R/ccme_cadmium.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_cadmium #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***cadmium***. +#' Environment for \strong{\emph{cadmium}}. #' #' Additional information is available from #'\insertRef{Cadmium}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_cadmium #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 36 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 36 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_chloride.R b/R/ccme_chloride.R index 5d0a5c0..f83c440 100644 --- a/R/ccme_chloride.R +++ b/R/ccme_chloride.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_chloride #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***chloride***. +#' Environment for \strong{\emph{chloride}}. #' #' Additional information is available from #'\insertRef{Chloride}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_chloride #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 28 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 28 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_data.R b/R/ccme_data.R index f38efa1..974742b 100644 --- a/R/ccme_data.R +++ b/R/ccme_data.R @@ -29,8 +29,8 @@ #' #' @name ccme_data #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 144 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 144 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_endosulfan.R b/R/ccme_endosulfan.R index ba47bd9..bc662c5 100644 --- a/R/ccme_endosulfan.R +++ b/R/ccme_endosulfan.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_endosulfan #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***endosulfan***. +#' Environment for \strong{\emph{endosulfan}}. #' #' Additional information is available from #'\insertRef{Endosulfan}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_endosulfan #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 12 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 12 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_glyphosate.R b/R/ccme_glyphosate.R index c826fbd..e0e18db 100644 --- a/R/ccme_glyphosate.R +++ b/R/ccme_glyphosate.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_glyphosate #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***glyphosate***. +#' Environment for \strong{\emph{glyphosate}}. #' #' Additional information is available from #'\insertRef{Glyphosate}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_glyphosate #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 18 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 18 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_silver.R b/R/ccme_silver.R index 5cf8033..4875071 100644 --- a/R/ccme_silver.R +++ b/R/ccme_silver.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_silver #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***silver***. +#' Environment for \strong{\emph{silver}}. #' #' Additional information is available from #'\insertRef{Silver}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_silver #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 9 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 9 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/ccme_uranium.R b/R/ccme_uranium.R index de0e369..8a674ed 100644 --- a/R/ccme_uranium.R +++ b/R/ccme_uranium.R @@ -1,7 +1,7 @@ #' CCME Species Sensitivity Data for ccme_uranium #' #' Species Sensitivity Data from the Canadian Council of Ministers of the -#' Environment for ***uranium***. +#' Environment for \strong{\emph{uranium}}. #' #' Additional information is available from #'\insertRef{Uranium}{ssddata} @@ -19,8 +19,8 @@ #' #' @name ccme_uranium #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 13 rows and 5 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 13 rows and 5 columns. #' @keywords datasets #' @examples #' diff --git a/R/csiro_chlorine_marine.R b/R/csiro_chlorine_marine.R index 65c80f6..34ba3e0 100644 --- a/R/csiro_chlorine_marine.R +++ b/R/csiro_chlorine_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for chlorine_marine #' #' Species Sensitivity Data provided by the Commonwealth Scientific and -#' Industrial Research Organisation of Australia for ***chlorine*** +#' Industrial Research Organisation of Australia for \strong{\emph{chlorine}} #' in marine water. #' #' These data were sourced from: @@ -25,8 +25,8 @@ #' #' @name csiro_chlorine_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 30 rows and 2 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 30 rows and 2 columns. #' @keywords datasets #' @examples #' diff --git a/R/csiro_cobalt_marine.R b/R/csiro_cobalt_marine.R index e7ff526..552a121 100644 --- a/R/csiro_cobalt_marine.R +++ b/R/csiro_cobalt_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for cobalt_marine #' #' Species Sensitivity Data provided by the Commonwealth Scientific and -#' Industrial Research Organisation of Australia for ***cobalt*** +#' Industrial Research Organisation of Australia for \strong{\emph{cobalt}} #' in marine water. #' #' These data were sourced from: @@ -30,8 +30,8 @@ #' #' @name csiro_cobalt_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 14 rows and 7 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 14 rows and 7 columns. #' @keywords datasets #' @examples #' diff --git a/R/csiro_data.R b/R/csiro_data.R index 5b6aabf..5e3f5ac 100644 --- a/R/csiro_data.R +++ b/R/csiro_data.R @@ -40,8 +40,8 @@ #' #' @name csiro_data #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 91 rows and 11 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 91 rows and 11 columns. #' @keywords datasets #' @examples #' diff --git a/R/csiro_lead_marine.R b/R/csiro_lead_marine.R index a51d820..62317eb 100644 --- a/R/csiro_lead_marine.R +++ b/R/csiro_lead_marine.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for lead_marine #' #' Species Sensitivity Data provided by the Commonwealth Scientific and -#' Industrial Research Organisation of Australia for ***lead*** +#' Industrial Research Organisation of Australia for \strong{\emph{lead}} #' in marine water. #' #' These data were sourced from: @@ -30,8 +30,8 @@ #' #' @name csiro_lead_marine #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 16 rows and 7 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 16 rows and 7 columns. #' @keywords datasets #' @examples #' diff --git a/R/csiro_nickel_fresh.R b/R/csiro_nickel_fresh.R index 1af1060..1425c24 100644 --- a/R/csiro_nickel_fresh.R +++ b/R/csiro_nickel_fresh.R @@ -1,7 +1,7 @@ #' Species Sensitivity Data for nickel_fresh #' #' Species Sensitivity Data provided by the Commonwealth Scientific and -#' Industrial Research Organisation of Australia for ***nickel*** +#' Industrial Research Organisation of Australia for \strong{\emph{nickel}} #' in freshwater. #' #' These data were sourced from: @@ -29,8 +29,8 @@ #' #' @name csiro_nickel_fresh #' @docType data -#' @format An object of class `tbl_df` (inherits from `tbl`, -#' `data.frame`) with 31 rows and 6 columns. +#' @format An object of class \code{tbl_df} (inherits from \code{tbl}, +#' \code{data.frame}) with 31 rows and 6 columns. #' @keywords datasets #' @examples #' diff --git a/data-raw/source_all.R b/data-raw/source_all.R index cb55a03..952834c 100644 --- a/data-raw/source_all.R +++ b/data-raw/source_all.R @@ -1,10 +1,5 @@ -files <- unlist(sapply(list.dirs("data-raw")[-1], FUN = function(x) { - list.files(x, pattern = "[.][rR]$", full.names = TRUE) -})) -# remove wqbench because this is documented manually -files <- setdiff(files, "data-raw/wqbench/DATASET.R") +datasets <- c("aims", "anon", "anzg", "ccme", "csiro") + +files <- file.path("data-raw", datasets, "DATASET.R") invisible(lapply(files, source)) -roxygen2md::roxygen2md() -# styler::style_pkg(filetype = c("R", "Rmd")) -devtools::document() diff --git a/man/aims_aluminium_marine.Rd b/man/aims_aluminium_marine.Rd index 1c52f32..f13cd2b 100644 --- a/man/aims_aluminium_marine.Rd +++ b/man/aims_aluminium_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Australian Institute of Marine -Science for \emph{\strong{aluminium}} in marine water. +Science for \strong{\emph{aluminium}} in marine water. } \details{ These data were sourced from: diff --git a/man/aims_gallium_marine.Rd b/man/aims_gallium_marine.Rd index 084f2da..bd9938d 100644 --- a/man/aims_gallium_marine.Rd +++ b/man/aims_gallium_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Australian Institute of Marine -Science for \emph{\strong{gallium}} in marine water. +Science for \strong{\emph{gallium}} in marine water. } \details{ These data were sourced from: diff --git a/man/aims_molybdenum_marine.Rd b/man/aims_molybdenum_marine.Rd index 3125bee..9019a8d 100644 --- a/man/aims_molybdenum_marine.Rd +++ b/man/aims_molybdenum_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Australian Institute of Marine -Science for \emph{\strong{molybdenum}} in marine water. +Science for \strong{\emph{molybdenum}} in marine water. } \details{ These data were sourced from: diff --git a/man/anzg_alpha_cypermethrin_fresh.Rd b/man/anzg_alpha_cypermethrin_fresh.Rd index 074fed4..86e3284 100644 --- a/man/anzg_alpha_cypermethrin_fresh.Rd +++ b/man/anzg_alpha_cypermethrin_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{alpha cypermethrin}} in freshwater. +for \strong{\emph{alpha cypermethrin}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_aluminium_marine.Rd b/man/anzg_aluminium_marine.Rd index f0ac0c9..ce4bca4 100644 --- a/man/anzg_aluminium_marine.Rd +++ b/man/anzg_aluminium_marine.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{aluminium}} in marine water. +for \strong{\emph{aluminium}} in marine water. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_ametryn_fresh.Rd b/man/anzg_ametryn_fresh.Rd index 64b59bb..b0e067b 100644 --- a/man/anzg_ametryn_fresh.Rd +++ b/man/anzg_ametryn_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{ametryn}} in freshwater. +for \strong{\emph{ametryn}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_ammonia_fresh.Rd b/man/anzg_ammonia_fresh.Rd index 4311e26..e39a310 100644 --- a/man/anzg_ammonia_fresh.Rd +++ b/man/anzg_ammonia_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{ammonia}} in freshwater. +for \strong{\emph{ammonia}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_bisphenol_a_fresh.Rd b/man/anzg_bisphenol_a_fresh.Rd index 1515f02..df101a8 100644 --- a/man/anzg_bisphenol_a_fresh.Rd +++ b/man/anzg_bisphenol_a_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{bisphenol a}} in freshwater. +for \strong{\emph{bisphenol a}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_bisphenol_a_marine.Rd b/man/anzg_bisphenol_a_marine.Rd index b4efdb9..c20182d 100644 --- a/man/anzg_bisphenol_a_marine.Rd +++ b/man/anzg_bisphenol_a_marine.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{bisphenol a}} in marine water. +for \strong{\emph{bisphenol a}} in marine water. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_boron_fresh.Rd b/man/anzg_boron_fresh.Rd index 5aa9eca..5f73f62 100644 --- a/man/anzg_boron_fresh.Rd +++ b/man/anzg_boron_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{boron}} in freshwater. +for \strong{\emph{boron}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_chromium_III_fresh.Rd b/man/anzg_chromium_III_fresh.Rd index bf45e30..42160a6 100644 --- a/man/anzg_chromium_III_fresh.Rd +++ b/man/anzg_chromium_III_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{chromium III}} in freshwater. +for \strong{\emph{chromium III}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/anzg_metolachlor_fresh.Rd b/man/anzg_metolachlor_fresh.Rd index 7614fbe..8ebbb94 100644 --- a/man/anzg_metolachlor_fresh.Rd +++ b/man/anzg_metolachlor_fresh.Rd @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \description{ Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia. This data underpins the ANZG default guideline -for \emph{\strong{metolachlor}} in freshwater. +for \strong{\emph{metolachlor}} in freshwater. } \details{ These data are licensed under CC BY 4.0 (summary of terms provided here: diff --git a/man/ccme_boron.Rd b/man/ccme_boron.Rd index a951002..97496a6 100644 --- a/man/ccme_boron.Rd +++ b/man/ccme_boron.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{boron}}. +Environment for \strong{\emph{boron}}. } \details{ Additional information is available from diff --git a/man/ccme_cadmium.Rd b/man/ccme_cadmium.Rd index 7fee2ef..3baba1a 100644 --- a/man/ccme_cadmium.Rd +++ b/man/ccme_cadmium.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{cadmium}}. +Environment for \strong{\emph{cadmium}}. } \details{ Additional information is available from diff --git a/man/ccme_chloride.Rd b/man/ccme_chloride.Rd index 34ab480..f69eeaa 100644 --- a/man/ccme_chloride.Rd +++ b/man/ccme_chloride.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{chloride}}. +Environment for \strong{\emph{chloride}}. } \details{ Additional information is available from diff --git a/man/ccme_endosulfan.Rd b/man/ccme_endosulfan.Rd index 98024c5..50b7958 100644 --- a/man/ccme_endosulfan.Rd +++ b/man/ccme_endosulfan.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{endosulfan}}. +Environment for \strong{\emph{endosulfan}}. } \details{ Additional information is available from diff --git a/man/ccme_glyphosate.Rd b/man/ccme_glyphosate.Rd index 95e0400..075b9a4 100644 --- a/man/ccme_glyphosate.Rd +++ b/man/ccme_glyphosate.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{glyphosate}}. +Environment for \strong{\emph{glyphosate}}. } \details{ Additional information is available from diff --git a/man/ccme_silver.Rd b/man/ccme_silver.Rd index d37741c..0dcf46d 100644 --- a/man/ccme_silver.Rd +++ b/man/ccme_silver.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{silver}}. +Environment for \strong{\emph{silver}}. } \details{ Additional information is available from diff --git a/man/ccme_uranium.Rd b/man/ccme_uranium.Rd index 967518c..c6096d4 100644 --- a/man/ccme_uranium.Rd +++ b/man/ccme_uranium.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data from the Canadian Council of Ministers of the -Environment for \emph{\strong{uranium}}. +Environment for \strong{\emph{uranium}}. } \details{ Additional information is available from diff --git a/man/csiro_chlorine_marine.Rd b/man/csiro_chlorine_marine.Rd index 24e14d6..b08c5e0 100644 --- a/man/csiro_chlorine_marine.Rd +++ b/man/csiro_chlorine_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Commonwealth Scientific and -Industrial Research Organisation of Australia for \emph{\strong{chlorine}} +Industrial Research Organisation of Australia for \strong{\emph{chlorine}} in marine water. } \details{ diff --git a/man/csiro_cobalt_marine.Rd b/man/csiro_cobalt_marine.Rd index 6d6a72c..a51e754 100644 --- a/man/csiro_cobalt_marine.Rd +++ b/man/csiro_cobalt_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Commonwealth Scientific and -Industrial Research Organisation of Australia for \emph{\strong{cobalt}} +Industrial Research Organisation of Australia for \strong{\emph{cobalt}} in marine water. } \details{ diff --git a/man/csiro_lead_marine.Rd b/man/csiro_lead_marine.Rd index 473d7ed..7fda753 100644 --- a/man/csiro_lead_marine.Rd +++ b/man/csiro_lead_marine.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Commonwealth Scientific and -Industrial Research Organisation of Australia for \emph{\strong{lead}} +Industrial Research Organisation of Australia for \strong{\emph{lead}} in marine water. } \details{ diff --git a/man/csiro_nickel_fresh.Rd b/man/csiro_nickel_fresh.Rd index 3f16a16..a1d5796 100644 --- a/man/csiro_nickel_fresh.Rd +++ b/man/csiro_nickel_fresh.Rd @@ -10,7 +10,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, } \description{ Species Sensitivity Data provided by the Commonwealth Scientific and -Industrial Research Organisation of Australia for \emph{\strong{nickel}} +Industrial Research Organisation of Australia for \strong{\emph{nickel}} in freshwater. } \details{ diff --git a/scripts/build.R b/scripts/build.R index 297ae36..d180e10 100644 --- a/scripts/build.R +++ b/scripts/build.R @@ -1,17 +1,22 @@ -roxygen2md::roxygen2md() -roxygen2::roxygenise() +# README +devtools::build_readme() -devtools::test() -devtools::document() +# Generate dataset R files +source("data-raw/source_all.R") -# if updating references -unlink("man", recursive = TRUE) +# Generate documentation devtools::document() +# Update pkgdown config +source("data-raw/build_pkgdown_yml.R") +# Build site pkgdown::build_site() + browseURL("docs/index.html") +devtools::test() + devtools::check() rcmdcheck::rcmdcheck(