CRAN submission

Author: andschar

.Rbuildignore

@@ -3,3 +3,8 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+
+^README.Rmd
+^README_files
+
+CONTRIBUTING

CONTRIBUTING

@@ -0,0 +1,40 @@
+# CONTRIBUTING #
+
+### Please contribute!
+We love collaboration.
+
+### Found a Bug?
+
+* Submit an issue on our Issues page [here](https://github.com/andschar/standartox/issues).
+
+### Code contributions?
+
+* **Fork** this repo to your Github account.
+* **Clone** your version on your account down to your machine from your account, e.g,. `git clone https://github.com/<yourgithubusername>/standartox.git`.
+* Make sure to **track upstream** progress (i.e., on our version of `standartox` at `andschar/standartox`) by doing `git remote add upstream https://github.com/andschar/standartox.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
+* Make your **changes** (bonus points for making changes on a new branch).
+* **Push** up to your account.
+* Submit a **pull request** to home base at `andschar/standartox`.
+
+### Code guidelines
+
+We do not have strong guideline for our contributions and are happy to help.
+
+1. Please follow [this](http://adv-r.had.co.nz/Style.html) styleguide for your contributions.
+
+We want to keep dependencies to a minimum:
+
+2. Please use the [`data.table`](https://github.com/Rdatatable/data.table) for data wrangling.
+
+3. Please use the lightweight [`jsonlite`](https://github.com/jeroenooms/jsonlite) package for handling JSON.
+
+4. Be nice to the resources! Use appropriate timeouts.
+
+5. Tests go into a separate tests branch and not in the master branch.
+
+### Questions? 
+
+Get in touch: [[email protected]](mailto:[email protected])
+
+### Thanks for contributing!
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: standartox
-Version: 0.0.0.9024
-Date: 2020-09-05
-Title: Ecotoxicological information from the standartox database
+Version: 0.0.1
+Date: 2021-04-30
+Title: Ecotoxicological Information from the Standartox Database
 Authors@R: c(
     person("Andreas", "Scharmüller",
             role = c("aut", "cre"),
@@ -16,6 +16,7 @@ Description: The <standartox.uni-landau.de> database offers cleaned,
 Depends:
     R (>= 3.5.0)
 Imports:
+    stats,
     httr (>= 1.4.1),
     curl (>= 3.4),
     jsonlite (>= 1.6.1),

NEWS

@@ -0,0 +1,4 @@
+standartox 0.0.1
+=============================
+
+initial release

R/standartox.R

@@ -59,18 +59,18 @@ stx_catalog = function(vers = NULL) {
 #' \donttest{
 #' # might fail if API is not available
 #' stx_query('1071-83-6')
-#' stx_query(casnr = '1071-83-6',
+#' stx_query(cas = '1071-83-6',
 #'           duration = c(48, 120),
 #'           concentration_unit = 'ug/l')
-#' stx_query(casnr = '1071-83-6',
+#' stx_query(cas = '1071-83-6',
 #'           duration = c(48, 120),
 #'           concentration_unit = 'ug/l',
 #'           endpoint = 'XX50')
 #' }
 #' 
 #' @export
 #'
-stx_query = function(casnr = NULL,
+stx_query = function(cas = NULL,
                      concentration_unit = NULL,
                      concentration_type = NULL,
                      duration = NULL,
@@ -86,13 +86,15 @@ stx_query = function(casnr = NULL,
                      region = NULL,
                      vers = NULL,
                      ...) {
+  # to avoid NOTE in R CMD check --as-cran
+  casnr = outlier = concentration = cname = NULL
   # debuging
   # browser() # debuging
-  # casnr = '1071-83-6'; concentration_unit = NULL; concentration_type = NULL; duration = NULL; endpoint = 'XX50'; effect = NULL; exposure = NULL; chemical_role = NULL; chemical_class = NULL; taxa = NULL; ecotox_grp = NULL; trophic_lvl = NULL; habitat = NULL; region = NULL; vers = NULL
+  # cas = '1071-83-6'; concentration_unit = NULL; concentration_type = NULL; duration = NULL; endpoint = 'XX50'; effect = NULL; exposure = NULL; chemical_role = NULL; chemical_class = NULL; taxa = NULL; ecotox_grp = NULL; trophic_lvl = NULL; habitat = NULL; region = NULL; vers = NULL
   # checks
   endpoint = match.arg(endpoint)
   # request
-  body = list(casnr = casnr,
+  body = list(casnr = cas,
               concentration_unit = concentration_unit,
               concentration_type = concentration_type,
               duration = duration,
@@ -237,11 +239,11 @@ stx_taxa = function() {
 
 # IDEA
 # microbenchmark::microbenchmark({
-# col_test = c('result_id', 'casnr', 'species_number', 'ref_number',
+# col_test = c('result_id', 'cas', 'species_number', 'ref_number',
 #              'concentration', 'concentration_unit', 'concentration_orig', 'concentration_unit_orig',
 #              'concentration_type', 'duration', 'duration_unit',
 #              'endpoint', 'effect', 'exposure', 'outlier')
-# col_chem = c('cname', 'iupac_name', 'cas', 'casnr', 'inchikey', 'inchi',
+# col_chem = c('cname', 'iupac_name', 'cas', 'cas', 'inchikey', 'inchi',
 #              'molecularweight',
 #              grep('cro|ccl', names(out_fil), value = TRUE))
 # col_taxa = c(
@@ -261,10 +263,13 @@ stx_taxa = function() {
 
 #' Function to aggregate filtered test results
 #' 
+#' 
 #' @author Andreas Scharmueller \email{andschar@@protonmail.com}
 #' @noRd
 #'  
 stx_aggregate = function(dat = NULL) {
+  # assign variables to avoid R CMD check NOTES
+  . = concentration = cname = cas = tax_taxon = gmn = gmnsd = n = NULL
   # checking
   if (is.null(dat)) stop('Provide table.')
   # aggregation

R/utils.R

@@ -105,7 +105,7 @@ gm_sd = function (x, na.rm = TRUE, sqrt.unbiased = TRUE) {
     warning("Non-positive values in 'x'")
     return(NA_real_)
   } else {
-    sd.log = sd(log(x))
+    sd.log = stats::sd(log(x))
     if (!sqrt.unbiased) {
       n = length(x)
       sd.log = sqrt((n - 1)/n) * sd.log
@@ -120,8 +120,8 @@ gm_sd = function (x, na.rm = TRUE, sqrt.unbiased = TRUE) {
 #' @noRd
 #' 
 flag_outliers = function(x, lim = 1.5, na.rm = TRUE, ...) {
-  qnt = quantile(x, probs = c(.25, .75), na.rm = na.rm)
-  H = lim * IQR(x, na.rm = na.rm)
+  qnt = stats::quantile(x, probs = c(.25, .75), na.rm = na.rm)
+  H = lim * stats::IQR(x, na.rm = na.rm)
   fifelse(x < qnt[1] - H | x > qnt[2] + H, TRUE, FALSE)
 }