fix #98, namespace base pkg fxn calls

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Species trait data from many different sources, including
     data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
     from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
     ('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
-Version: 0.2.0.9418
+Version: 0.2.3.9100
 Authors@R: c(
     person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"),
     person("Zachary", "Foster", role = "aut", email = "zacharyfoster1989@gmail.com"),
@@ -21,9 +21,6 @@ VignetteBuilder: knitr
 Depends:
     R (>= 2.10)
 Imports:
-    methods,
-    stats,
-    utils,
     jsonlite (>= 0.9.19),
     httr (>= 1.1.0),
     dplyr (>= 0.4.3),

NAMESPACE

@@ -37,18 +37,13 @@ importFrom(httr,content)
 importFrom(httr,stop_for_status)
 importFrom(httr,warn_for_status)
 importFrom(jsonlite,fromJSON)
-importFrom(methods,is)
 importFrom(readr,read_delim)
 importFrom(rvest,html_table)
-importFrom(stats,na.omit)
-importFrom(stats,setNames)
 importFrom(taxize,classification)
 importFrom(taxize,get_tsn)
 importFrom(taxize,get_uid)
 importFrom(taxize,itis_native)
 importFrom(taxize,iucn_id)
-importFrom(utils,URLencode)
-importFrom(utils,read.csv)
 importFrom(xml2,read_xml)
 importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_text)

R/coral.R

@@ -86,7 +86,7 @@ coral_GET <- function(url, args, ...) {
   res <- GET(url, query = args, ...)
   stop_for_status(res)
   txt <- content(res, "text", encoding = "UTF-8")
-  dplyr::tbl_df(read.csv(text = txt, header = TRUE, stringsAsFactors = FALSE))
+  dplyr::tbl_df(utils::read.csv(text = txt, header = TRUE, stringsAsFactors = FALSE))
 }
 
 coralbase <- function() 'http://coraltraits.org'

R/eol_invasive.R

@@ -145,5 +145,5 @@ eol_invasive_ <- function(name = NULL, dataset="all", searchby = grep, page=NULL
   df$db <- dataset
   names(df)[c(1,3)] <- c("searched_name","eol_object_id")
   row.names(df) <- NULL
-  if (!count) df else length(na.omit(df$eol_object_id))
+  if (!count) df else length(stats::na.omit(df$eol_object_id))
 }

R/g_invasive.R

@@ -61,7 +61,7 @@ g_invasive <- function(x, simplify = FALSE, verbose=TRUE) {
 			  one <- tryCatch(xml2::xml_text(xml2::xml_find_all(doc, "//span[@class='ListNote']"))[[1]],
                         error = function(e) e)
 			  two <- paste(xml2::xml_text(xml2::xml_find_all(doc, "//span[@class='Info']")), collapse = "; ")
-			  out[i, 2] <- paste(if (is(one, "simpleError")) NULL else one, two, sep = "; ")
+			  out[i, 2] <- paste(if (inherits(one, "simpleError")) NULL else one, two, sep = "; ")
 			} else {
         out[i, 2] <- "Invasive"
 			}

R/leda.R

@@ -41,7 +41,7 @@
 #' sapply(out, NROW)
 #' }
 leda <- function(trait = "age_first_flowering", ...) {
-  tt <- GET(URLencode(paste0(leda_base(), pick_file_name(trait))), ...)
+  tt <- GET(utils::URLencode(paste0(leda_base(), pick_file_name(trait))), ...)
   out <- rawToChar(content(tt, "raw", encoding = "UTF-8"))
   stop_for_status(tt)
   out <- iconv(out, "latin1", "UTF-8")

R/traits-package.r

@@ -29,9 +29,6 @@
 #'
 #' @importFrom httr GET POST content stop_for_status warn_for_status authenticate
 #' @importFrom jsonlite fromJSON
-#' @importFrom methods is
-#' @importFrom stats setNames na.omit
-#' @importFrom utils read.csv URLencode
 #' @importFrom xml2 read_xml xml_find_all xml_text
 #' @importFrom rvest html_table
 #' @importFrom taxize get_uid classification get_tsn itis_native iucn_id

R/zzz.R

@@ -53,7 +53,7 @@ trydefault <- function (expr, default, quiet = FALSE){
 }
 
 low_names <- function(x) {
-  if (is(x, "data.frame")) {
+  if (inherits(x, "data.frame")) {
     stats::setNames(x, tolower(names(x)))
   } else {
     x