Merge pull request #178 from ldecicco-USGS/master

Remove plyr dependency
DOI-USGS · Feb 12, 2016 · 83dc1c6 · 83dc1c6
2 parents bb116e3 + 38f8657
commit 83dc1c6
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Showing 5 changed files with 11 additions and 32 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,9 @@ Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     person("David","Lorenz", role=c("aut"),
     email = "[email protected]"),
     person("Jordan", "Read", role = c("ctb"),
-    email = "[email protected]"))
+    email = "[email protected]"),
+    person("Lindsay","Carr", role=c("ctb"),
+    email = "[email protected]"))
 Description: Collection of functions to help retrieve U.S. Geological Survey
     (USGS) and U.S. Environmental Protection Agency (EPA) water quality and
     hydrology data from web services. USGS web services are discovered from the
@@ -29,7 +31,6 @@ Imports:
     RCurl,
     reshape2,
     lubridate,
-    plyr,
     stats,
     utils,
     dplyr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -52,10 +52,10 @@ importFrom(XML,xpathSApply)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate_)
 importFrom(dplyr,mutate_each_)
+importFrom(dplyr,rbind_all)
 importFrom(dplyr,select_)
 importFrom(lubridate,fast_strptime)
 importFrom(lubridate,parse_date_time)
-importFrom(plyr,rbind.fill.matrix)
 importFrom(readr,col_character)
 importFrom(readr,col_number)
 importFrom(readr,cols)

diff --git a/R/AAA.R b/R/AAA.R
@@ -1,4 +1,5 @@
 pkg.env <- new.env()
 .onLoad = function(libname, pkgname){
   suppressMessages(setAccess('public'))
+  options(Access.dataRetrieval = NULL)
 }
diff --git a/R/importWaterML1.r b/R/importWaterML1.r
@@ -133,7 +133,6 @@ importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
 
   timeSeries <- xpathApply(doc, "//ns1:timeSeries", namespaces = ns)
 
-
   if(0 == length(timeSeries)){
     df <- data.frame()
     attr(df, "queryInfo") <- queryInfo
@@ -287,16 +286,7 @@ importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
                 datetime <- datetime - tzHours*60*60
               }
             }
-
-#             if(tz != ""){
-#               attr(datetime, "tzone") <- tz
-#               df$tz_cd <- rep(tz, nrow(df))
-#             } else {
-#               attr(datetime, "tzone") <- "UTC"
-#               df$tz_cd <- rep("UTC", nrow(df))
-#             }
 
-
           } else {
 
             datetime <- as.character(datetime)

diff --git a/R/importWaterML2.r b/R/importWaterML2.r
@@ -19,7 +19,7 @@
 #' @importFrom XML xmlValue
 #' @importFrom XML xmlAttrs
 #' @importFrom XML xmlName
-#' @importFrom plyr rbind.fill.matrix
+#' @importFrom dplyr rbind_all
 #' @examples
 #' baseURL <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0"
 #' URL <- paste(baseURL, "sites=01646500",
@@ -83,16 +83,7 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
     chunk <- xmlDoc(timeSeries[[i]])
     chunk <- xmlRoot(chunk)
     chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE)
-
-#     xp <- xpathApply(chunk, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", 
-#                      xpathSApply, ".//*[not(*)]", 
-#                      function(x) setNames(ifelse(nzchar(xmlValue(x)), 
-#                                        xmlValue(x), 
-#                                           ifelse("qualifier" == xmlName(x),
-#                                                 xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x) 
-#                                                     xmlName(x)), 
-#                      namespaces = chunkNS)
-
+
     xp <- xpathApply(chunk, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", 
                      xpathSApply, ".//*[not(*)]", 
                      function(x) setNames(ifelse(nzchar(xmlValue(x)), 
@@ -108,9 +99,9 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
       xp <- xp[-1]
     }
 
-
-    DF2 <- do.call(rbind.fill.matrix, lapply(xp, t))
-    DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
+    y <- lapply(xp,t)
+    z <- lapply(y, as.data.frame)
+    DF2 <- suppressWarnings(rbind_all(z))
 
     names(DF2)[grep("wml2",names(DF2))] <- sub("wml2:","",names(DF2)[grep("wml2",names(DF2))])
 
@@ -150,11 +141,7 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
     } else {
       DF2$qualifier <- rep(defaultQualifier,nrow(DF2))
     }
-
-
-#     DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
-#                                ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
-
+
 #########################################
 
     id <- as.character(xpathApply(chunk, "//gml:identifier", xmlValue, namespaces = chunkNS))