CRAN Release

rmendels · Jun 4, 2019 · 8b61bae · 8b61bae
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diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2019-05-29.
+This package was submitted to CRAN on 2019-06-03.
 Once it is accepted, delete this file and tag the release (commit 4c2ea05e5e).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,32 +1,40 @@
 Package: rerddapXtracto
 Type: Package
-Title: Extracts Environmental Data from ERD's ERDDAP Web Service
-Version: 0.3.5.900
+Title: Extracts Environmental Data from 'ERDDAP' Web Services
+Version: 0.3.5
 Authors@R: person("Roy", "Mendelssohn", email = "[email protected]", role = c("aut","cre"))
-Description: The xtractomatic package contains three functions that access
-    environmental data from ERD's ERDDAP service. The rxtracto function extracts
+Description: Contains three functions that access
+    environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts
     data along a trajectory for a given "radius" around the point. The
-    rxtracto_3D function extracts data in a box. The rxtractogon function
-    extracts data in a polygon. There are also two helper functions to obtain
-    information about available data.
-    These functions differ from those in the xtractomatic package in that they
-    use the `rerddap` package to access gridded data on any ERDDAP server, but
-    they require the user to provide initial information about the data
-    to be extracted.
+    rxtracto_3D() function extracts data in a box. The rxtractogon() function
+    extracts data in a polygon. All of those three function use the 'rerddap' package
+    to extract the data, and should work with any 'ERDDAP' server.
+    There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
+    package to simplify the creation of maps of the data.
 URL: https://github.com/rmendels/rerddapXtracto
 BugReports: https://github.com/rmendels/rerddapXtracto/issues
+Depends:
+    R(>= 3.5.0)
 License: CC0
-LazyData: TRUE
 Imports:
     abind,
+    dplyr,
+    ggplot2,
+    httr,
     methods,
     ncdf4,
     parsedate,
-    rerddap,
+    plotdap,
+    readr,
+    rerddap (>= 0.6.0),
     sp,
-    stats
+    stats,
 Suggests:
-    ggplot2,
+    gganimate,
     knitr,
     mapdata,
-RoxygenNote: 6.0.1
+    rmarkdown
+RoxygenNote: 6.1.1
+Encoding: UTF-8
+LazyData: TRUE
+VignetteBuilder: knitr
diff --git a/R/rxtracto.R b/R/rxtracto.R
@@ -1,9 +1,9 @@
-#' Extract environmental data along a trajectory from an ERDDAP server using rerddap.
+#' Extract environmental data along a trajectory from an 'ERDDAP' server using 'rerddap'.
 #'
-#' \code{rxtracto} uses the R program rerddap to extract environmental
-#' data from an ERDDAP server along a (x,y,z, time) trajectory.
+#' \code{rxtracto} uses the R program 'rerddap' to extract environmental
+#' data from an 'ERDDAP' server along a (x,y,z, time) trajectory.
 #' @export
-#' @param dataInfo - the return from an rerddap "info" call to an ERDDAP server
+#' @param dataInfo - the return from an 'rerddap::info' call to an 'ERDDAP' server
 #' @param parameter - character string containing the name of the parameter to extract
 #' @param xcoord - a real array with the x-coordinates of the trajectory (if longitude in #'   decimal degrees East, either 0-360 or -180 to 180)
 #' @param ycoord -  a real array with the y-coordinate of the trajectory (if latitude in
@@ -14,11 +14,10 @@
 #' @param xlen - real array defining the longitude box around the given point (xlen/2 around the point)
 #' @param ylen - real array defining the latitude box around the given point (ylen/2 around the point)
 #' @param zlen - real array defining the depth or altitude box around the given point (zlen/2 around the point)
-#' @param xName - character string with name of the xcoord in the ERDDAP dataset (default "longitude")
-#' @param yName - character string with name of the ycoord in the ERDDAP dataset (default "latitude")
-#' @param zName - character string with name of the zcoord in the ERDDAP dataset (default "altitude")
-#' @param tName - character string with name of the tcoord in the ERDDAP dataset (default "time")
-#' @param urlbase - base URL of the ERDDAP server being accessed - default "http://upwell.pfeg.noaa.gov/erddap"
+#' @param xName - character string with name of the xcoord in the 'ERDDAP' dataset (default "longitude")
+#' @param yName - character string with name of the ycoord in the 'ERDDAP' dataset (default "latitude")
+#' @param zName - character string with name of the zcoord in the 'ERDDAP' dataset (default "altitude")
+#' @param tName - character string with name of the tcoord in the 'ERDDAP' dataset (default "time")
 #' @param verbose - logical variable (default FALSE)
 #'                   if the the URL request should be verbose
 #' @return A dataframe containing:
@@ -36,42 +35,28 @@
 #'  \item column 11 = median absolute deviation of data within search radius
 #'  }
 #' @examples
-#' urlbase <- 'https://upwell.pfeg.noaa.gov/erddap'
-#' dataInfo <- rerddap::info('erdMBsstd8day')
+#' # toy example to show use
+#' # but keep execution time down
+#' \donttest{
+#' dataInfo <- rerddap::info('erdHadISST')
+#' }
 #' parameter <- 'sst'
-#' xcoord <- c(230, 231)
-#' ycoord <- c(40, 41)
-#' tcoord <- c('2006-01-15', '2006-01-20')
-#' zcoord <- c(0., 0.)
-#' xlen <- 0.5
-#' ylen <- 0.5
+#' xcoord <- c(-130.5)
+#' ycoord <- c(40.5)
+#' tcoord <- c('2006-01-16')
+#' xlen <- 0.01
+#' ylen <- 0.01
 #' extract <- rxtracto(dataInfo, parameter = parameter, xcoord = xcoord,
-#'                     ycoord = ycoord, tcoord= tcoord, zcoord = zcoord,
+#'                     ycoord = ycoord, tcoord= tcoord,
 #'                     xlen = xlen, ylen = ylen)
+#' \donttest{
 #' # 2-D example getting bathymetry
 #' dataInfo <- rerddap::info('etopo360')
 #' parameter <- 'altitude'
 #' extract <- rxtracto(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord,
 #'                     xlen = xlen, ylen = ylen)
+#' }
 #'
-#' # Example where grid is not latitude-longitude
-#' dataInfo <- rerddap::info('glos_tds_5912_ca66_3f41')
-#' parameter <- 'temp'
-#' xName <- 'nx'
-#' yName <- 'ny'
-#' zName <- 'nsigma'
-#' xcoord <- c(10, 11)
-#' ycoord <- c(10, 11)
-#' zcoord <- c(1, 1)
-#'  # time span changes in this dataset - get last three times
-#'  myURL <- "https://upwell.pfeg.noaa.gov/erddap/griddap/glos_tds_5912_ca66_3f41.csv0?time[last - 2:1:last]"
-#' myTimes <- utils::read.csv(utils::URLencode(myURL), header = FALSE, stringsAsFactors = FALSE)[[1]]
-#' tcoord <- c(myTimes[1], myTimes[3])
-#' xlen <- 0
-#' ylen <- 0
-#' extract <- rxtracto(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord,
-#'                     zcoord = zcoord, tcoord = tcoord, xlen = xlen,
-#'                     ylen = ylen, xName = xName, yName = yName, zName = zName)
 
 
 
@@ -80,15 +65,14 @@ rxtracto <- function(dataInfo, parameter = NULL, xcoord=NULL, ycoord = NULL,
                   zcoord = NULL, tcoord = NULL, xlen = 0., ylen = 0., zlen = 0.,
                   xName = 'longitude', yName = 'latitude', zName = 'altitude',
                   tName = 'time',
-                  urlbase = 'https://upwell.pfeg.noaa.gov/erddap',
                   verbose = FALSE) {
 
   # Check Passed Info -------------------------------------------------------
   rerddap::cache_setup(temp_dir = TRUE)
   callDims <- list(xcoord, ycoord, zcoord, tcoord)
   names(callDims) <- c(xName, yName, zName, tName)
   dataInfo1 <- dataInfo
-
+  urlbase <- dataInfo1$base_url
   # Check that the non-null input vectors are the same length
   dimLengths <- lapply(callDims, length)
   dimLengths[dimLengths == 0] <- NULL
@@ -243,7 +227,6 @@ oldDataFrame <- out_dataframe[1, ]
      # will try 5 times,  if failure will stop and save data
      tryn <- 0
      goodtry <- -1
-     options(warn = 2)
      while ((tryn <= numtries) & (goodtry == -1)) {
        tryn <- tryn + 1
        extract <- try(do.call(rerddap::griddap, griddapCmd ))
@@ -254,7 +237,9 @@ oldDataFrame <- out_dataframe[1, ]
     # extract <- do.call(rerddap::griddap, griddapCmd )
     if (goodtry == -1) {
       print(griddapCmd)
-      print("There was an error in the url call, perhaps a time out.  See message on screen and URL called")
+      text1 <- "There was an error in the url call, perhaps a time out."
+      text2 <- "See message on screen and URL called"
+      print(paste(text1, text2))
       print("Returning incomplete download")
       out_dataframe <- out_dataframe[1:(i - 1), ]
       remove('paramdata')
@@ -297,7 +282,7 @@ oldDataFrame <- out_dataframe[1, ]
    oldDataFrame <- out_dataframe[i,]
 
  }
-out_dataframe <- structure(out_dataframe, class = 'rxtractoTrack')
+out_dataframe <- structure(out_dataframe, class = c('list', 'rxtractoTrack'))
 return(out_dataframe)
 }
 

diff --git a/R/rxtracto_3D.R b/R/rxtracto_3D.R
@@ -1,24 +1,24 @@
-#' Extract environmental data in a 3-dimnesional box from an ERDDAP server using rerddap.
+#' Extract environmental data in a 3-dimensional box from an 'ERDDAP' server using 'rerddap'.
 #'
-#' \code{rxtracto_3D} uses the R program rerddap to extract environmental data
-#' from an ERDDAP server in an (x,y,z, time) bounding box.
+#' \code{rxtracto_3D} uses the R program 'rerddap' to extract environmental data
+#' from an 'ERDDAP' server in an (x,y,z, time) bounding box.
 #' The same call could be made directly in rerddap,
 #' but function is maintained as it is used in the polygon routine.
 #' @export
-#' @param dataInfo - the return from an rerddap "info" call to an ERDDAP server
+#' @param dataInfo - the return from an 'rerddap:info' call to an 'ERDDAP' server
 #' @param parameter - character string containing the name of the parameter to extract
 #' @param xcoord - a real array with the x-coordinates of the trajectory (if longitude in #'   decimal degrees East, either 0-360 or -180 to 180)
 #' @param ycoord -  a real array with the y-coordinate of the trajectory (if latitude in
 #'   decimal degrees N; -90 to 90)
 #' @param zcoord -  a real array with the z-coordinate (usually altitude or depth)
 #' @param tcoord - a character array with the times of the trajectory in
 #'   "YYYY-MM-DD" - for now restricted to be time.
-#' @param xName - character string with name of the xcoord in the ERDDAP dataset (default "longitude")
-#' @param yName - character string with name of the ycoord in the ERDDAP dataset (default "latitude")
-#' @param zName - character string with name of the zcoord in the ERDDAP dataset (default "altitude")
-#' @param tName - character string with name of the tcoord in the ERDDAP dataset (default "time")
-#' @param urlbase - base URL of the ERDDAP server being accessed - default "http://upwell.pfeg.noaa.gov/erddap"
+#' @param xName - character string with name of the xcoord in the 'ERDDAP' dataset (default "longitude")
+#' @param yName - character string with name of the ycoord in the 'ERDDAP' dataset (default "latitude")
+#' @param zName - character string with name of the zcoord in the 'ERDDAP' dataset (default "altitude")
+#' @param tName - character string with name of the tcoord in the 'ERDDAP' dataset (default "time")
 #' @param verbose - logical variable (default FALSE) if the the URL request should be verbose
+#' @param cache_remove - logical variable (default TRUE) whether to delete 'rerddap' cache
 #' @return structure with data and dimensions:
 #' \itemize{
 #'   \item extract$data - the data array dimensioned (lon,lat,time)
@@ -29,38 +29,23 @@
 #'   \item extract$time - the times of the extracts
 #'   }
 #' @examples
-#' urlbase <- 'https://upwell.pfeg.noaa.gov/erddap'
-#' dataInfo <- rerddap::info('erdMBsstd8day')
+#' # toy example to show use
+#' # and keep execution time low
+#' \donttest{
+#' dataInfo <- rerddap::info('erdHadISST')
+#' }
 #' parameter <- 'sst'
-#' xcoord <- c(230, 235)
-#' ycoord <- c(40, 45)
-#' tcoord <- c('2006-01-15', '2006-01-20')
-#' zcoord <- c(0., 0.)
+#' xcoord <- c(-130.5, -130.5)
+#' ycoord <- c(40.5, 40.5)
+#' tcoord <- c('2006-01-16', '2006-01-16')
 #' extract <- rxtracto_3D(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord,
-#'                        tcoord = tcoord, zcoord = zcoord)
+#'                        tcoord = tcoord)
 #'
+#' \donttest{
 #' # 2-D example getting bathymetry
 #' dataInfo <- rerddap::info('etopo360')
 #' parameter <- 'altitude'
 #' extract <- rxtracto_3D(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord)
-#'
-#' # Example where grid is not latitude-longitude
-#' dataInfo <- rerddap::info('glos_tds_5912_ca66_3f41')
-#' parameter = 'temp'
-#' xName <- 'nx'
-#' yName <- 'ny'
-#' zName <- 'nsigma'
-#' xcoord <- c(10, 11)
-#' ycoord <- c(10, 11)
-#' zcoord <- c(1, 1)
-#'  # time span changes in this dataset - get last three times
-#'  myURL <- "https://upwell.pfeg.noaa.gov/erddap/griddap/glos_tds_5912_ca66_3f41.csv0?time[last - 2:1:last]"
-#' myTimes <- utils::read.csv(utils::URLencode(myURL), header = FALSE, stringsAsFactors = FALSE)[[1]]
-#' tcoord <- c(myTimes[1], myTimes[3])
-#' extract <- rxtracto_3D(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord,
-#'                        zcoord = zcoord, tcoord = tcoord, xName = xName,
-#'                        yName = yName, zName = zName)
-#'
 #' # Dataset that has depth also
 #' # 3 months of subsurface temperature at 70m depth from SODA 2.2.4
 #' dataInfo <- rerddap::info('erdSoda331oceanmday')
@@ -75,16 +60,22 @@
 #' extract <- rxtracto_3D(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord,
 #'                        zcoord = zcoord, tcoord = tcoord, xName = xName,
 #'                        yName = yName, zName = zName)
+#' }
 #'
 
-rxtracto_3D <- function(dataInfo, parameter = NULL, xcoord = NULL, ycoord = NULL, zcoord = NULL, tcoord = NULL, xName = 'longitude', yName = 'latitude', zName = 'altitude', tName = 'time', urlbase = 'https://upwell.pfeg.noaa.gov/erddap/', verbose=FALSE) {
+rxtracto_3D <- function(dataInfo, parameter = NULL, xcoord = NULL,
+                        ycoord = NULL, zcoord = NULL, tcoord = NULL,
+                        xName = 'longitude', yName = 'latitude',
+                        zName = 'altitude', tName = 'time',
+                        verbose=FALSE, cache_remove = TRUE) {
 
 
 # Check Passed Info -------------------------------------------------------
  rerddap::cache_setup(temp_dir = TRUE)
  callDims <- list(xcoord, ycoord, zcoord, tcoord)
  names(callDims) <- c(xName, yName, zName, tName)
  dataInfo1 <- dataInfo
+ urlbase <- dataInfo1$base_url
  urlbase <- checkInput(dataInfo1, parameter, urlbase, callDims)
 
 
@@ -217,20 +208,11 @@ if (grepl('etopo',extract[[2]])) {
 
 }
 
-# copy netcdf file from cache to the present directory and rename
-copyFile <- paste0(getwd(), '/', parameter, '.nc')
-iFile <- 1
-while (file.exists(copyFile)) {
-  copyFile <- paste0(getwd(), '/', parameter, '_', iFile, '.nc')
-  iFile <- iFile + 1
-}
-fcopy <- file.copy(griddapExtract$summary$filename, copyFile)
-if (!fcopy) {
-  print('copying and renaming downloaded file from default ~/.rerddap failed')
-}
 # remove netcdf file from cache
-rerddap::cache_delete(griddapExtract)
-extract <- structure(extract, class = 'rxtracto3D')
+if (cache_remove) {
+  rerddap::cache_delete(griddapExtract)
+}
+extract <- structure(extract, class = c('list', 'rxtracto3D'))
 return(extract)
 }