v0.4.6

rmendels · Jan 10, 2020 · 8225f71 · 8225f71
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,8 @@
 Package: rerddapXtracto
 Type: Package
 Title: Extracts Environmental Data from 'ERDDAP' Web Services
-Version: 0.4.5
+Version: 0.4.6
+Date: 2020-01-08
 Authors@R: person("Roy", "Mendelssohn", email = "[email protected]", role = c("aut","cre"))
 Description: Contains three functions that access
     environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts
@@ -25,7 +26,7 @@ Imports:
     methods,
     ncdf4,
     parsedate,
-    plotdap,
+    plotdap (>= 0.0.5),
     readr,
     rerddap (>= 0.6.0),
     sf,
@@ -38,7 +39,7 @@ Suggests:
     maptools,
     rgdal,
     rmarkdown
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Encoding: UTF-8
 LazyData: TRUE
 VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# rerddapXtracto 0.4.6
+
+Changed vignette to work with latest version of 'plotdap' that now uses the colors from the 'cmocean' package
+
 # rerddapXtracto 0.4.5
 
 Added maptools and rgdal to Suggests to be consistent with of plotdap v0.0.4

diff --git a/R/plotBBox.R b/R/plotBBox.R
@@ -5,7 +5,7 @@
 #'
 #' @export
 #' @param resp data frame returned from 'rxtracto()'
-#' @param plotColor the color to use in plot from 'rerddap'
+#' @param plotColor the color to use in plot from 'cmocean'
 #' @param time a function to map multi-time to one, or else identity
 #'  for animation
 #' @param myFunc function of one argument to transform the data
@@ -30,7 +30,7 @@
 #'                        tcoord = tcoord, zcoord = zcoord)
 #' }
 #' # low resolution selected to keep time to render down
-#' p <- plotBBox(MBsst, plotColor = 'temperature', maxpixels = 300)
+#' p <- plotBBox(MBsst, plotColor = 'thermal', maxpixels = 300)
 
 plotBBox <- function(resp, plotColor = 'viridis', time = NA, myFunc = NA,
                 mapData = NULL, crs = NULL,
@@ -106,8 +106,8 @@ plotBBox <- function(resp, plotColor = 'viridis', time = NA, myFunc = NA,
               ggplot2::guides(fill = ggplot2::guide_colourbar(title = name)))
   }
   if (animate) {
-    xlim <- c(min(myStruct$longitude), max(myStruct$longitude))
-    ylim <- c(min(myStruct$latitude), max(myStruct$latitude))
+    xlim <- c(min(myStruct$data$lon), max(myStruct$data$lon))
+    ylim <- c(min(myStruct$data$lat), max(myStruct$data$lat))
     suppressMessages(myplot <- plotdap::add_ggplot(
       myplot, ggplot2::coord_sf(
         crs = myplot$crs, datum = myplot$datum,

diff --git a/R/plotTrack.R b/R/plotTrack.R
@@ -7,7 +7,7 @@
 #' @param ycoord passed to 'rxtracto()'
 #' @param tcoord passed to 'rxtracto()'
 #' @param resp data frame returned from 'rxtracto()'
-#' @param plotColor the color to use in plot from 'rerddap'
+#' @param plotColor the color to use in plot from 'cmocean'
 #' @param myFunc function of one argument to transform the data
 #' @param mapData map data from 'maps' or 'mapdata', must be of class 'map'
 #' @param crs valid crs string
@@ -30,7 +30,7 @@
 #' swchl <- rxtracto(swchlInfo, parameter = 'chlorophyll', xcoord = xpos,
 #'         ycoord = ypos, tcoord = tpos, zcoord = zpos, xlen = .2, ylen = .2)
 #' }
-#' p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'chlorophyll')
+#' p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'algae')
 
 plotTrack <- function(resp, xcoord, ycoord, tcoord, plotColor = 'viridis', myFunc = NA,
                       mapData = NULL, crs = NULL,

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
-## update Version 0.4.5
+## update Version 0.4.6
 
-Minor update, added maptools and rgdal to Suggests to be consistent with plotdap v0.0.4.
+Minor update so that the vignette is consistent with 'plotdap' version 0.0.5
 
 
 ## Test environments

diff --git a/data/cmocean.RData b/data/cmocean.RData
diff --git a/man/cmocean.Rd b/man/cmocean.Rd
diff --git a/man/plotBBox.Rd b/man/plotBBox.Rd
diff --git a/man/plotTrack.Rd b/man/plotTrack.Rd
diff --git a/man/rerddapXtracto.Rd b/man/rerddapXtracto.Rd
diff --git a/man/rxtracto.Rd b/man/rxtracto.Rd
diff --git a/man/rxtracto_3D.Rd b/man/rxtracto_3D.Rd
diff --git a/man/rxtractogon.Rd b/man/rxtractogon.Rd
diff --git a/vignettes/UsingrerddapXtracto.Rmd b/vignettes/UsingrerddapXtracto.Rmd
@@ -197,7 +197,7 @@ We plot the track line with the locations colored according to the mean of the s
 require("ggplot2")
 require("plotdap")
 
-myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'chlorophyll')
+myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'algae')
 myPlot
 ```
 
@@ -209,7 +209,7 @@ To make a cumulative animation of the track:
 
 <span id="animateTrack"></span>
 ```{r animateTrack, echo = TRUE, eval = FALSE}
-myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'chlorophyll',
+myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'algae',
                     animate = TRUE, cumulative = TRUE)
 
 ```
@@ -232,7 +232,7 @@ xlim <- c(-160, -105)
 topoInfo <- rerddap::info('etopo360')
 topo <- rxtracto(topoInfo, parameter = 'altitude', xcoord = xpos, ycoord = ypos, xlen = .1, ylen = .1)
 myFunc = function(x) -x
-topoPlot <- plotTrack(topo, xpos, ypos, NA, plotColor = 'density', name = 'Depth', myFunc = myFunc)
+topoPlot <- plotTrack(topo, xpos, ypos, NA, plotColor = 'dense', name = 'Depth', myFunc = myFunc)
 topoPlot
 ```
 
@@ -325,7 +325,7 @@ We can map the data using `plotBBox()`:
 require("ggplot2")
 require("plotdap")
 myFunc <- function(x) log(x)
-chlalogPlot <- plotBBox(VIIRS, plotColor = 'chlorophyll', myFunc = myFunc)
+chlalogPlot <- plotBBox(VIIRS, plotColor = 'algae', myFunc = myFunc)
 chlalogPlot
 ```
 
@@ -408,7 +408,7 @@ myFunc <- function(x) log(x)
 sanctchl1 <- sanctchl
 sanctchl1$chla <- sanctchl1$chla[, , 2]
 sanctchl1$time <- sanctchl1$time[2]
-sanctchlPlot <- plotBBox(sanctchl1, plotColor = 'chlorophyll', myFunc = myFunc)
+sanctchlPlot <- plotBBox(sanctchl1, plotColor = 'algae', myFunc = myFunc)
 sanctchlPlot
 ```
 
@@ -421,7 +421,7 @@ require("gganimate")
 require("ggplot2")
 require("plotdap")
 myFunc <- function(x) log(x)
-sanctchlPlot <- plotBBox(sanctchl, plotColor = 'chlorophyll', myFunc = myFunc, time = identity, animate = TRUE)
+sanctchlPlot <- plotBBox(sanctchl, plotColor = 'algae', myFunc = myFunc, time = identity, animate = TRUE)
 ```
 
 ![Sanctuary Animation](sanctuary.gif)
@@ -444,7 +444,7 @@ Mapping the data to show the canyon:
 require("ggplot2")
 require("mapdata")
 myFunc = function(x) -x
-bathyPlot <- suppressMessages((plotBBox(bathy, plotColor = 'density', myFunc = myFunc, name = 'Depth')))
+bathyPlot <- suppressMessages((plotBBox(bathy, plotColor = 'dense', myFunc = myFunc, name = 'Depth')))
 bathyPlot
 ```
 
@@ -470,7 +470,7 @@ str(soda70)
 ```{r soda70Plot, fig.width = 6, fig.height = 3, fig.align = 'center', warning = FALSE}
 require("ggplot2")
 require("plotdap")
-sodaPlot <- plotBBox(soda70, plotColor = 'temperature', name = 'temp_at_70m', maxpixels = 30000)
+sodaPlot <- plotBBox(soda70, plotColor = 'thermal', name = 'temp_at_70m', maxpixels = 30000)
 sodaPlot
 
 ```
@@ -497,7 +497,7 @@ NAtlSSS <- rxtracto_3D(dataInfo, parameter = parameter, xcoord = sssLons, ycoord
 ```{r NAtlSSSplot, eval = FALSE, echo = TRUE}
 require("ggplot2")
 require("plotdap")
-NAtlSSSPlot <- plotBBox(NAtlSSS, plotColor = 'salinity', name = "salinity", maxpixels = 30000)
+NAtlSSSPlot <- plotBBox(NAtlSSS, plotColor = 'haline', name = "salinity", maxpixels = 30000)
 NAtlSSSPlot
 ```
 
@@ -537,8 +537,8 @@ Plotting the results using `plotBBox()`:
 ```{r ifrPSALplot, fig.width = 6, fig.height = 3, fig.align='center', warning = FALSE}
 require("ggplot2")
 require("plotdap")
-ifrPSALPlot <- plotBBox(ifrPSAL, plotColor = 'salinity', name = "salinity", maxpixels = 30000)
-print(ifrPSALPlot)
+ifrPSALPlot <- plotBBox(ifrPSAL, plotColor = 'haline', name = "salinity", maxpixels = 30000)
+ifrPSALPlot
 ```