Fixed vignette

ropensci · Mar 2, 2017 · e5cd8a4 · e5cd8a4
1 parent c6b08da
commit e5cd8a4
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Showing 19 changed files with 104 additions and 100 deletions.
diff --git a/R/MOPEX.R b/R/MOPEX.R
@@ -177,6 +177,7 @@ tsMOPEX <- function(stationID, plotOption = FALSE, timeExtent = NULL){
   #      6: daily minimum air temperature (Celsius)
 
   myTS <- zoo::zoo(x[,2:6], order.by = as.Date(x$date))
+  myTS$Q[myTS$Q == -99] <- NA
 
   if (!is.null(timeExtent)){
 

diff --git a/vignettes/TRMM.png b/vignettes/TRMM.png
diff --git a/vignettes/figure/unnamed-chunk-14-1.png b/vignettes/figure/unnamed-chunk-14-1.png
diff --git a/vignettes/figure/unnamed-chunk-18-1.png b/vignettes/figure/unnamed-chunk-18-1.png
diff --git a/vignettes/figure/unnamed-chunk-18-2.png b/vignettes/figure/unnamed-chunk-18-2.png
diff --git a/vignettes/figure/unnamed-chunk-19-1.png b/vignettes/figure/unnamed-chunk-19-1.png
diff --git a/vignettes/figure/unnamed-chunk-22-1.png b/vignettes/figure/unnamed-chunk-22-1.png
diff --git a/vignettes/figure/unnamed-chunk-24-1.png b/vignettes/figure/unnamed-chunk-24-1.png
diff --git a/vignettes/hddtools_vignette.R b/vignettes/hddtools_vignette.R
@@ -1,4 +1,4 @@
-## ----echo=FALSE----------------------------------------------------------
+## ----init, echo=FALSE----------------------------------------------------
 knitr::opts_chunk$set(
   comment = "#>",
   collapse = TRUE,
@@ -8,22 +8,22 @@ knitr::opts_chunk$set(
   eval = FALSE
 )
 
-## ------------------------------------------------------------------------
+## ----dependencies--------------------------------------------------------
 #  packs <- c("zoo", "sp", "RCurl", "XML", "rnrfa", "Hmisc", "raster",
 #             "stringr", "devtools", "leaflet")
 #  new_packages <- packs[!(packs %in% installed.packages()[,"Package"])]
 #  if(length(new_packages)) install.packages(new_packages)
 
-## ------------------------------------------------------------------------
+## ----installation1-------------------------------------------------------
 #  install.packages("hddtools")
 
-## ------------------------------------------------------------------------
+## ----installation2-------------------------------------------------------
 #  devtools::install_github("ropensci/hddtools")
 
-## ---- eval = TRUE--------------------------------------------------------
+## ----loading, eval = TRUE------------------------------------------------
 library("hddtools")
 
-## ---- eval = TRUE--------------------------------------------------------
+## ----KGClimateClass, eval = TRUE-----------------------------------------
 # Define a bounding box
 areaBox <- raster::extent(-10, 5, 48, 62)
 
@@ -33,32 +33,32 @@ KGClimateClass(areaBox = areaBox, updatedBy = "Peel")
 # Extract climate zones from Kottek's map:
 KGClimateClass(areaBox = areaBox, updatedBy = "Kottek")
 
-## ---- eval = FALSE-------------------------------------------------------
+## ----catalogueGRDC1, eval = FALSE----------------------------------------
 #  # GRDC full catalogue
 #  GRDC_catalogue_all <- catalogueGRDC()
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC2------------------------------------------------------
 #  # Filter GRDC catalogue based on a country code
 #  GRDC_catalogue_countrycode <- catalogueGRDC(columnName = "country_code",
 #                                              columnValue = "IT")
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC3------------------------------------------------------
 #  # Filter GRDC catalogue based on rivername
 #  GRDC_catalogue_river <- catalogueGRDC(columnName = "river", columnValue = "PO")
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC4------------------------------------------------------
 #  # Filter GRDC catalogue based on numerical value, for instance select all the stations for which daily data is available since 2000
 #  GRDC_catalogue_dstart <- catalogueGRDC(columnName = "d_start",
 #                                         columnValue = ">=2000")
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC5------------------------------------------------------
 #  # Define a bounding box
 #  areaBox <- raster::extent(-10, 5, 48, 62)
 #  
 #  # Filter GRDC catalogue based on a bounding box
 #  GRDC_catalogue_bbox <- catalogueGRDC(areaBox = areaBox)
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC6------------------------------------------------------
 #  # Define a bounding box
 #  areaBox <- raster::extent(-10, 5, 48, 62)
 #  
@@ -67,19 +67,19 @@ KGClimateClass(areaBox = areaBox, updatedBy = "Kottek")
 #                                             columnName = "statistics",
 #                                             columnValue = 1)
 
-## ------------------------------------------------------------------------
+## ----catalogueGRDC7------------------------------------------------------
 #  # Visualise outlets on an interactive map
 #  library(leaflet)
 #  leaflet(data = GRDC_catalogue_bbox_stats) %>%
 #    addTiles() %>%  # Add default OpenStreetMap map tiles
 #    addMarkers(~long, ~lat, popup = ~station)
 
-## ---- eval = TRUE--------------------------------------------------------
-# Monthly data extraction
-WolfeToneBridge <- tsGRDC(stationID = catalogueGRDC()$grdc_no[7126],
-                          plotOption = TRUE)
+## ----tsGRDC--------------------------------------------------------------
+#  # Monthly data extraction
+#  WolfeToneBridge <- tsGRDC(stationID = catalogueGRDC()$grdc_no[7126],
+#                            plotOption = TRUE)
 
-## ---- eval = FALSE-------------------------------------------------------
+## ----TRMM----------------------------------------------------------------
 #  # Define a bounding box
 #  areaBox <- raster::extent(-10, 5, 48, 62)
 #  
@@ -92,57 +92,57 @@ WolfeToneBridge <- tsGRDC(stationID = catalogueGRDC()$grdc_no[7126],
 #  library(raster)
 #  plot(TRMMfile)
 
-## ---- eval = TRUE--------------------------------------------------------
+## ----catalogueData60UK1, eval = TRUE-------------------------------------
 # Data60UK full catalogue
 Data60UK_catalogue_all <- catalogueData60UK()
 
 # Filter Data60UK catalogue based on bounding box
 areaBox <- raster::extent(-4, -3, 51, 53)
 Data60UK_catalogue_bbox <- catalogueData60UK(areaBox = areaBox)
 
-## ------------------------------------------------------------------------
+## ----catalogueData60UK2--------------------------------------------------
 #  # Visualise outlets on an interactive map
 #  library(leaflet)
 #  leaflet(data = Data60UK_catalogue_bbox) %>%
 #    addTiles() %>%  # Add default OpenStreetMap map tiles
 #    addMarkers(~Longitude, ~Latitude, popup = ~Location)
 
-## ---- eval = TRUE--------------------------------------------------------
-# Extract time series 
-stationID <- catalogueData60UK()$stationID[1]
-
-# Extract only the time series
-MorwickTS <- tsData60UK(stationID, plotOption = FALSE)
-plot(MorwickTS)
-
-# Extract time series for a specified temporal window
-twindow <- seq(as.Date("1988-01-01"), as.Date("1989-12-31"), by = "days")
-MorwickTSplot <- tsData60UK(stationID = stationID, 
-                            plotOption = TRUE,
-                            twindow = twindow)
-
-## ---- eval = TRUE--------------------------------------------------------
-# MOPEX full catalogue
-MOPEX_catalogue_all <- catalogueMOPEX()
-
-# Extract time series 
-BroadRiver <- tsMOPEX(stationID = MOPEX_catalogue_all$stationID[1], 
-                      plotOption = TRUE)
+## ----catalogueData60UK3--------------------------------------------------
+#  # Extract time series
+#  stationID <- catalogueData60UK()$stationID[1]
+#  
+#  # Extract only the time series
+#  MorwickTS <- tsData60UK(stationID, plotOption = FALSE)
+#  plot(MorwickTS)
+#  
+#  # Extract time series for a specified temporal window
+#  twindow <- seq(as.Date("1988-01-01"), as.Date("1989-12-31"), by = "days")
+#  MorwickTSplot <- tsData60UK(stationID = stationID,
+#                              plotOption = TRUE,
+#                              twindow = twindow)
+
+## ----MOPEX---------------------------------------------------------------
+#  # MOPEX full catalogue
+#  MOPEX_catalogue_all <- catalogueMOPEX()
+#  
+#  # Extract time series
+#  BroadRiver <- tsMOPEX(stationID = MOPEX_catalogue_all$stationID[1],
+#                        plotOption = TRUE)
 
-## ---- eval = FALSE-------------------------------------------------------
+## ----SEPA1, eval = FALSE-------------------------------------------------
 #  # SEPA unofficial catalogue
 #  SEPA_catalogue_all <- catalogueSEPA()
 
-## ------------------------------------------------------------------------
+## ----SEPA2, eval = FALSE-------------------------------------------------
 #  # Single time series extraction
 #  Kilphedir <- tsSEPA(stationID = catalogueSEPA()$stationId[1],
 #                      plotOption = TRUE)
 
-## ---- eval = TRUE--------------------------------------------------------
-# Multiple time series extraction
-y <- tsSEPA(stationID = c("234253", "234174", "234305"))
-plot(y[[1]], ylim = c(0, max(y[[1]], y[[2]], y[[3]])), 
-     xlab = "", ylab = "Water level [m]")
-lines(y[[2]], col = "red")
-lines(y[[3]], col = "blue")
+## ----SEPA3---------------------------------------------------------------
+#  # Multiple time series extraction
+#  y <- tsSEPA(stationID = c("234253", "234174", "234305"))
+#  plot(y[[1]], ylim = c(0, max(y[[1]], y[[2]], y[[3]])),
+#       xlab = "", ylab = "Water level [m]")
+#  lines(y[[2]], col = "red")
+#  lines(y[[3]], col = "blue")