vignettes cleaned up and rebuilt

Author: peterson-tim-j

man/makeNetCDF_file.Rd

@@ -1,5 +1,5 @@
 ---
-title: "Make and update source data grids"
+title: "Make source data grids"
 description: >
   This vignette shows how to build the netCDF data file and then
   update it to new start and end dates.
@@ -10,7 +10,7 @@ vignette: >
   %\usepackage[utf8]{inputenc}
 ---
 
-``` r
+```{r setup}
 library(AWAPer, warn.conflicts = FALSE)
 ```
 This example shows how to build the required data files and then update them.

vignettes/A_Make_data_grids.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Make and update source data grids"
+title: "Make source data grids"
 description: >
   This vignette shows how to build the netCDF data file and then
   update it to new start and end dates.
@@ -10,7 +10,7 @@ vignette: >
   %\usepackage[utf8]{inputenc}
 ---
 
-``` r
+```{r setup}
 library(AWAPer, warn.conflicts = FALSE)
 ```
 This example shows how to build the required data files and then update them.

vignettes/A_Make_data_grids.Rnw

@@ -26,8 +26,14 @@ The first step is to create the netCDF files. Here only one netCDF file is creat
 
 The netCDF file contains grids of daily rainfall for all of Australia and is used below to extract data at points of interest. Often users run _makeNetCDF_file_ once to build netCDF data files that contain all variables over the entire record length (which requires ~5GB disk storage) and then use the netCDFs grids for multiple projects, rather than re-building the netCDF for each project. Also, if _makeNetCDF_file_ is run with the the netCDF file names pointing to existing files and _updateFrom=NA_ then the netCDF files will be updated to yesterday.
 
+To start to create the grids, the file name for the netCDF grids need to be defined. Here we'll just use temporary files. You should change this to a non-temporary file name and folder.
 ```{r}
-fnames = makeNetCDF_file(ncdfFilename ='AWAP_demo.nc',
+# Set names for netCDF files (in the system temp. directory).
+ncdfFilename = tempfile(fileext='.nc')
+```
+
+```{r}
+fnames = makeNetCDF_file(ncdfFilename = ncdfFilename,
                          updateFrom=as.Date("2010-08-01","%Y-%m-%d"),
                          updateTo=as.Date("2010-10-01","%Y-%m-%d"),
                          urlTmin=NA, urlTmax=NA, urlVprp=NA, urlSolarrad=NA)
@@ -50,7 +56,7 @@ Extract the daily precipitation at the two locations. The data is extracted from
 
 The other AWAPer variables are not extracted because _getTmin_, _getTmax_, _getVprp_, _getSolarrad_ and _getET_ are set to _F_. Note the netCDF file _ncdfFilename_ must be in the working directory or the full file path must be given.
 ```{r}
-climateData.data = extractCatchmentData(ncdfFilename='AWAP_demo.nc',
+climateData.data = extractCatchmentData(ncdfFilename=ncdfFilename,
                                         extractFrom=as.Date("2010-08-01","%Y-%m-%d"),
                                         extractTo=as.Date("2010-10-01","%Y-%m-%d"),
                                         locations=coordinates.data,
@@ -60,7 +66,7 @@ climateData.data = extractCatchmentData(ncdfFilename='AWAP_demo.nc',
 ## Plot the daily precipitation at each site
 Plot time series of the etracted daily precipitation.
 
-```{r}
+```{r, fig.width= 8, fig.heght=8}
 for (i in 1:nrow(coordinates.data)){
   filt = climateData.data$CatchmentID.ID == coordinates.data$ID[i]
 
@@ -77,8 +83,9 @@ legend('topright',legend=c('Bore-10084446','Rain-63005'),lty=2:3)
 ```
 
 ## Check AWAPer data against precipitation gauge date
-Use the following observed precipitation (from gauge_63005) to check the AWAPer data. Note, the observed data is hardcoded in and sourced from the Australian Bureau of Meteorology.
+Use the following observed precipitation (from gauge_63005) to check the AWAPer data.
 
+First let's hard-code in and sourced from the Australian Bureau of Meteorology.
 ```{r}
 obsPrecip <- data.frame(
   year= c(2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010,
@@ -91,16 +98,21 @@ obsPrecip <- data.frame(
   precip_mm = c(0.6, 5.2, 0.8, 0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 15.8, 15.6, 7.6, 0.7, 0.4, 1.4, 1.0, 0.0, 0.0, 30.4, 1.0, 0.0,
                 0.0, 5.0, 2.2, 0.3, 0.8, 13.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 13.8, 15.2, 0.4, 0.2, 0.0, 0.0, 12.4, 0.9,
                 0.0, 0.0, 0.1, 13.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.3, 0.0, 0.0, 0.0, 0.0))
+```
+Now let's compare the extracted rainfall against the gauge rainfall data.
+
+The left plot shows that the gauge and extracted data plot along the 1:1. This shows that the extracted data is unbiased. The scatter does, however, show that there is some difference in the estimates. This arises because the source grids are at a 0.05 degree resolution, or about 5 km x 5 km, and this introduces some error with the gauge is not at the centre of the grid cell and the location to be extracted is not also at the centre.
+
+```{r, fig.width= 8, fig.heght=8}
+par(mfrow = c(1, 2))
 
-# Plot the observed vs AWAPer rainfall at gauge ID 63005
 filt2 = climateData.data$CatchmentID.ID=='Rain-63005'
 plot(obsPrecip$precip_mm,climateData.data$precip_mm[filt2],
      xlim = c(0,35),ylim = c(0,35),
      main='Obs. vs. AWAPer precip.',
      xlab='Obs. [mm/d]', ylab='AWAPer [mm/d]', cex=0.2)
 abline(0,1, col='grey', lty=2)
 
-# Plot the cumulative observed vs AWAPer rainfall at gauge ID 63005
 plot(cumsum(obsPrecip$precip_mm),cumsum(climateData.data$precip_mm[filt2]),
      xlim = c(0,175),ylim = c(0,175),
      main='Cum. obs. vs. AWAPer precip.',

vignettes/B_Point_rainfall.Rmd

@@ -26,8 +26,14 @@ The first step is to create the netCDF files. Here only one netCDF file is creat
 
 The netCDF file contains grids of daily rainfall for all of Australia and is used below to extract data at points of interest. Often users run _makeNetCDF_file_ once to build netCDF data files that contain all variables over the entire record length (which requires ~5GB disk storage) and then use the netCDFs grids for multiple projects, rather than re-building the netCDF for each project. Also, if _makeNetCDF_file_ is run with the the netCDF file names pointing to existing files and _updateFrom=NA_ then the netCDF files will be updated to yesterday.
 
+To start to create the grids, the file name for the netCDF grids need to be defined. Here we'll just use temporary files. You should change this to a non-temporary file name and folder.
 ```{r}
-fnames = makeNetCDF_file(ncdfFilename ='AWAP_demo.nc',
+# Set names for netCDF files (in the system temp. directory).
+ncdfFilename = tempfile(fileext='.nc')
+```
+
+```{r}
+fnames = makeNetCDF_file(ncdfFilename = ncdfFilename,
                          updateFrom=as.Date("2010-08-01","%Y-%m-%d"),
                          updateTo=as.Date("2010-10-01","%Y-%m-%d"),
                          urlTmin=NA, urlTmax=NA, urlVprp=NA, urlSolarrad=NA)
@@ -50,7 +56,7 @@ Extract the daily precipitation at the two locations. The data is extracted from
 
 The other AWAPer variables are not extracted because _getTmin_, _getTmax_, _getVprp_, _getSolarrad_ and _getET_ are set to _F_. Note the netCDF file _ncdfFilename_ must be in the working directory or the full file path must be given.
 ```{r}
-climateData.data = extractCatchmentData(ncdfFilename='AWAP_demo.nc',
+climateData.data = extractCatchmentData(ncdfFilename=ncdfFilename,
                                         extractFrom=as.Date("2010-08-01","%Y-%m-%d"),
                                         extractTo=as.Date("2010-10-01","%Y-%m-%d"),
                                         locations=coordinates.data,
@@ -60,7 +66,7 @@ climateData.data = extractCatchmentData(ncdfFilename='AWAP_demo.nc',
 ## Plot the daily precipitation at each site
 Plot time series of the etracted daily precipitation.
 
-```{r}
+```{r, fig.width= 8, fig.heght=6}
 for (i in 1:nrow(coordinates.data)){
   filt = climateData.data$CatchmentID.ID == coordinates.data$ID[i]
 
@@ -77,8 +83,9 @@ legend('topright',legend=c('Bore-10084446','Rain-63005'),lty=2:3)
 ```
 
 ## Check AWAPer data against precipitation gauge date
-Use the following observed precipitation (from gauge_63005) to check the AWAPer data. Note, the observed data is hardcoded in and sourced from the Australian Bureau of Meteorology.
+Use the following observed precipitation (from gauge_63005) to check the AWAPer data.
 
+First let's hard-code in and sourced from the Australian Bureau of Meteorology.
 ```{r}
 obsPrecip <- data.frame(
   year= c(2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010,
@@ -91,16 +98,21 @@ obsPrecip <- data.frame(
   precip_mm = c(0.6, 5.2, 0.8, 0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 15.8, 15.6, 7.6, 0.7, 0.4, 1.4, 1.0, 0.0, 0.0, 30.4, 1.0, 0.0,
                 0.0, 5.0, 2.2, 0.3, 0.8, 13.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 13.8, 15.2, 0.4, 0.2, 0.0, 0.0, 12.4, 0.9,
                 0.0, 0.0, 0.1, 13.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.3, 0.0, 0.0, 0.0, 0.0))
+```
+Now let's compare the extracted rainfall against the gauge rainfall data.
+
+The left plot shows that the gauge and extracted data plot along the 1:1. This shows that the extracted data is unbiased. The scatter does, however, show that there is some difference in the estimates. This arises because the source grids are at a 0.05 degree resolution, or about 5 km x 5 km, and this introduces some error with the gauge is not at the centre of the grid cell and the location to be extracted is not also at the centre.
+
+```{r, fig.width= 8, fig.heght=6}
+par(mfrow = c(1, 2))
 
-# Plot the observed vs AWAPer rainfall at gauge ID 63005
 filt2 = climateData.data$CatchmentID.ID=='Rain-63005'
 plot(obsPrecip$precip_mm,climateData.data$precip_mm[filt2],
      xlim = c(0,35),ylim = c(0,35),
      main='Obs. vs. AWAPer precip.',
      xlab='Obs. [mm/d]', ylab='AWAPer [mm/d]', cex=0.2)
 abline(0,1, col='grey', lty=2)
 
-# Plot the cumulative observed vs AWAPer rainfall at gauge ID 63005
 plot(cumsum(obsPrecip$precip_mm),cumsum(climateData.data$precip_mm[filt2]),
      xlim = c(0,175),ylim = c(0,175),
      main='Cum. obs. vs. AWAPer precip.',