Merge pull request #227 from jread-usgs/master

vignette for CRAN v1.1.3

inst/doc/geoknife.R

@@ -0,0 +1,231 @@
+## ----setup, include=FALSE---------------------------------
+library(rmarkdown)
+options(continue=" ")
+options(width=60)
+library(knitr)
+library(geoknife)
+
+
+## ---- eval=FALSE------------------------------------------
+#  install.packages("geoknife",
+#      repos = c("http://owi.usgs.gov/R","http://cran.rstudio.com/"),
+#      dependencies = TRUE)
+
+## ---- eval=FALSE------------------------------------------
+#  install.packages("devtools")
+#  devtools::install_github('USGS-R/geoknife')
+
+## ---------------------------------------------------------
+library(geoknife)
+
+## ---------------------------------------------------------
+stencil <- simplegeom(c(-89, 46.23))
+
+## ---------------------------------------------------------
+stencil <- simplegeom(data.frame(
+              'point1' = c(-89, 46), 
+              'point2' = c(-88.6, 45.2)))
+
+## ---------------------------------------------------------
+stencil <- webgeom('state::New Hampshire')
+stencil <- webgeom('state::New Hampshire,Wisconsin,Alabama')
+
+## ---------------------------------------------------------
+stencil <- webgeom('HUC8::09020306,14060009')
+# display stencil:
+stencil
+
+## ---------------------------------------------------------
+HUCs <- query(stencil, 'values')
+# there are thousands of results, but head() will only display a few of them
+head(HUCs) 
+
+## ---------------------------------------------------------
+fabric <- webdata('prism')
+fabric
+
+## ---------------------------------------------------------
+times(fabric) <- c('1990-01-01','2010-01-01')
+variables(fabric) <- c('ppt','tmx', 'tmn')
+fabric
+
+## ---------------------------------------------------------
+job <- geoknife(stencil, fabric)
+
+## ---------------------------------------------------------
+check(job)
+running(job)
+error(job)
+successful(job)
+
+## ---------------------------------------------------------
+job <- cancel(job)
+
+## ---------------------------------------------------------
+job <- geoknife(stencil, fabric, wait = TRUE)
+
+## ---- fig.height=3.5, fig.width=7-------------------------
+data <- result(job)
+plot(data[,1:2], ylab = variables(fabric))
+
+## ---- eval=FALSE------------------------------------------
+#  job <- geoknife(webgeom('state::Wisconsin'), fabric = 'prism', email = '[email protected]')
+
+## ---------------------------------------------------------
+stencil <- simplegeom(c(-89, 45.43))
+
+## ---------------------------------------------------------
+stencil <- simplegeom(data.frame(
+              'point1' = c(-89, 46), 
+              'point2' = c(-88.6, 45.2)))
+
+## ---------------------------------------------------------
+library(sp)
+Sr1 = Polygon(cbind(c(2,4,4,1,2),c(2,3,5,4,2)))
+Sr2 = Polygon(cbind(c(5,4,2,5),c(2,3,2,2)))
+Sr3 = Polygon(cbind(c(4,4,5,10,4),c(5,3,2,5,5)))
+Sr4 = Polygon(cbind(c(5,6,6,5,5),c(4,4,3,3,4)), hole = TRUE)
+
+Srs1 = Polygons(list(Sr1), "s1")
+Srs2 = Polygons(list(Sr2), "s2")
+Srs3 = Polygons(list(Sr3, Sr4), "s3/4")
+stencil <- simplegeom(Srl = list(Srs1,Srs2,Srs3), proj4string = CRS("+proj=longlat +datum=WGS84"))
+
+## ---------------------------------------------------------
+stencil <- webgeom()
+
+## ---------------------------------------------------------
+stencil
+
+## ---------------------------------------------------------
+geom(stencil) <- "derivative:CONUS_States"
+version(stencil)
+attribute(stencil) <- "STATE"
+values(stencil) <- c("Wisconsin","Maine")
+
+## ---------------------------------------------------------
+stencil <- webgeom('state::Wisconsin')
+stencil
+query(stencil, 'values')
+webgeom('state::Wisconsin,Maine')
+webgeom('HUC8::09020306,14060009')
+webgeom('ecoregion::Colorado Plateaus,Driftless Area')
+
+head(query(webgeom('ecoregion::Colorado Plateaus,Driftless Area'), 'values'), 10)
+
+## ---------------------------------------------------------
+query(stencil, 'geoms')
+query(stencil, 'attributes')
+query(stencil, 'values')
+
+## ---------------------------------------------------------
+fabric <- webdata()
+
+## ---------------------------------------------------------
+fabric
+
+## ---------------------------------------------------------
+times(fabric)
+url(fabric) <- 'http://cida.usgs.gov/thredds/dodsC/prism'
+variables(fabric) <- 'ppt'
+
+times(fabric)[1] <- as.POSIXct('1990-01-01')
+
+## ---------------------------------------------------------
+webdatasets = query('webdata')
+length(webdatasets)
+
+## ---------------------------------------------------------
+webdatasets[61:65]
+
+## ---------------------------------------------------------
+title(webdatasets[87])
+abstract(webdatasets[87])
+
+## ---------------------------------------------------------
+fabric <- webdata(webdatasets[99])
+evapotran <- webdata(webdatasets['Monthly Conterminous U.S. actual evapotranspiration data'])
+
+## ---------------------------------------------------------
+times(fabric) <- c('1990-01-01','2005-01-01')
+
+## ---- eval=FALSE------------------------------------------
+#  query(fabric, 'times')
+#  query(fabric, 'variables')
+
+## ---------------------------------------------------------
+fabric = webdata(url='dods://apdrc.soest.hawaii.edu/dods/public_data/satellite_product/AVHRR/avhrr_mon')
+
+## ---- eval=FALSE------------------------------------------
+#  variables(fabric) <- 'sst'
+#  query(fabric, 'times')
+#  
+#  times(fabric) <- c('1990-01-01','1999-12-31')
+
+## ---- eval=FALSE------------------------------------------
+#  sst = result(geoknife(data.frame('caspian.sea'=c(51,40)), fabric, wait = TRUE))
+#  head(sst)
+#  july.idx <- months(sst$DateTime) == 'July'
+#  plot(sst$DateTime[july.idx], sst$caspian.sea[july.idx], type='l', lwd=2, col='dodgerblue', ylab='Sea Surface Temperature (degC)',xlab=NA)
+#  
+
+## ---------------------------------------------------------
+fabric = webdata('prism')
+variables(fabric) <- 'ppt'
+query(fabric, 'times')
+
+## ---------------------------------------------------------
+query(fabric, 'variables')
+
+## ---------------------------------------------------------
+variables(fabric) <- NA
+
+## ----eval=FALSE-------------------------------------------
+#  query(fabric, 'times')
+
+## ---------------------------------------------------------
+knife <- webprocess()
+query(knife, 'algorithms')
+
+## ---------------------------------------------------------
+url(knife) <- 'http://cida-test.er.usgs.gov/gdp/process/WebProcessingService'
+query(knife, 'algorithms')
+
+## ---------------------------------------------------------
+knife <- webprocess()
+algorithm(knife)
+algorithm(knife) <- query(knife, 'algorithms')[1]
+algorithm(knife)
+# -- or --
+algorithm(knife) <- list('Area Grid Statistics (weighted)' = 
+                           "gov.usgs.cida.gdp.wps.algorithm.FeatureWeightedGridStatisticsAlgorithm")
+
+## ---------------------------------------------------------
+url(knife)
+url(knife) <- 'http://cida-test.er.usgs.gov/gdp/process/WebProcessingService'
+
+## ---------------------------------------------------------
+knife <- webprocess(wait = TRUE)
+knife
+
+## ---------------------------------------------------------
+knife <- webprocess(email = '[email protected]')
+knife
+
+## ---------------------------------------------------------
+job <- geoknife(stencil, fabric = 'prism', wait = FALSE)
+check(job)
+
+## ---- eval=FALSE------------------------------------------
+#  running(job)
+#  error(job)
+#  successful(job)
+
+## ---------------------------------------------------------
+id(job)
+job <- cancel(job)
+id(job)
+
+## ---------------------------------------------------------
+cancel()
+