fixes for CRAN (release 2.5.8)

NAMESPACE

@@ -1,98 +1,102 @@
-# R 3.3 compatibility:
-importFrom("grDevices", "rgb", "convertColor")
-
-importFrom("graphics", "axis", "legend", "mtext", "rect", "segments",
-             "text", "plot")
-
-importFrom("stats", "aggregate", "complete.cases", "na.omit", "as.formula", "splinefun", "weighted.mean")
-
-importFrom("utils", "URLencode", "download.file", "object.size",
-             "read.csv", "read.table", "setTxtProgressBar",
-             "txtProgressBar", "write.table", "type.convert")
-
-importFrom("methods", "slot<-")
-
-importFrom(reshape2, 
-  dcast,
-  melt
-)
-
-importFrom(raster,
-  readAll,
-  raster,
-  extent
-)
-
-importFrom(lattice, 
-  panel.abline
-)
-
-importFrom(plyr, 
-  ddply,
-  llply,
-  ldply,
-  dlply,
-  join,
-  summarize
-)
-
-
-importFrom(sp,
-  spTransform,
-  CRS,
-  proj4string,
-  "coordinates<-",
-  "proj4string<-",
-  SpatialPolygonsDataFrame,
-  SpatialPointsDataFrame,
-  SpatialPoints,
-  spChFIDs
-)
-
-importFrom(curl,
-  curl,
-  new_handle
-)
-
-importFrom(xml2,
-  read_html,
-  xml_text
-)
-
-
-importFrom(aqp, 
-  "depths<-", 
-  "site<-",
-  site,
-  idname,
-  parseMunsell,
-  diagnostic_hz,
-  horizonDepths,
-  "diagnostic_hz<-",
-  restrictions,
-  "restrictions<-",
-  SoilTextureLevels,
-  hzDepthTests, 
-  munsell2rgb,
-  rgb2munsell,
-  horizons,
-  "horizons<-",
-  metadata,
-  "metadata<-",
-  hzidname,
-  "hzidname<-",
-  hzdesgnname,
-  'hzdesgnname<-',
-  hztexclname,
-  'hztexclname<-',
-  profile_id
-)
-
-importMethodsFrom(aqp, "plot")
-importMethodsFrom(aqp, "length")
-importMethodsFrom(aqp, "nrow")
-importClassesFrom(aqp, "SoilProfileCollection")
-
-
-
-exportPattern("^[^\\.]")
+# R 3.3 compatibility:
+importFrom("grDevices", "rgb", "convertColor")
+
+importFrom("graphics", "axis", "legend", "mtext", "rect", "segments",
+             "text", "plot")
+
+importFrom("stats", "aggregate", "complete.cases", "na.omit", "as.formula", "splinefun", "weighted.mean")
+
+importFrom("utils", "URLencode", "download.file", "object.size",
+             "read.csv", "read.table", "setTxtProgressBar",
+             "txtProgressBar", "write.table", "type.convert")
+
+importFrom("methods", "slot<-")
+
+importFrom(data.table, 
+           data.table,
+           as.data.table)
+
+importFrom(reshape2, 
+  dcast,
+  melt
+)
+
+importFrom(raster,
+  readAll,
+  raster,
+  extent
+)
+
+importFrom(lattice, 
+  panel.abline
+)
+
+importFrom(plyr, 
+  ddply,
+  llply,
+  ldply,
+  dlply,
+  join,
+  summarize
+)
+
+
+importFrom(sp,
+  spTransform,
+  CRS,
+  proj4string,
+  "coordinates<-",
+  "proj4string<-",
+  SpatialPolygonsDataFrame,
+  SpatialPointsDataFrame,
+  SpatialPoints,
+  spChFIDs
+)
+
+importFrom(curl,
+  curl,
+  new_handle
+)
+
+importFrom(xml2,
+  read_html,
+  xml_text
+)
+
+
+importFrom(aqp, 
+  "depths<-", 
+  "site<-",
+  site,
+  idname,
+  parseMunsell,
+  diagnostic_hz,
+  horizonDepths,
+  "diagnostic_hz<-",
+  restrictions,
+  "restrictions<-",
+  SoilTextureLevels,
+  hzDepthTests, 
+  munsell2rgb,
+  rgb2munsell,
+  horizons,
+  "horizons<-",
+  metadata,
+  "metadata<-",
+  hzidname,
+  "hzidname<-",
+  hzdesgnname,
+  'hzdesgnname<-',
+  hztexclname,
+  'hztexclname<-',
+  profile_id,
+  aqp_df_class,
+  'aqp_df_class<-'
+)
+
+importMethodsFrom(aqp, "plot")
+importMethodsFrom(aqp, "length")
+importMethodsFrom(aqp, "nrow")
+importClassesFrom(aqp, "SoilProfileCollection")
+
+exportPattern("^[^\\.]")

NEWS.md

@@ -12,6 +12,7 @@
  * bug fix for `fetchSDA_spatial` with `chunk.size` > 1 resulting in duplicate data in result
  * major improvements to `fetchSDA_spatial` to handle queries that exceed JSON Serialization Limit
  * add `fetchSoilGrids` for point data queries to SoilGrids v2 API with SoilProfileCollection output
+ * `fetchKSSL(..., returnGeochemicalData=TRUE)` now returns geochemical, optical and XRD/thermal data
 
 # soilDB 2.5.6 (2020-06-16)
  * bug fixes in `fetchKSSL` related to vectorization, all arguments vectorized except for `bbox`

R/SDA-spatial.R

@@ -24,7 +24,7 @@
 #' @param g name of column in \code{d} containing WKT geometry
 #' @param p4s PROJ4 CRS definition, typically GCS WGS84
 #' 
-#' @details The SDA website can be found at \url{http://sdmdataaccess.nrcs.usda.gov}. See the \href{http://ncss-tech.github.io/AQP/soilDB/SDA-tutorial.html}{SDA Tutorial} for detailed examples.
+#' @details The SDA website can be found at \url{https://sdmdataaccess.nrcs.usda.gov}. See the \href{http://ncss-tech.github.io/AQP/soilDB/SDA-tutorial.html}{SDA Tutorial} for detailed examples.
 #' 
 #' @note This function requires the `httr`, `jsonlite`, `XML`, and `rgeos` packages.
 #' 

R/SDA_query.R

@@ -91,7 +91,7 @@ format_SQL_in_statement <- function(x) {
 #' 
 #' @description Submit a query to the Soil Data Access (SDA) REST/JSON web-service and return the results as a data.frame. There is a 100,000 record limit and 32Mb JSON serializer limit, per query. Queries should contain a WHERE statement or JOIN condition to limit the number of rows affected / returned. Consider wrapping calls to \code{SDA_query} in a function that can iterate over logical chunks (e.g. areasymbol, mukey, cokey, etc.). The function \code{makeChunks} can help with such iteration.
 #' 
-#' @details The SDA website can be found at \url{http://sdmdataaccess.nrcs.usda.gov} and query examples can be found at \url{http://sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx}. A library of query examples can be found at \url{https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=SDA-SQL_Library_Home}.
+#' @details The SDA website can be found at \url{https://sdmdataaccess.nrcs.usda.gov} and query examples can be found at \url{https://sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx}. A library of query examples can be found at \url{https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=SDA-SQL_Library_Home}.
 #' 
 #' SSURGO (detailed soil survey) and STATSGO (generalized soil survey) data are stored together within SDA. This means that queries that don't specify an area symbol may result in a mixture of SSURGO and STATSGO records. See the examples below and the \href{http://ncss-tech.github.io/AQP/soilDB/SDA-tutorial.html}{SDA Tutorial} for details.
 #' 

R/mapunit_geom_by_ll_bbox.R

@@ -8,7 +8,7 @@
 #' 
 #' @param bbox 	a bounding box in WGS coordinates
 #' @param source the source database, currently limited to soil data access (SDA)
-#' @details The SDA website can be found at http://sdmdataaccess.nrcs.usda.gov. See examples for bounding box formatting.
+#' @details The SDA website can be found at \url{https://sdmdataaccess.nrcs.usda.gov}. See examples for bounding box formatting.
 #' @return A SpatialPolygonsDataFrame of map unit polygons, in WGS84 (long,lat) coordinates.
 #' @note SDA does not return the spatial intersection of map unit polygons and bounding box. Rather, just those polygons that are completely within the bounding box / overlap with the bbox. This function requires the 'rgdal' package.
 #' 

man/OSDquery.Rd

@@ -54,8 +54,7 @@
 \value{a \code{data.frame} object containing soil series names that match patterns supplied as arguments.}
 
 \references{
-
-  \url{http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/home/?cid=nrcs142p2_053587}
+  \url{https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/home/?cid=nrcs142p2_053587}
 }
 
 \author{D.E. Beaudette}

man/us_ss_timeline.Rd

@@ -30,55 +30,4 @@ This data was web scraped from the NRCS Soils Website. The scraping procedure an
 https://www.nrcs.usda.gov/wps/portal/nrcs/soilsurvey/soils/survey/state/
 }
 
-\examples{
-\donttest{
-if (requireNamespace("curl") &
-    curl::has_internet() &
-    require("XML") & 
-    require("RCurl") &
-    require("ggplot2") & 
-    require("gridExtra")
-) {
-
-data(state)
-st <- paste0(c(state.abb, "PR", "DC", "VI", "PB"))
-us_ss_timeline <- {
-  lapply(st, function(x) {
-    cat("getting", x, "\n")
-    url <- getURL(paste0(
-      "https://www.nrcs.usda.gov/wps/portal/nrcs/surveylist/soils/survey/state/?stateId=", x)
-    )
-    df  <- readHTMLTable(url, which = 22, stringsAsFactors = FALSE)
-    df$state <- x
-    return(df)
-  }) ->.;
-  do.call("rbind", .) ->.;
-  names(.) <- c("ssa", "year", "pdf", "wss", "state")
-  .[!grepl(.$year, pattern="current"), ] ->.;
-}
-us_ss_timeline <- within(us_ss_timeline, {
-  ssa  = sapply(ssa, function(x) strsplit(x, "\r")[[1]][1])
-  year = as.numeric(substr(year, 3,6))
-  pdf  = ifelse(pdf == "Yes", TRUE, FALSE)
-  wss  = NULL
-})
-
-test <- as.data.frame(table(us_ss_timeline$year), stringsAsFactors = FALSE)
-
-g1 <- ggplot(data = test, aes(x = Var1, y = Freq)) +
-  geom_histogram(stat = "identity") + 
-  xlab("Year") + 
-  ylab("Count") +
-  theme(aspect.ratio = 1) + 
-  ggtitle("Number of Published \n US Soil Surveys by Year")
-g2 <- ggplot(test, aes(x = Var1, y = cumsum(Freq))) +
-  geom_histogram(stat = "identity") + 
-  xlab("Year") + 
-  ylab("Count") +
-  theme(aspect.ratio = 1) +
-  ggtitle("Cumulative Number of Published \n US Soil Surveys by Year")
-
-grid.arrange(g1, g2, ncol = 2)
-
-}}}
 \keyword{datasets}

misc/man-deprecated/fetchOSD.Rd

@@ -63,7 +63,7 @@ These last two cases are problematic for analysis that makes use of morphology a
 \value{a \code{SoilProfileCollection} object containing basic soil morphology and taxonomic information.}
 
 \references{
-USDA-NRCS OSD search tools: \url{http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/home/?cid=nrcs142p2_053587}
+USDA-NRCS OSD search tools: \url{https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/home/?cid=nrcs142p2_053587}
 }
 
 \author{D.E. Beaudette}