Fix or remove dead links

inst/CITATION

@@ -30,5 +30,5 @@ bibentry(bibtype = "Manual",
 	 author = c(person("Sean", "Tuck"), person("Helen", "Phillips")),
 	 year = year,
 	 note = note,
-	 url = "http://cran.r-project.org/package=MODISTools"
+	 url = "https://cran.r-project.org/package=MODISTools"
 )

man/GetBands.Rd

@@ -8,11 +8,7 @@
 }
 \value{A character vector; containing the codes for each data band.}
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSubsets]{MODISSubsets}}}

man/GetDates.Rd

@@ -10,11 +10,7 @@
 }
 \value{A character vector; each element representing a time-step (in MODIS date format) where data is available.}
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSubsets]{MODISSubsets}}}

man/GetProducts.Rd

@@ -6,11 +6,7 @@
 \arguments{No input.}
 \value{A character vector; containing the codes for each product.}
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSubsets]{MODISSubsets}}}

man/GetSubset.Rd

@@ -27,11 +27,7 @@ subset=The downloaded data, as a vector of character strings, with length number
 
 This data frame is then passed to MODISSubsets.}
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSubsets]{MODISSubsets}}}

man/MODISGrid.Rd

@@ -13,12 +13,12 @@
   }
   \item{SubDir}{Logical; if TRUE, all ASCII raster grids created from one MODIS data file will be collected under a subdirectory, within \code{DirName}, that has the same name as the MODIS data file from which it was created. If FALSE all ASCII raster grids will simply be written to \code{DirName}, with no nested file structure.
   }
-  \item{NoDataValues}{Named list; the no data values for all the data bands contained in the files. Should be specified as a list of vectors: the names for the list elements should be the product codes and each element should contain a named vector of no data values for bands within that product. For guidance, see the example below. All data bands found in the MODIS data files should be listed in this argument. These values are neccessary to identify pixels with missing data. The correct no data values for the data bands of interest can be found at \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}.
+  \item{NoDataValues}{Named list; the no data values for all the data bands contained in the files. Should be specified as a list of vectors: the names for the list elements should be the product codes and each element should contain a named vector of no data values for bands within that product. For guidance, see the example below. All data bands found in the MODIS data files should be listed in this argument. These values are neccessary to identify pixels with missing data. The correct no data values for the data bands of interest can be found at on the ORNL LPDAAC website.
   }
 }
 \details{A raster grid file is created for each grid found in a MODIS data file (i.e. a new file is written for each date that occurs in a time series). In other words, where the MODIS data file may follow a tile of pixels over time, the raster grids split up each tile to create a new file for that tile at each new date. Therefore, multiple raster grids may be created from one MODIS data file. These files can be stored in one directory or nested in subdirectories for each MODIS data file, using the optional argument \code{SubDir}. By default, the subdirectories are created to retain the spatial structure.
 
-The data are in the MODIS projection system. To combine a raster grid with a projection, the two files must be stored in the same directory with the same file name. Every raster grid needs a respective PRJ file. The projection (PRJ) file for each ASCII raster grid is included in the function output. This PRJ file can be accessed online at \url{https://daac.ornl.gov/MODIS/modis.prj}.
+The data are in the MODIS projection system. To combine a raster grid with a projection, the two files must be stored in the same directory with the same file name. Every raster grid needs a respective PRJ file. The projection (PRJ) file for each ASCII raster grid is included in the function output.
 }
 \value{Multiple ASCII raster grid files, with PRJ files, containing a tile of MODIS pixels at a given date, either all written to one directory or separated into subdirectories for each MODIS data file found. The file names for each raster grid created are composed of the following: "GRID_", the file name of the relevant MODIS data file, the data band that the grid pertains to, and finally the MODIS acquisition date for the grid (in Julian date format).
 }

man/MODISSubsets.Rd

@@ -31,11 +31,7 @@ SaveDir = ".", StartDate = FALSE, TimeSeriesLength = 0, Transect = FALSE)
 \value{An ASCII file written for each unique time-series (unique location, or unique time-series at a duplicated location), containing all data requested, for each band, for every pixel in the specified tile size. A subset download CSV file will also be written, that contains all the unique time-series information, and a status report for each time-series telling the user if the respective time-series was downloaded successfully or identifying any problems with that particular download.
 }
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link{MODISSummaries}}

man/MODISSummaries.Rd

@@ -55,11 +55,7 @@ One file (MODIS_Summary...) contains summary statistics and computed values for
 The second file (MODIS_Data...) that has the information from the original file inputted (which should have been used in MODISSubsets too) with computed means of the MODIS data tagged on, coupling the input with the output in one form ready for use, such as modelling. In the second file, each nth column of MODIS data, if more than one, will be for each pixel within the whole tile of n pixels collected for the time-series on that row.
 }
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{ \code{\link[MODISTools:MODISSubsets]{MODISSubsets}}

man/MODISTools-package.Rd

@@ -6,11 +6,7 @@
 \details{Imports RCurl and XML. The main purpose of this package is to employ the MODIS SOAP Web Service to remotely interrogate the MODIS archive and locally download the requested datasets. The most important function is MODISSubsets, which allows the user to request subsets from a given MODIS product for multiple time-series. Each time-series is defined by a coordinate location (WGS-1984), a specified surrounding extent of pixels, and a start and end date. The relevant MODIS product data is then extracted for these location/time combinations. Automating this as a batch process greatly reduces time, effort, and human error. Alternatively, MODISTransects expands upon MODISSubsets by extracting MODIS data along a transect, and its surrounding neighbourhood. Downloaded subsets are saved in ascii files, which are then accessed by MODISSummaries for computing summary statistics. It also organises downloaded data back with the original input data into a csv file that can be easily used for modelling; this provides efficient storage of data and a transparent process from data collection, to processing, to a form that is ready for final use.}
 \author{Sean Tuck}
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 
   \url{https://cran.r-project.org/package=RCurl}
 

man/MODISTransects.Rd

@@ -33,11 +33,7 @@ The transects lengths requested must be longer than the requested pixel size. Th
 \value{ASCII file written for each location, containing the specified time-series for each band of data requested. File name states the transect ID that the location is within, and a unique ID for that specific location.
 }
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSubsets]{MODISSubsets}}}

man/QualityCheck.Rd

@@ -28,11 +28,7 @@ QualityCheck(Data, Product, Band, NoDataFill, QualityBand, QualityScores,
 \value{Data, as it was, but with poor quality data and no data fill values replaced with NAs.
 }
 \references{
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html}
-
-  \url{https://daac.ornl.gov/MODIS/MODIS-menu/products.html}
-
-  \url{https://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
+  \url{https://daacmodis.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl}
 }
 \author{Sean Tuck}
 \seealso{\code{\link[MODISTools:MODISSummaries]{MODISSummaries}}}

man/WritePRJ.Rd

@@ -11,7 +11,7 @@ WritePRJ(Path)
   \item{Path}{The file path for the MODIS PRJ file that will be written.
   }
 }
-\value{A PRJ (plain text) file containing the definitions for the MODIS projection system. This PRJ file can be accessed online at \url{https://daac.ornl.gov/MODIS/modis.prj}.
+\value{A PRJ (plain text) file containing the definitions for the MODIS projection system.
 }
 \author{Sean Tuck
 }

man/daacmodis.Rd

@@ -1,6 +1,7 @@
 \name{daacmodis}
 \alias{daac}
 \alias{daacmodis}
+\alias{wsdl_loc}
 \docType{data}
 \title{
 Base URLs for MODIS downloads and the web service location