Merge pull request #31 from ropensci/fix-crs

Update projection following GDAL, PROJ
ropensci · Jul 2, 2020 · 2a5ce33 · 2a5ce33
2 parents 560bb7a + ddd3bf0
commit 2a5ce33
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -36,7 +36,7 @@ Suggests:
     rmarkdown,
     asnipe
 SystemRequirements: GEOS (>= 3.2.0)
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 BugReports: https://github.com/ropensci/spatsoc/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,5 @@
 # v 0.1.14 
+* updated tests, man and vignettes following new handling of projections in sp ([PR 31](https://github.com/ropensci/spatsoc/pull/31), [R spatial information](https://www.r-spatial.org/r/2020/03/17/wkt.html))
 * clarified explicit drop of NAs in dyadID in edge list vignette
 
 # v 0.1.13 (2020-03-25)

diff --git a/R/build_lines.R b/R/build_lines.R
@@ -3,11 +3,7 @@
 #'
 #' \code{build_lines} creates a \code{SpatialLines} object from a \code{data.table}. The function accepts a \code{data.table} with relocation data, individual identifiers a sorting column and a \code{projection}. The relocation data is transformed into \code{SpatialLines} for each individual and optionally, each \code{splitBy}. Relocation data should be in two columns representing the X and Y coordinates.
 #'
-#' The \code{DT} must be a \code{data.table}. If your data is a \code{data.frame}, you can convert it by reference using \code{\link[data.table:setDT]{data.table::setDT}}.
-#'
-#' The \code{id}, \code{coords}, \code{sortBy} (and optional \code{splitBy}) arguments expect the names of respective columns in \code{DT} which correspond to the individual identifier, X and Y coordinates, sorting column, and additional splitting columns.
-#'
-#' The \code{projection} expects a \code{PROJ.4} character string (such as those available on \url{https://spatialreference.org/}).
+#' The \code{projection} argument expects a character string defining the EPSG code. For example, for UTM zone 21N (EPSG 32736), the projection argument is "+init=epsg:32736". See \url{https://spatialreference.org/}) for a list of EPSG codes. Please note, R spatial has followed updates to GDAL and PROJ for handling projections, see more at \url{https://www.r-spatial.org/r/2020/03/17/wkt.html}.
 #'
 #' The \code{sortBy} is used to order the input \code{data.table} when creating \code{SpatialLines}. It must a \code{POSIXct} to ensure the rows are sorted by date time.
 #'
@@ -20,6 +16,7 @@
 #' An error is returned when an individual has less than 2 relocations, making it impossible to build a line.
 #'
 #' @inheritParams group_lines
+#' @inheritParams build_polys
 #'
 #' @export
 #'
@@ -38,8 +35,8 @@
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
-#' # Proj4 string for example data
-#' utm <- '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+#' # EPSG code for example data
+#' utm <- '+init=epsg:32736'
 #'
 #' # Build lines for each individual
 #' build_lines(DT, projection = utm, id = 'ID', coords = c('X', 'Y'),

diff --git a/R/build_polys.R b/R/build_polys.R
@@ -6,7 +6,7 @@
 #'
 #' The \code{id}, \code{coords} (and optional \code{splitBy}) arguments expect the names of respective columns in \code{DT} which correspond to the individual identifier, X and Y coordinates, and additional grouping columns.
 #'
-#' The \code{projection} expects a \code{PROJ.4} character string (such as those available on \url{https://spatialreference.org/}). \code{build_polys} expects planar coordinates (not unprojected latitude, longitude).
+#' The \code{projection} argument expects a character string defining the EPSG code. For example, for UTM zone 21N (EPSG 32736), the projection argument is "+init=epsg:32736". See \url{https://spatialreference.org/}) for a list of EPSG codes. Please note, R spatial has followed updates to GDAL and PROJ for handling projections, see more at \url{https://www.r-spatial.org/r/2020/03/17/wkt.html}.
 #'
 #' The \code{hrType} must be either one of "kernel" or "mcp". The \code{hrParams} must be a named list of arguments matching those of \code{adehabitatHR::kernelUD} and \code{adehabitatHR::getverticeshr} or \code{adehabitatHR::mcp}.
 #'
@@ -21,7 +21,7 @@
 #'
 #' @inheritParams group_polys
 #' @param spPts alternatively, provide solely a SpatialPointsDataFrame with one column representing the ID of each point.
-#'
+#' @param projection character string defining the EPSG code. For example, for UTM zone 21N (EPSG 32736), the projection argument is "+init=epsg:32736". See details.
 #' @export
 #'
 #' @family Build functions
@@ -37,8 +37,8 @@
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
-#' # Proj4 string for example data
-#' utm <- '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+#' # EPSG code for example data
+#' utm <- '+init=epsg:32736'
 #'
 #' # Build polygons for each individual using kernelUD and getverticeshr
 #' build_polys(DT, projection = utm, hrType = 'kernel',

diff --git a/R/get_gbi.R b/R/get_gbi.R
@@ -46,7 +46,8 @@
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #' DT[, yr := year(datetime)]
 #'
-#' utm <- '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+#' # EPSG code for example data
+#' utm <- '+init=epsg:32736'
 #'
 #' group_polys(DT, area = FALSE, hrType = 'mcp',
 #'             hrParams = list(percent = 95),

diff --git a/R/group_lines.R b/R/group_lines.R
@@ -19,11 +19,11 @@
 #' sorting, timegroup (generated by \code{group_times}) and additional grouping
 #' columns.
 #'
+#' The \code{projection} argument expects a character string defining the EPSG code. For example, for UTM zone 21N (EPSG 32736), the projection argument is "+init=epsg:32736". See \url{https://spatialreference.org/}) for a list of EPSG codes. Please note, R spatial has followed updates to GDAL and PROJ for handling projections, see more at \url{https://www.r-spatial.org/r/2020/03/17/wkt.html}.
+#'
 #' The \code{sortBy} is used to order the input \code{data.table} when creating
 #' \code{SpatialLines}. It must a \code{POSIXct} to ensure the rows are sorted
-#' by date time. The \code{projection} expects a \code{PROJ.4} character string
-#' (such as those available on \url{https://spatialreference.org/}). \code{group_lines}
-#' expects planar coordinates (not unprojected latitude, longitude).
+#' by date time.
 #'
 #' The \code{threshold} must be provided in the units of the coordinates. The
 #' \code{threshold} can be equal to 0 if strict overlap is required, else it
@@ -59,7 +59,7 @@
 #'
 #'
 #' @inheritParams group_pts
-#' @param projection PROJ.4 character string
+#' @inheritParams build_polys
 #' @param threshold The width of the buffer around the lines in the units of the
 #'   projection. Supply 0 to compare intersection without buffering.
 #' @param spLines Alternatively to providing a DT, provide a SpatialLines object
@@ -86,8 +86,8 @@
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
-#' # Proj4 string for example data
-#' utm <- '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+#' # EPSG code for example data
+#' utm <- '+init=epsg:32736'
 #'
 #' \donttest{group_lines(DT, threshold = 50, projection = utm, sortBy = 'datetime',
 #'             id = 'ID', coords = c('X', 'Y'))}

diff --git a/R/group_polys.R b/R/group_polys.R
@@ -13,14 +13,11 @@
 #' \code{data.frame}, you can convert it by reference using
 #' \code{\link[data.table:setDT]{data.table::setDT}}.
 #'
-#'
 #' The \code{id}, \code{coords} (and optional \code{splitBy}) arguments expect
 #' the names of respective columns in \code{DT} which correspond to the
 #' individual identifier, X and Y coordinates, and additional grouping columns.
 #'
-#' The \code{projection} expects a \code{PROJ.4} character string (such as those
-#' available on \url{https://spatialreference.org/}). \code{group_polys} expects planar
-#' coordinates (not unprojected latitude, longitude).
+#' The \code{projection} argument expects a character string defining the EPSG code. For example, for UTM zone 21N (EPSG 32736), the projection argument is "+init=epsg:32736". See \url{https://spatialreference.org/}) for a list of EPSG codes. Please note, R spatial has followed updates to GDAL and PROJ for handling projections, see more at \url{https://www.r-spatial.org/r/2020/03/17/wkt.html}.
 #'
 #' The \code{hrType} must be either one of "kernel" or "mcp". The
 #' \code{hrParams} must be a named list of arguments matching those of
@@ -48,6 +45,7 @@
 #'
 #' @inheritParams group_pts
 #' @inheritParams group_lines
+#' @inheritParams build_polys
 #' @param area boolean indicating either overlap group (when \code{FALSE}) or
 #'   area and proportion of overlap (when \code{TRUE})
 #' @param hrType type of HR estimation, either 'mcp' or 'kernel'
@@ -69,15 +67,15 @@
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
-#' # Proj4 string for example data
-#' utm <- '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+#' # EPSG code for example data
+#' utm <- '+init=epsg:32736'
 #'
-#' group_polys(DT, area = FALSE, 'mcp', list(percent = 95),
-#'             projection = utm,
+#' group_polys(DT, area = FALSE, hrType = 'mcp',
+#'             hrParams = list(percent = 95), projection = utm,
 #'             id = 'ID', coords = c('X', 'Y'))
 #'
-#' areaDT <- group_polys(DT, area = TRUE, 'mcp', list(percent = 95),
-#'                       projection = utm,
+#' areaDT <- group_polys(DT, area = TRUE, hrType = 'mcp',
+#'                       hrParams = list(percent = 95), projection = utm,
 #'                       id = 'ID', coords = c('X', 'Y'))
 group_polys <-
   function(DT = NULL,

diff --git a/codemeta.json b/codemeta.json
@@ -19,14 +19,14 @@
   ],
   "issueTracker": "https://github.com/ropensci/spatsoc/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.1.13",
+  "version": "0.1.14",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "4.0.0",
+    "version": "4.0.2",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.0.0 (2020-04-24)",
+  "runtimePlatform": "R version 4.0.2 (2020-06-22)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -227,7 +227,7 @@
   ],
   "releaseNotes": "https://github.com/ropensci/spatsoc//blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/spatsoc/blob/master/README.md",
-  "fileSize": "662.408KB",
+  "fileSize": "663.098KB",
   "contIntegration": "https://codecov.io/gl/robit.a/spatsoc",
   "developmentStatus": "http://www.repostatus.org/#active",
   "review": {

diff --git a/man/DT.Rd b/man/DT.Rd
diff --git a/man/build_lines.Rd b/man/build_lines.Rd
diff --git a/man/build_polys.Rd b/man/build_polys.Rd
diff --git a/man/get_gbi.Rd b/man/get_gbi.Rd
diff --git a/man/group_lines.Rd b/man/group_lines.Rd
diff --git a/man/group_polys.Rd b/man/group_polys.Rd
diff --git a/tests/testthat/test-build-lines.R b/tests/testthat/test-build-lines.R
@@ -4,8 +4,7 @@ library(spatsoc)
 
 DT <- fread('../testdata/DT.csv')
 
-utm <-
-  '+proj=utm +zone=36 +south +ellps=WGS84 +datum=WGS84 +units=m +no_defs'
+utm <- '+init=epsg:32736'
 
 DT[, datetime := as.POSIXct(datetime)]