Merge pull request #38 from ropensci/fix-crs2

Fix crs (2)

R/build_lines.R

@@ -1,19 +1,37 @@
 #' Build Lines
 #'
 #'
-#' \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{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{splitBy} argument offers further control building \code{SpatialLines}. If in your \code{DT}, you have multiple temporal groups (e.g.: years) for example, you can provide the name of the column which identifies them and build \code{SpatialLines} for each individual in each year.
-#'
-#' \code{build_lines} is used by \code{group_lines} for grouping overlapping lines created from relocations.
-#'
-#' @return \code{build_lines} returns a \code{SpatialLines} object with a line for each individual (and optionally \code{splitBy} combination).
-#'
-#' An error is returned when an individual has less than 2 relocations, making it impossible to build a line.
+#' \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{projection} argument expects a character string defining the EPSG
+#' code. For example, for UTM zone 36N (EPSG 32736), the projection argument is
+#'  '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{splitBy} argument offers further control building \code{SpatialLines}.
+#' If in your \code{DT}, you have multiple temporal groups (e.g.: years) for
+#' example, you can provide the name of the column which identifies them and
+#' build \code{SpatialLines} for each individual in each year.
+#'
+#' \code{build_lines} is used by \code{group_lines} for grouping overlapping
+#' lines created from relocations.
+#'
+#' @return \code{build_lines} returns a \code{SpatialLines} object with a line
+#' for each individual (and optionally \code{splitBy} combination).
+#'
+#' 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
@@ -36,7 +54,7 @@
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
 #' # EPSG code for example data
-#' utm <- '+init=epsg:32736'
+#' utm <- 'EPSG:32736'
 #'
 #' # Build lines for each individual
 #' build_lines(DT, projection = utm, id = 'ID', coords = c('X', 'Y'),
@@ -131,13 +149,14 @@ build_lines <-
     if (length(lst) == 0) {
       return(NULL)
     } else {
+      proj4string <- sp::CRS(projection)
       l <- lapply(seq_along(lst), function(i) {
         sp::SpatialLines(list(sp::Lines(sp::Line(
           cbind(lst[[i]][[coords[1]]],
                 lst[[i]][[coords[2]]])
         ),
         names(lst)[[i]])),
-        proj4string = sp::CRS(projection))
+        proj4string = proj4string)
       })
       return(do.call(sp::rbind.SpatialLines, l))
     }

R/build_polys.R

@@ -1,27 +1,59 @@
 #' Build Polygons
 #'
-#' \code{build_polys} creates a \code{SpatialPolygons} object from a \code{data.table}. The function accepts a \code{data.table} with relocation data, individual identifiers, a \code{projection}, \code{hrType} and \code{hrParams}. The relocation data is transformed into \code{SpatialPolygons} 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} (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} 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}.
-#'
-#' The \code{splitBy} argument offers further control building \code{SpatialPolygons}. If in your \code{DT}, you have multiple temporal groups (e.g.: years) for example, you can provide the name of the column which identifies them and build \code{SpatialPolygons} for each individual in each year.
-#'
-#' \code{group_polys} uses \code{build_polys} for grouping overlapping polygons created from relocations.
-#'
-#' @return \code{build_polys} returns a \code{SpatialPolygons} object with a polyon for each individual (and optionally \code{splitBy} combination).
-#'
-#' An error is returned when \code{hrParams} do not match the arguments of the \code{hrType} \code{adehabitatHR} function.
+#' \code{build_polys} creates a \code{SpatialPolygons} object from a
+#' \code{data.table}. The function accepts a \code{data.table} with
+#' relocation data, individual identifiers, a \code{projection},
+#' \code{hrType} and \code{hrParams}. The relocation data is transformed
+#' into \code{SpatialPolygons} 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} (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} argument expects a character string defining
+#' the EPSG code. For example, for UTM zone 36N (EPSG 32736), the projection
+#' argument is "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}. It is likely
+#' that \code{build_polys} will return "Warning in proj4string(xy) :
+#' CRS object has comment, which is lost in output" due to these changes.
+#'
+#' 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}.
+#'
+#' The \code{splitBy} argument offers further control building
+#' \code{SpatialPolygons}. If in your \code{DT}, you have multiple
+#' temporal groups (e.g.: years) for example, you can provide the
+#' name of the column which identifies them and build \code{SpatialPolygons}
+#' for each individual in each year.
+#'
+#' \code{group_polys} uses \code{build_polys} for grouping overlapping
+#' polygons created from relocations.
+#'
+#' @return \code{build_polys} returns a \code{SpatialPolygons} object
+#' with a polyon for each individual (and optionally \code{splitBy}
+#' combination).
+#'
+#' An error is returned when \code{hrParams} do not match the arguments
+#' of the \code{hrType} \code{adehabitatHR} function.
 #'
 #'
 #' @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.
+#' @param spPts alternatively, provide solely a SpatialPointsDataFrame with one
+#' column representing the ID of each point.
+#' @param projection character string defining the projection to be passed to
+#' \code{sp::CRS}. For example, for UTM zone 36S (EPSG 32736),
+#' the projection argument is 'EPSG:32736'. See details.
 #' @export
 #'
 #' @family Build functions
@@ -38,7 +70,7 @@
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
 #' # EPSG code for example data
-#' utm <- '+init=epsg:32736'
+#' utm <- 'EPSG:32736'
 #'
 #' # Build polygons for each individual using kernelUD and getverticeshr
 #' build_polys(DT, projection = utm, hrType = 'kernel',

R/extdata.R

@@ -5,7 +5,7 @@
 #'
 #' @format A data.table with 14297 rows and 5 variables: \describe{
 #'   \item{ID}{individual identifier} \item{X}{X coordinate of the relocation
-#'   (UTM 21N)} \item{Y}{Y coordinate of the relocation (UTM 21N)}
+#'   (UTM 36N)} \item{Y}{Y coordinate of the relocation (UTM 36N)}
 #'   \item{datetime}{character string representing the date time}
 #'   \item{population}{sub population within the individuals} }
 #'

R/get_gbi.R

@@ -47,7 +47,7 @@
 #' DT[, yr := year(datetime)]
 #'
 #' # EPSG code for example data
-#' utm <- '+init=epsg:32736'
+#' utm <- 'EPSG:32736'
 #'
 #' group_polys(DT, area = FALSE, hrType = 'mcp',
 #'             hrParams = list(percent = 95),

R/group_lines.R

@@ -19,7 +19,14 @@
 #' 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{projection} argument expects a character string defining
+#' the EPSG code. For example, for UTM zone 36N (EPSG 32736), the projection
+#' argument is "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}. It is likely
+#' that \code{build_polys} will return "Warning in proj4string(xy) :
+#' CRS object has comment, which is lost in output" due to these changes.
 #'
 #' 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
@@ -87,7 +94,7 @@
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
 #' # EPSG code for example data
-#' utm <- '+init=epsg:32736'
+#' utm <- 'EPSG:32736'
 #'
 #' \donttest{group_lines(DT, threshold = 50, projection = utm, sortBy = 'datetime',
 #'             id = 'ID', coords = c('X', 'Y'))}

R/group_polys.R

@@ -17,7 +17,14 @@
 #' 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} 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{projection} argument expects a character string defining the EPSG
+#' code. For example, for UTM zone 36N (EPSG 32736), the projection argument is
+#'  '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}. It is likely
+#' that \code{build_polys} will return "Warning in proj4string(xy) :
+#' CRS object has comment, which is lost in output" due to these changes.
 #'
 #' The \code{hrType} must be either one of "kernel" or "mcp". The
 #' \code{hrParams} must be a named list of arguments matching those of
@@ -68,7 +75,7 @@
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'
 #' # EPSG code for example data
-#' utm <- '+init=epsg:32736'
+#' utm <- 'EPSG:32736'
 #'
 #' group_polys(DT, area = FALSE, hrType = 'mcp',
 #'             hrParams = list(percent = 95), projection = utm,

README.Rmd

@@ -36,7 +36,7 @@ For more details, see the [blog post](https://ropensci.org/blog/2018/12/04/spats
 
 
 ## News
-New edge-list generating functions added:
+Edge-list generating functions added:
 
   * `edge_nn`
   * `edge_dist`
@@ -47,23 +47,23 @@ and dyad id function:
 
 (feedback welcome as always!)
 
-Both documented further in a new vignette: [Using edge list and dyad id functions](https://docs.ropensci.org/spatsoc/articles/using-edge-and-dyad.html).
+Both documented further in a vignette: [Using edge list and dyad id functions](https://docs.ropensci.org/spatsoc/articles/using-edge-and-dyad.html).
 
 
-Also, our article describing `spatsoc` was just published at Methods in Ecology and Evolution. [Link here](https://doi.org/10.1111/2041-210X.13215) and thanks to reviewers and editors at [rOpenSci](https://github.com/ropensci/software-review/issues/237) and at [MEE](https://besjournals.onlinelibrary.wiley.com/journal/2041210x). 
+Also, our article describing `spatsoc` is published at Methods in Ecology and Evolution. [Link here](https://doi.org/10.1111/2041-210X.13215). Thanks to reviewers and editors at [rOpenSci](https://github.com/ropensci/software-review/issues/237) and at [MEE](https://besjournals.onlinelibrary.wiley.com/journal/2041210x). 
 
 
 More detailed news [here](https://docs.ropensci.org/spatsoc/news/index.html).
 
 
 ## Installation
-Install the latest version with `remotes`.  
 
 ```{r install}
-remotes::install_github('ropensci/spatsoc')
-
-# or CRAN
+# Stable release
 install.packages('spatsoc')
+
+# Development version
+remotes::install_github('ropensci/spatsoc')
 ```
 
 `spatsoc` depends on `rgeos` and requires [GEOS](https://trac.osgeo.org/geos/) installed on the system.