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Feret Jean-Baptiste
biodivMapR
Commits
729ad162
Commit
729ad162
authored
Nov 07, 2019
by
floriandeboissieu
Browse files
fix: CRS comparison in diversity_from_plots, removed get_projection
parent
06f1204a
Changes
4
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NAMESPACE
View file @
729ad162
...
...
@@ -2,7 +2,6 @@
export(check_data)
export(diversity_from_plots)
export(get_projection)
export(list_shp)
export(map_alpha_div)
export(map_beta_div)
...
...
@@ -28,7 +27,6 @@ importFrom(matrixStats,rowSds)
importFrom(methods,is)
importFrom(raster,projection)
importFrom(raster,raster)
importFrom(raster,shapefile)
importFrom(raster,writeRaster)
importFrom(rgdal,readOGR)
importFrom(rgdal,writeOGR)
...
...
NEWS.md
View file @
729ad162
...
...
@@ -6,6 +6,7 @@
-
moved examples to repository root: example files are not installed with package anymore.
-
removed Plots reprojection from
`diversity_from_plots`
:
now, Plots and Raster must be in the same projection. Changed example Plots projection accordingly.
-
removed
`get_projection`
(useless)
# biodivMapR v1.0.1 (Release date: 2019-09-27)
...
...
R/Lib_Validation_biodivMapR.R
View file @
729ad162
...
...
@@ -10,26 +10,6 @@
# the main goal is to validate ground data associated with biodiversity metrics
# ==============================================================================
#' get projection of a raster or a vector
#' @param file path for a raster or vector (shapefile)
#' @param type 'raster' or 'vector'
#' @return projection
#' @importFrom raster raster shapefile projection
#' @importFrom rgdal readOGR
#' @import tools
#' @export
get_projection
<-
function
(
file
,
type
=
'raster'
){
if
(
type
==
'raster'
){
obj
<-
raster
(
file
)
}
else
if
(
type
==
'vector'
){
Shp.Path
=
dirname
(
file
)
Shp.Name
=
file_path_sans_ext
(
basename
(
file
))
obj
=
readOGR
(
dsn
=
Shp.Path
,
layer
=
Shp.Name
,
verbose
=
FALSE
)
}
projstr
<-
projection
(
obj
)
return
(
projstr
)
}
#' Get list of shapefiles in a directory
#'
#' @param x character or list. Directory containing shapefiles
...
...
@@ -141,6 +121,7 @@ get_alpha_metrics = function(Distrib){
#' @param NbClusters numeric. Number of clusters defined in k-Means.
#' @param Name_Plot character. Name of the plots defined in the shapefile
#' @return alpha and beta diversity metrics
#' @importFrom raster raster projection
#' @importFrom rgdal readOGR
#' @import tools
#' @export
...
...
@@ -173,10 +154,8 @@ diversity_from_plots = function(Raster, Plots, NbClusters = 50, Name_Plot = FALS
if
(
file.exists
(
paste
(
file_path_sans_ext
(
File.Vector
),
'.shp'
,
sep
=
''
))){
Plot
=
readOGR
(
Dir.Vector
,
Name.Vector
[[
ip
]],
verbose
=
FALSE
)
# check if vector and rasters are in the same referential
Projection.Plot
=
get_projection
(
File.Vector
,
'vector'
)
Projection.Raster
=
get_projection
(
Raster
,
'raster'
)
# if not, convert vector file
if
(
compareCRS
(
Projection.
Raster
,
Projection.
Plot
)){
if
(
!
compareCRS
(
raster
(
Raster
)
,
Plot
)){
stop
(
'Raster and Plots have different projection. Plots should be reprojected to Raster CRS, see help('
)
}
}
else
if
(
file.exists
(
paste
(
File.Vector
,
'kml'
,
'sep'
=
'.'
))){
...
...
man/get_projection.Rd
deleted
100644 → 0
View file @
06f1204a
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Lib_Validation_biodivMapR.R
\name{get_projection}
\alias{get_projection}
\title{get projection of a raster or a vector}
\usage{
get_projection(file, type = "raster")
}
\arguments{
\item{file}{path for a raster or vector (shapefile)}
\item{type}{'raster' or 'vector'}
}
\value{
projection
}
\description{
get projection of a raster or a vector
}
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