Using R as GIS
Objects, Functions etc...
Franziska Faupel
MOSaIC
Structure
- Load Spatial Objects
- Create Spatial Objects
- Manipulate Spatial Objects
- Reproject Spatial Data
- Plot Spatial Objects
- Summary
Packages
Packages
| Package | Properties | |
|---|---|---|
raster |
Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported. | https://cran.r-project.org/web/packages/raster/raster.pdf |
rgdal |
Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. | https://cran.r-project.org/web/packages/rgdal/rgdal.pdf |
spded |
collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree... | https://cran.r-project.org/web/packages/spdep/spdep.pdf |
1. Load Spatial Objects
1. Load Spatial Objects | Spatial Points Data Frame
library(rgdal)
file_gravemounds <- "gravemounds"
spdf_gm <- readOGR("2data", file_gravemounds)
## OGR data source with driver: ESRI Shapefile
## Source: "2data", layer: "gravemounds"
## with 24 features
## It has 17 fields
class(spdf_gm)
## [1] "SpatialPointsDataFrame"
## attr(,"package")
## [1] "sp"
SpatialPointsDataFrame | Data
str(spdf_gm@data)
## 'data.frame': 24 obs. of 17 variables:
## $ Nekropole : Factor w/ 24 levels "Beckenmatt","Dachhuebel-Birklach",..: 18 12 24 3 20 5 7 11 2 1 ...
## $ Gravemound: int 8 6 33 14 12 16 7 18 20 31 ...
## $ Inhumation: Factor w/ 1 level "y": 1 NA 1 NA 1 1 1 NA 1 1 ...
## $ Incrematio: Factor w/ 1 level "y": 1 NA 1 1 1 1 1 1 1 NA ...
## $ Epoche : Factor w/ 3 levels "BA","both","IA": 2 1 2 1 2 1 2 1 1 1 ...
## $ Excavated : int 8 1 12 5 7 9 7 9 7 26 ...
## $ Literature: Factor w/ 2 levels "Schaeffer 1926",..: 1 1 2 1 2 1 2 1 1 1 ...
## $ Bronze : int 43 NA 13 12 29 7 14 4 23 15 ...
## $ Ceramics : int 8 NA 9 3 9 9 4 11 13 24 ...
## $ Amber : int 9 NA NA 3 1 NA NA NA 4 NA ...
## $ Gold : int NA NA NA 1 NA NA NA NA NA NA ...
## $ Glass : int 1 NA NA 2 NA NA NA NA NA NA ...
## $ Iron : int 1 NA NA NA NA NA NA NA NA NA ...
## $ Stone : int 1 NA NA NA NA 1 2 NA NA NA ...
## $ Coral : int NA NA NA NA NA NA NA NA NA NA ...
## $ X : num 3419142 3417717 3421495 3423415 3419884 ...
## $ Y : num 5416936 5415907 5415052 5413753 5414973 ...
SpatialPointsDataFrame | Coordinates
str(spdf_gm@coords.nrs)
## num(0)
SpatialPointsDataFrame | Coordinates
str(spdf_gm@coords)
## num [1:24, 1:2] 3419142 3417717 3421495 3423415 3419884 ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:2] "coords.x1" "coords.x2"
SpatialPointsDataFrame | Bonding Box
str(spdf_gm@bbox)
## num [1:2, 1:2] 3404224 5404405 3425604 5418083
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:2] "coords.x1" "coords.x2"
## ..$ : chr [1:2] "min" "max"
SpatialPointsDataFrame | Projection Information
str(spdf_gm@proj4string)
## Formal class 'CRS' [package "sp"] with 1 slot
## ..@ projargs: chr "+proj=tmerc +lat_0=0 +lon_0=9 +k=1 +x_0=3500000 +y_0=0 +datum=potsdam +units=m +no_defs +ellps=bessel +towgs84=598.1,73.7,418.2"| __truncated__
SpatialPointsDataFrame
plot(spdf_gm)
1. Load Spatial Objects | Spatial Grid Data Frame
library(raster)
file_srtm <- "3geodata/bw_srtm.asc" # path to srtm DTM
sgdf_srtm <- read.asciigrid(file_srtm)
class(sgdf_srtm)
## [1] "SpatialGridDataFrame"
## attr(,"package")
## [1] "sp"
1. Load Spatial Objects | Spatial Grid Data Frame
plot(sgdf_srtm)
SpatialGridDataFrame | Data
str(sgdf_srtm@data)
## 'data.frame': 15860650 obs. of 1 variable:
## $ 3geodata/bw_srtm.asc: num 197 197 197 197 197 ...
SpatialGridDataFrame | Grid
str(sgdf_srtm@grid)
## Formal class 'GridTopology' [package "sp"] with 3 slots
## ..@ cellcentre.offset: num [1:2] 3347909 5206717
## ..@ cellsize : num [1:2] 90 90
## ..@ cells.dim : int [1:2] 4225 3754
SpatialGridDataFrame | Bonding Box
str(sgdf_srtm@bbox)
## num [1:2, 1:2] 3347864 5206672 3728114 5544532
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:2] "min" "max"
SpatialGridDataFrame | Projection Information
str(sgdf_srtm@proj4string)
## Formal class 'CRS' [package "sp"] with 1 slot
## ..@ projargs: chr NA
2. Create Spatial Objects
2. Create Spatial Objects | Spatial Points Data Frame
file_gm <- "2data/gravemounds.csv"
crs1 <- "+proj=tmerc +lat_0=0 +lon_0=9 +k=1 +x_0=3500000 +y_0=0 +ellps=WGS84 +units=m +no_defs" # gk3
df_gm <- read.table(file_gm, sep=';', header=TRUE)
spdf_gm01 <- df_gm
coordinates(spdf_gm01)=~X+Y
projection(spdf_gm01) <- crs1
class(spdf_gm01)
## [1] "SpatialPointsDataFrame"
## attr(,"package")
## [1] "sp"
2. Create Spatial Objects | Spatial Points Data Frame
plot(spdf_gm01)
2. Create Spatial Objects | Spatial Lines Data Frame
library(spdep)
fs_nb_del <- tri2nb(coordinates(spdf_gm)) # Creating a List of Neighbours
coords <- as.matrix(coordinates(spdf_gm)) # extracting gravemound coordinates as a matrix
# Creating a Delauny Graph as a Spatial Lines Data Frame
del <- nb2lines(fs_nb_del, coords=coords, proj4string = CRS(as.character(crs1)))
class(del)
## [1] "SpatialLinesDataFrame"
## attr(,"package")
## [1] "sp"
2. Create Spatial Objects | Spatial Lines Data Frame
plot(del)
SpatialLinesDataFrame | Data
str(del@data)
## 'data.frame': 118 obs. of 5 variables:
## $ i : int 1 1 1 1 1 2 2 2 2 2 ...
## $ j : int 2 3 5 14 22 1 5 6 7 8 ...
## $ i_ID:Class 'AsIs' chr [1:118] "1" "1" "1" "1" ...
## $ j_ID:Class 'AsIs' chr [1:118] "2" "3" "5" "14" ...
## $ wt : num 1 1 1 1 1 1 1 1 1 1 ...
SpatialLinesDataFrame | Lines
str(del@lines)
## List of 118
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
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## .. .. .. .. ..@ coords: num [1:2, 1:2] 3419142 3417717 5416936 5415907
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "1"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
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## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
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## .. ..@ ID : chr "2"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
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## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
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## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
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## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
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## .. .. .. .. ..@ coords: num [1:2, 1:2] 3412957 3421628 5404536 5408831
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "90"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3412957 3419741 5404536 5408021
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "91"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3412957 3411268 5404536 5404405
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "92"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3411268 3412431 5404405 5412258
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "93"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3411268 3412957 5404405 5404536
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "94"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3411268 3406774 5404405 5406406
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "95"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3406774 3412431 5406406 5412258
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "96"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3406774 3411268 5406406 5404405
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "97"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3406774 3406705 5406406 5411437
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "98"
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3406774 3405413 5406406 5410742
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "99"
## [list output truncated]
SpatialLinesDataFrame | Lines > Coordinates
str(del@lines$coords)
## NULL
str(del@lines[1])
## List of 1
## $ :Formal class 'Lines' [package "sp"] with 2 slots
## .. ..@ Lines:List of 1
## .. .. ..$ :Formal class 'Line' [package "sp"] with 1 slot
## .. .. .. .. ..@ coords: num [1:2, 1:2] 3419142 3417717 5416936 5415907
## .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : chr [1:2] "xx" "yy"
## .. ..@ ID : chr "1"
3. Manipulate Spatial Objects
3. Manipulate Spatial Objects | How to crop?
ext <- extent(3404224, 3425604, 5404405, 5418083)
raster_srtm <- raster(sgdf_srtm)
sgdf_ai <- crop(raster_srtm, ext, snap='near', overwrite=TRUE)
sgdf_alsace <- as(sgdf_ai, 'SpatialGridDataFrame')
plot(sgdf_alsace)
Raster
class(raster)
## [1] "standardGeneric"
## attr(,"package")
## [1] "methods"
plot(raster_srtm)
Raster | File
str(raster_srtm@file)
## Formal class '.RasterFile' [package "raster"] with 13 slots
## ..@ name : chr ""
## ..@ datanotation: chr "FLT4S"
## ..@ byteorder : chr "little"
## ..@ nodatavalue : num -Inf
## ..@ NAchanged : logi FALSE
## ..@ nbands : int 1
## ..@ bandorder : chr "BIL"
## ..@ offset : int 0
## ..@ toptobottom : logi TRUE
## ..@ blockrows : int 0
## ..@ blockcols : int 0
## ..@ driver : chr ""
## ..@ open : logi FALSE
Raster | Data
str(raster_srtm@data)
## Formal class '.SingleLayerData' [package "raster"] with 13 slots
## ..@ values : num [1:15860650] 197 197 197 197 197 ...
## ..@ offset : num 0
## ..@ gain : num 1
## ..@ inmemory : logi TRUE
## ..@ fromdisk : logi FALSE
## ..@ isfactor : logi FALSE
## ..@ attributes: list()
## ..@ haveminmax: logi TRUE
## ..@ min : num 35.5
## ..@ max : num 3452
## ..@ band : int 1
## ..@ unit : chr ""
## ..@ names : chr "X3geodata.bw_srtm.asc"
Raster | Legend & Title
str(raster_srtm@legend)
## Formal class '.RasterLegend' [package "raster"] with 5 slots
## ..@ type : chr(0)
## ..@ values : logi(0)
## ..@ color : logi(0)
## ..@ names : logi(0)
## ..@ colortable: logi(0)
str(raster_srtm@title)
## chr(0)
Raster | Extent, Coulmns & Rows
str(raster_srtm@extent)
## Formal class 'Extent' [package "raster"] with 4 slots
## ..@ xmin: num 3347864
## ..@ xmax: num 3728114
## ..@ ymin: num 5206672
## ..@ ymax: num 5544532
str(raster_srtm@ncols)
## int 4225
str(raster_srtm@nrows)
## int 3754
Raster | Others...
str(raster_srtm@rotated)
## logi FALSE
str(raster_srtm@rotation)
## Formal class '.Rotation' [package "raster"] with 2 slots
## ..@ geotrans: num(0)
## ..@ transfun:function ()
Raster | Others...
str(raster_srtm@crs)
## Formal class 'CRS' [package "sp"] with 1 slot
## ..@ projargs: chr NA
str(raster_srtm@history)
## list()
str(raster_srtm@z)
## list()
4. Reproject Spatial Data
4. Reproject Spatial Data
Gauss Krueger , http://www.geocontent.de/uploads/RTEmagicC_karte_gk.jpg.jpg
WGS 1984 , http://earth-info.nga.mil/GandG/publications/tr8350.2/TR8350.2-b/Sections%201-5.pdf
4. Reproject Spatial Data
# creating a spdf, if not allready existing
coordinates(spdf)=~x+y
# Project Corrdinates
coo <- project(cbind(spdf@coords[,1], spdf@coords[,2]),crs1)
# create a spdf
spdf <- SpatialPointsDataFrame(coo , as.data.frame(df)
,proj4string=CRS(as.character(crs1)))
5. Plot Spatial Objects
5. Plot Spatial Objects
plot(sgdf_alsace, col = grey.colors(50, start=0.98, end=0.1), main="Gravemounds of Haguenau")
5. Plot Spatial Objects
plot(sgdf_alsace, col = grey.colors(50, start=0.98, end=0.1), main="Gravemounds of Haguenau")
points(spdf_gm, col="dark red", pch=15)
legend("bottomright", cex=0.7, legend=c("Gravemounds"), pch=15,col="dark red")
5. Plot Spatial Objects
plot(sgdf_alsace, col = grey.colors(50, start=0.98, end=0.1), main="Gravemounds of Haguenau")
points(spdf_gm, col="dark red", pch=15)
lines(del, col="black")
legend("bottomright", cex=0.7, legend=c("Gravemounds"), pch=15,col="dark red")
6. Summary
6. Summary
| Spatial Object | Short | Slots | function |
|---|---|---|---|
| Spatial Points Data Frame | spdf | @data; @coords.nrs; @coords; @bbox; @porj4string | SpatialPointsDataFrame() |
| Spatial Grid Data Frame | sgdf | @data; @grid; @bbox; @porj4string | SpatialGridDataFrame() |
| Spatial Lines Data Frame | sldf | @data; @lines | SpatialLinesDataFrame() |
| raster | ras | @file; @data; @legend; @title; @extent; @rotated; @rotation; @ncols; @nrows; @crs; @history; @z | raster() |
Presentations
Monday, 5th of September
Tuesday, 6th of September
Wednesday, 7th of September
- Modelling Interaction: Cultural & Geographic Distance
- Workshop: Geographical and Economic Distances
- Workshop: Cultural Distances
Thursday, 8th of September
- Modelling Interaction: Network Approaches
- Workshop: Pointpattern Analysis
- Workshop: Network Analysis