Spatial example

library(rpostgis)

## Loading required package: RPostgreSQL

## Loading required package: DBI

library(RPostgreSQL)
library(sf)

## Linking to GEOS 3.5.1, GDAL 2.1.2, PROJ 4.9.3

library(mapview)
library(leaflet.extras)

## Loading required package: leaflet

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(raster)

## Loading required package: sp

## 
## Attaching package: 'raster'

## The following object is masked from 'package:dplyr':
## 
##     select

library(elevatr)
library(tmap)
library(gdistance)

## Loading required package: igraph

## 
## Attaching package: 'igraph'

## The following object is masked from 'package:raster':
## 
##     union

## The following objects are masked from 'package:dplyr':
## 
##     as_data_frame, groups, union

## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum

## The following object is masked from 'package:base':
## 
##     union

## Loading required package: Matrix

## 
## Attaching package: 'gdistance'

## The following object is masked from 'package:igraph':
## 
##     normalize

conn <- dbConnect("PostgreSQL", host = "postgis", dbname = "nateng" ,user = "docker", password = "docker")
grassland<-st_read(conn,query="select * from calc_grass")
transects<-st_read(conn,query="select * from transects")
counts<-st_read(conn,query="select * from counts")
dbDisconnect(conn)

## [1] TRUE

grassland<-st_zm(grassland)
tmap_mode("view")

## tmap mode set to interactive viewing

tm_shape(grassland) +tm_fill() +  tm_borders() + tm_scale_bar() + tm_compass(type = "8star", position = c("left", "top")) + tm_basemap(server = "OpenTopoMap") -> map
tmap_mode("plot")

## tmap mode set to plotting

map

library(raster)
grassland$bin<-1

raster_template <- raster(extent(grassland), resolution = 100,
                         crs = st_crs(grassland)$proj4string)

grass<-rasterize(grassland, raster_template, field = "bin")
grass2<-grass
grass2[is.na(grass2)]<-100
tr<-transition(grass2,transitionFunction = mean,directions=8)

points<-as(counts, "Spatial")
p<-unique(coordinates(points))

test<-shortestPath(tr,p[1,],p[19,],output="SpatialLines")

plot(grass)
points(points)
lines(test)