inst/doc/use-cases.R

In rpostgisLT: Managing Animal Movement Data with 'PostGIS' and R

## ----eval=FALSE----------------------------------------------------------
#  library(rpostgisLT)
#  con <- dbConnect("PostgreSQL", dbname = <dbname>, host = <host>, user = <user>, password = <password>)

## ----eval=FALSE----------------------------------------------------------
#  pgtrajSchema(con)

## ----eval=FALSE----------------------------------------------------------
#  data(ibexraw)
#  ibexraw
#  is.regular(ibexraw)
#  ## FALSE
#  
#  ## Note that there is an issue with the time zone. In 'ibexraw', the
#  ## time zone is not set:
#  attr(ld(ibexraw)$date, "tzone")
#  ## This means that it is assumed to be UTC, and is thus converted to
#  ## local time zone on display (EDT2EST for me):
#  head(ld(ibexraw)$date)                    # Note that the first timestamp
#                                            # should be '2003-06-01
#                                            # 00:00:56'
#  ## We need to fix that upfront:
#  ibex <- ld(ibexraw)
#  attr(ibex$date, "tzone") <- "Europe/Paris"
#  ibex <- dl(ibex)
#  
#  ltraj2pgtraj(con, ibex)                   # Default should be in schema
#                                            # 'traj' and use ltraj name
#                                            # ('ibex') as pgtraj name.
#  ibexTest <- pgtraj2ltraj(con, "ibex")     # Default should look into
#                                            # 'traj' schema.
#  all.equal(ibex, ibexTest)
#  ## TRUE

## ----eval=FALSE----------------------------------------------------------
#  attr(ltraj, "proj4string") <- CRS("+proj=longlat +datum=WGS84")

## ----eval=FALSE----------------------------------------------------------
#  refda <- strptime("2003-06-01 00:00", "%Y-%m-%d %H:%M", tz = "Europe/Paris")
#  (ibex <- setNA(ibex, refda, 4, units = "hour"))
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)
#  ## TRUE

## ----eval=FALSE----------------------------------------------------------
#  (ibex <- sett0(ibex, refda, 4, units = "hour"))
#  ibex.ref <- ibex                        # At this stage, 'ibex' is our
#                                          # reference data
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)
#  ## TRUE

## ----eval=FALSE----------------------------------------------------------
#  ## 1. In space
#  summary(ld(ibex)$dist)
#  (ibex <- redisltraj(ibex, 400))
#  ibex <- removeinfo(ibex)
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)
#  ## R uses fractional seconds (PostGIS doesn't), so dates are not exactly equal
#  
#  ## 2. In time
#  ibex <- ibex.ref
#  (ibex <- redisltraj(na.omit(ibex), 14400, type = "time"))
#  ibex <- removeinfo(ibex)
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)
#  ## TRUE

## ----eval=FALSE----------------------------------------------------------
#  ## 1. Subset on given parameters
#  ibex <- ibex.ref
#  ## We work on the data frame from the trajectory, which we subset, and
#  ## then rebuild the ltraj without recomputing trajectory parameters;
#  ## this is essentially what 'hab::subset' does.
#  ## Note that the steps are not continuous any more.
#  ibex <- ld(ibex)
#  ibex <- droplevels(ibex[ibex$dist < 400 & !is.na(ibex$dist), ])
#  dlfast <- function(x) {
#      trajnam <- c("x", "y", "date", "dx", "dy", "dist", "dt",
#          "R2n", "abs.angle", "rel.angle")
#      idd <- tapply(as.character(x$id), x$burst, unique)
#      traj <- split(x[, names(x) %in% trajnam], x$burst)
#      names(traj) <- NULL
#      class(traj) <- c("ltraj", "list")
#      attr(traj, "typeII") <- TRUE
#      attr(traj, "regular") <- is.regular(traj)
#      for (i in (1:length(traj))) {
#          attr(traj[[i]], "id") <- as.character(idd[i])
#          attr(traj[[i]], "burst") <- names(idd[i])
#      }
#      return(traj)
#  }
#  ibex <- dlfast(ibex)
#  head(ibex[[1]])
#  attr(ibex, "proj4string") <- CRS()
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)
#  
#  ## 2. Subsample on the temporal sequence
#  ibex <- ibex.ref
#  (ibex <- subsample(ibex, 14400*2))
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)

## ----eval=FALSE----------------------------------------------------------
#  ## 1. Cut if there is a step greater than 3000 m
#  ibex <- ibex.ref
#  (ibex <- cutltraj(ibex, "dist > 3000"))
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)

## ----eval=FALSE----------------------------------------------------------
#  ## 2. Bind back by individual:
#  (ibex <- bindltraj(ibex))   # Note that this adds "infolocs" to the ltraj
#                              # which are also stored in the pgtraj data structure
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)

## ----eval=FALSE----------------------------------------------------------
#  ibex <- ibex.ref
#  ibex2 <- ibex
#  burst(ibex2) <- paste(burst(ibex2), "2", sep = "-")
#  (ibex <- c(ibex, ibex2)[order(id(c(ibex, ibex2)))])
#  attr(ibex, "proj4string") <- CRS()
#  
#  ltraj2pgtraj(con, ibex, overwrite = TRUE)
#  ibexTest <- pgtraj2ltraj(con, "ibex")
#  all.equal(ibex, ibexTest)