inst/doc/spThin_vignette.R

In spThin: Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models

## ----load_package--------------------------------------------------------
library( spThin )

## ------------------------------------------------------------------------
data( Heteromys_anomalus_South_America )
head( Heteromys_anomalus_South_America )

## ------------------------------------------------------------------------
table( Heteromys_anomalus_South_America$REGION )

## ------------------------------------------------------------------------
thinned_dataset_full <-
  thin( loc.data = Heteromys_anomalus_South_America, 
        lat.col = "LAT", long.col = "LONG", 
        spec.col = "SPEC", 
        thin.par = 10, reps = 100, 
        locs.thinned.list.return = TRUE, 
        write.files = FALSE, 
        write.log.file = FALSE)

## ---- eval=FALSE---------------------------------------------------------
#  thinned_dataset_full <-
#    thin( loc.data = Heteromys_anomalus_South_America,
#          lat.col = "LAT", long.col = "LONG",
#          spec.col = "SPEC",
#          thin.par = 10, reps = 100,
#          locs.thinned.list.return = TRUE,
#          write.files = TRUE,
#          max.files = 5,
#          out.dir = "hanomalus_thinned_full/", out.base = "hanomalus_thinned",
#          write.log.file = TRUE,
#          log.file = "hanomalus_thinned_full_log_file.txt" )

## ------------------------------------------------------------------------
plotThin( thinned_dataset_full )

## ------------------------------------------------------------------------
thinned_dataset_mainland <-
  thin( loc.data = Heteromys_anomalus_South_America[ which( Heteromys_anomalus_South_America$REGION == "mainland" ) , ], 
        lat.col = "LAT", long.col = "LONG", 
        spec.col = "SPEC", 
        thin.par = 10, reps = 100, 
        locs.thinned.list.return = TRUE, 
        write.files = FALSE, 
        write.log.file = FALSE)

## ------------------------------------------------------------------------
thinned_dataset_trin <-
  thin( loc.data = Heteromys_anomalus_South_America[ which( Heteromys_anomalus_South_America$REGION == "trin" ) , ], 
        lat.col = "LAT", long.col = "LONG", 
        spec.col = "SPEC", 
        thin.par = 10, reps = 10, 
        locs.thinned.list.return = TRUE, 
        write.files = FALSE, 
        write.log.file = FALSE)

## ------------------------------------------------------------------------
thinned_dataset_mar <-
  thin( loc.data = Heteromys_anomalus_South_America[ which( Heteromys_anomalus_South_America$REGION == "mar" ) , ], 
        lat.col = "LAT", long.col = "LONG", 
        spec.col = "SPEC", 
        thin.par = 10, reps = 10, 
        locs.thinned.list.return = TRUE, 
        write.files = FALSE, 
        write.log.file = FALSE )

## ------------------------------------------------------------------------
thinned_dataset_tobago <-
  thin( loc.data = Heteromys_anomalus_South_America[ which( Heteromys_anomalus_South_America$REGION == "tobago" ) , ], 
        lat.col = "LAT", long.col = "LONG", 
        spec.col = "SPEC", 
        thin.par = 10, reps = 10, 
        locs.thinned.list.return = TRUE, 
        write.files = FALSE, 
        write.log.file = FALSE )