gbm.cons: Conservation Area Mapping

In SimonDedman/gbm.auto: Automated Boosted Regression Tree Modelling and Mapping Suite

Conservation Area Mapping

Description

Runs gbm.auto for multiple subsets of the same overall dataset and scales the combined results, leading to maps which highlight areas of high conservation importance for multiple species in the same study area e.g. using juvenile and adult female subsets to locate candidate nursery grounds and spawning areas respectively.

Usage

gbm.cons(
  mygrids,
  subsets,
  alerts = TRUE,
  map = TRUE,
  BnW = TRUE,
  resvars,
  gbmautos = TRUE,
  savedir = tempdir(),
  expvars,
  tcs = NULL,
  lrs = rep(list(c(0.01, 0.005)), length(resvars)),
  bfs = rep(0.5, length(resvars)),
  ZIs = rep("CHECK", length(resvars)),
  colss = rep(list(grey.colors(1, 1, 1)), length(resvars)),
  linesfiless = rep(FALSE, length(resvars)),
  savegbms = rep(TRUE, length(resvars)),
  varints = rep(TRUE, length(resvars)),
  maps = rep(TRUE, length(resvars)),
  RSBs = rep(TRUE, length(resvars)),
  BnWs = rep(TRUE, length(resvars)),
  zeroes = rep(TRUE, length(resvars)),
  shape = NULL,
  pngtype = c("cairo-png", "quartz", "Xlib"),
  gridslat = 2,
  gridslon = 1,
  grids = NULL
)

Arguments

mygrids	Gridded lat+long+data object to predict to.
subsets	Subset name(s): character; single or vector, corresponding to matching-named dataset objects e.g. read in by read.csv().
alerts	Play sounds to mark progress steps.
map	Produce maps.
BnW	Also produce B&W maps?
resvars	Vector of resvars cols from dataset objects for gbm.autos, length(subsets)*species, no default.
gbmautos	Do gbm.auto runs for species? Default TRUE, set FALSE if already run and output files in expected directories.
savedir	Save outputs to a temporary directory (default) else change to current directory e.g. "/home/me/folder". Do not use getwd() here.
expvars	List object of expvar vectors for gbm.autos, length = no. of subsets * no. of species. No default.
tcs	Gbm.auto parameters, auto-calculated below if not provided by user.
lrs	Gbm.auto parameter, uses defaults if not provided by user.
bfs	Gbm.auto parameter, uses defaults if not provided by user.
ZIs	Gbm.auto parameter, autocalculated below if not provided by user. Choose one entry.
colss	Gbm.auto parameter, uses defaults if not provided by user.
linesfiless	Gbm.auto parameter, uses defaults if not provided by user.
savegbms	Gbm.auto parameter, uses defaults if not provided by user.
varints	Gbm.auto parameter, uses defaults if not provided by user.
maps	Gbm.auto parameter, uses defaults if not provided by user.
RSBs	Gbm.auto parameter, uses defaults if not provided by user.
BnWs	Gbm.auto parameter, uses defaults if not provided by user.
zeroes	For breaks.grid, include zero-only category in colour breakpoints and subsequent legend. Defaults to TRUE.
shape	Coastline file for gbm.map.
pngtype	File-type for png files, alternatively try "quartz" on Mac. Choose one.
gridslat	Per Gbm.auto defaults to 2.
gridslon	Per Gbm.auto defaults to 1.
grids	Dummy param for package testing for CRAN, ignore.

Value

Maps via gbm.map & saved data as csv file.

Author(s)

Simon Dedman, [e-mail]

Examples

# Not run: downloads and saves external data.
data(grids)
gbm.cons(mygrids = grids, subsets = c("Juveniles","Adult_Females"),
         resvars = c(44:47,11:14),
         expvars = list(c(4:11,15,17,21,25,29,37),
                        c(4:11,15,18,22,26,30,38),
                        c(4:11,15,19,23,27,31),
                        c(4:11,15,20,24,28,32,39),
                        4:10, 4:10, 4:10, 4:10),
         tcs = list(c(2,14), c(2,14), 13, c(2,14), c(2,6), c(2,6), 6,
         c(2,6)),
         lrs = list(c(0.01,0.005), c(0.01,0.005), 0.005, c(0.01,0.005),
               0.005, 0.005, 0.001, 0.005),
         ZIs = rep(TRUE, 8),
         savegbms = rep(FALSE, 8),
         varints = rep(FALSE, 8),
         RSBs = rep(FALSE, 8),
         BnWs = rep(FALSE, 8),
         zeroes = rep(FALSE,8))
         

SimonDedman/gbm.auto documentation built on Oct. 9, 2024, 8:57 p.m.