gbm.cons {gbm.auto}

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))