pfSimpleGrid: Produce simple gridded maps of paleofire data
In paleofire/paleofire: Analysis of Charcoal Records from the Global Charcoal Database

Description Usage Arguments Details Value Author(s) References See Also Examples

Produce gridded map graphics representing spatial variability in charcoal data from the Global Charcoal Database.

pfSimpleGrid(
  TR,
  tarAge,
  hw,
  binhw = 0.5 * mean(diff(tarAge)),
  fun = mean,
  n.boot = 0,
  prob.CI = c(0.025, 0.975),
  test.val = 0,
  proj4 = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs",
  res = 5,
  ext = c(-180, 180, -90, 90),
  fig.file.name = NULL,
  show.plots = TRUE,
  title.text = "",
  cols = NULL,
  cuts = NULL,
  zlim = NULL,
  base.map = "coasts",
  base.map.col = grey(0.7),
  base.map.lwd = 0.5
)

`TR`	An object returned by `pfTransform`
`tarAge`	Numeric, the target ages for prebinning given in years (e.g. tarAge = seq(0, 10000, 20)). If unspecified the sequence is defined as tarAge=seq(from=min age, to=max Age, by=median resolution).
`hw`	Numeric, the half window width for the locfit procedure (in years).
`binhw`	Numeric, bin half width for the prebinning procedure (use the same value as tarAge intervals for overlapping bins or tarAge intervals/2 for non-overlapping bins).
`fun`	Function to be used for aggregating across sites.
`n.boot`	Number of bootstrap replicates to use when creating confidence intervals around each grid-cell value.
`prob.CI`	Vector of two quantiles to define the bootstrap CI for significance testing
`test.val`	Test value for bootstrap significance test.
`proj4`	proj.4 string representing the desired projection for plotted maps. Default is unprojected. See http://www.spatialreference.org to look up the string for your favorite projections.
`res, ext`	Desired grid resolution and extent. If `grd.res` is a single number, the grid will be defined with equal x/y resolution; a two-element vector (x,y) can also be supplied for unequal resolution. `grd.ext` is specified as a vector, matrix, or Extent object, as for the function raster::extent.
`fig.file.name`	Character sequence representing the file name for the output figures. Can be preceded by a path as long as all directories in the path exist. The file will be a PDF with one figure per time bin, each on a separate page.
`show.plots`	Logical indicating whether plots will be printed to the screen.
`title.text`	Character sequence for labeling figures. Time bin bounds will be added automatically.
`cols,`	cuts Vectors of color specifications and values defining the plot legend. Grid-cell values will be binned by `cuts` and assigned the colors in `cols`. If either are NULL, the function tries to guess at a good scheme. `cuts` may also be a single value specifying the number of bins.
`cuts`	Defines range and resolution of color scale
`zlim`	Two-element vector representing the bounds of the color scale. Ignored if `cuts` is fully specified, but otherwise used in defining the color bins.
`base.map`	Currently, either `'coasts'` or `'countries'` to choose which base map (from required library `'rworldmap'`) to be plotted as the base map for all plots. Could easily be modified to accept any SpatialPolygons object.
`base.map.col,`	Color specifications for plotting the basemap.
`base.map.lwd`	Line width specifications for plotting the basemap.

Takes any pfTransform object as input, and allows any set of one or more time bins to be specified for plotting (one plot per bin). Time bins are specified as for pfCompositeLF (which is called by pfSimpleGrid. The extent, resolution, and projection of the desired grid are also user-specified.

Records are first composited, and then aggregated with other sites falling in the same grid cell according to the specified function 'fun' (defauts to mean). This is a considerably simpler approach than the distance-based spatial binning used by pfDotMap, although it has its own tradeoffs (e.g. grid cells are unlikely to represent equal area).

A flexible bootstrapped significance test is implemented. Within each time bin X grid cell combination, composite z-score values are randomly sampled (with replacement) from sites within the grid cell. The function is applied to the sampled values. Quantiles of all bootstrap function evaluations are computed, and significance is reported if a user-specified test value is outside of these bootstrap CI. Note that bootstrap CI calculated here reflect only spatial variability, as no temporal resampling is performed.

Plots are produced on the current device and/or in pdf files according to input arguments. In addition, a named list of useful objects is returned:

`COMP`	The binned composite generated for plotting.
`tarAge`	The list of target ages used for temporal binning.
`sg.rast`	A `Raster-class` object containing the gridded output data
`sg.plots`	A list of trellis objects representing the composed plots. Note that these objects can be edited to some degree with the `update.trellis` function, and plotted or used in layouts as any other trellis graphics can.

R. Kelly

Power, M., J. Marlon, N. Ortiz, P. Bartlein, S. Harrison, F. Mayle, A. Ballouche, R. Bradshaw, C. Carcaillet, C. Cordova, S. Mooney, P. Moreno, I. Prentice, K. Thonicke, W. Tinner, C. Whitlock, Y. Zhang, Y. Zhao, A. Ali, R. Anderson, R. Beer, H. Behling, C. Briles, K. Brown, A. Brunelle, M. Bush, P. Camill, G. Chu, J. Clark, D. Colombaroli, S. Connor, A. L. Daniau, M. Daniels, J. Dodson, E. Doughty, M. Edwards, W. Finsinger, D. Foster, J. Frechette, M. J. Gaillard, D. Gavin, E. Gobet, S. Haberle, D. Hallett, P. Higuera, G. Hope, S. Horn, J. Inoue, P. Kaltenrieder, L. Kennedy, Z. Kong, C. Larsen, C. Long, J. Lynch, E. Lynch, M. McGlone, S. Meeks, S. Mensing, G. Meyer, T. Minckley, J. Mohr, D. Nelson, J. New, R. Newnham, R. Noti, W. Oswald, J. Pierce, P. Richard, C. Rowe, M. Sanchez Goni, B. Shuman, H. Takahara, J. Toney, C. Turney, D. Urrego-Sanchez, C. Umbanhowar, M. Vandergoes, B. Vanniere, E. Vescovi, M. Walsh, X. Wang, N. Williams, J. Wilmshurst, and J. Zhang. 2008. Changes in fire regimes since the Last Glacial Maximum: an assessment based on a global synthesis and analysis of charcoal data. Climate Dynamics 30:887-907.

pfGridding

## Not run: 
ID=pfSiteSel(continent=="North America", l12==1 & long<(-130))
plot(ID)

## Transform data
res3=pfTransform(ID,method=c("MinMax","Box-Cox","Z-Score"),BasePeriod=c(200,4000))

## Plot maps for 1000-yr bins spanning 3-0 kBP
# dev.new(width=10,height=10) # A big plot area helps. 
gridmap = pfSimpleGrid( TR=res3, tarAge=seq(0,2000,1000), hw=500, ext=c(-170,-80,40,80))
summary(gridmap)

# Plot the mean map from the first time bin
newmap = update(gridmap$sg.plots[[1]], main="A relabeled map")
newmap

## End(Not run)