title	subtitle	date	output	editor_options	citation-style	link-citations	always_allow_html
timeSinceFire Manual	v.1.2.1	Last updated: 2022-11-08	bookdown::html_document2 toc toc_float theme number_sections df_print keep_md true true sandstone false paged true	chunk_output_type bibliography console citations/references_timeSinceFire.bib	citations/ecology-letters.csl	true	true

timeSinceFire Module

(ref:timeSinceFire) timeSinceFire

Authors:

Steve G Cumming stevec@sbf.ulaval.ca [aut, cre], Alex M Chubaty achubaty@for-cast.ca [ctb]

Module Overview

Module summary

Yet Another Age Map Maintainer. This one is peculiar to the LandWeb application.

ageMap is incremented without bound on all flammable cells; cells identified as having been burned in the current year are set to 0.

Any statistics on age structure are to be calculated here, but none are yet implemented...because with the current fire model they would be pretty boring.

Module inputs and parameters

Table @ref(tab:moduleInputs-timeSinceFire) shows the full list of module inputs.

(\#tab:moduleInputs-timeSinceFire)List of (ref:timeSinceFire) input objects and their description.

objectName	objectClass	desc	sourceURL
NA	NA	NA	NA

A summary of user-visible parameters is provided in Table @ref(tab:moduleParams-timeSinceFire).

(\#tab:moduleParams-timeSinceFire)List of (ref:timeSinceFire) parameters and their description.

paramName	paramClass	default	min	max	paramDesc
.plots	character	screen	NA	NA	Used by Plots function, which can be optionally used here
.plotInitialTime	numeric	start(sim)	NA	NA	Describes the simulation time at which the first plot event should occur.
.plotInterval	numeric	NA	NA	NA	Describes the simulation time interval between plot events.
.saveInitialTime	numeric	NA	NA	NA	Describes the simulation time at which the first save event should occur.
.saveInterval	numeric	NA	NA	NA	This describes the simulation time interval between save events.
.studyAreaName	character	NA	NA	NA	Human-readable name for the study area used - e.g., a hash of the studyarea obtained using `reproducible::studyAreaName()`
.seed	list		NA	NA	Named list of seeds to use for each event (names).
.useCache	logical	FALSE	NA	NA	Should caching of events or module be used?

Events

Init

The Init event creates the RasterLayer rstTimeSinceFire. To do this, it rasterizes the template vegetation map LCC05 using the FireReturnInterval field of the SpatialPoygonDataFrame shpStudyRegion. This procedure retains the NAs which mask the actual study region within the template bounding rectangle.

Then, the RasterLayer rstFlammable is used to mask out areas of open water, rock, etc which can't burn and thus for which timeSinceFire is not applicable. These become NAs in rstTimeSinceFire.

The results is that all flammable cells within each polygon in the shapefile are set to the fire return interval specified for that polygon / ecoregion. Under the basic van Wagner model being implemented, this is the expected landscape mean age. The ecoregion age structure will equilibrate to the exponential distribution within a few multiples of the return interval.

No colour ramp or legend is created for this layer.

In the short term, this initial uniform age distribution will result in very high proportions of cells with tsf's greater than the return interval. If this becomes a problem, one could initialize to the regional median age. This can be done by multiplying the FireReturnInterval by $log(2)$ and then rounding; or some other lower quantile could be chosen: see the wikipedia page for the general quantile function.

Alternatively, a random exponential age structure could be generated for each ecoregion from the current rstTimeSinceFire, roughly as follows. See the wiki page for details and possible alternative methods.

U_ <- runif(ncell(rstTimeSinceFire))
T_ <- (-log(U_)) * rstTimeSinceFire[]
rstTimeSinceFire[] <- round(T_)

Plotting

A bare call to Plot(sim$rstTimeSinceFire). If you really want to see this, you'll have to live with the automated colour scheme and legend, or hack Init to your satisfaction.

Saving

Nothing is saved at present.

Age

This is the main event. rstFlammable is incremented by one. Then burned cells, as specified in the input vector burnLoci are set to age 0.

Module outputs

Description of the module outputs (Table @ref(tab:moduleOutputs-timeSinceFire)).

(\#tab:moduleOutputs-timeSinceFire)List of (ref:timeSinceFire) outputs and their description.

objectName	objectClass	desc
NA	NA	NA

Code and data availability

Code available from https://github.com/fRI-Research/timeSinceFire.

Links to other modules

Originally developed as part of the LandWeb project.