title	fireSense_IgnitionFit Manual
subtitle	v.1.0.0
date	Last updated: 2025-04-08
output	bookdown::html_document2 toc toc_float theme number_sections df_print keep_md true true sandstone false paged true
editor_options	chunk_output_type console
bibliography	citations/references_fireSense_IgnitionFit.bib
link-citations	true
always_allow_html	true

fireSense_IgnitionFit Module

(ref:fireSense-IgnitionFit) fireSense_IgnitionFit

Authors:

Jean Marchal jean.d.marchal@gmail.com [aut], Eliot McIntire eliot.mcintire@nrcan-rncan.gc.ca [aut], Ian Eddy ian.eddy@nrcan-rncan.gc.ca [aut, cre], Alex M Chubaty achubaty@for-cast.ca [ctb]

Module Overview

This module fits a statistical model to estimate the contributions of climate and fuel to fire ignition.

Estimate fire ignition (TODO: fill this out) - [@Marchal:2017a; @Marchal:2017b; @Marchal:2019]

Module summary

Fit a model of fire ignition from climate and fuel covariates.

Module inputs and parameters

Describe input data required by the module and how to obtain it (e.g., directly from online sources or supplied by other modules) .

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

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

objectName	objectClass	desc	sourceURL
climateVariablesForFire	list	The column name(s) in the `fireSense_ignitionCovariates` that is climate, in a named list, .e.g. `climateVariablesForFire = list('ignition' = 'MDC')`	NA
fireSense_ignitionCovariates	data.frame	table of aggregated ignition covariates with annual ignitions	NA
flammableRTM	SpatRaster	RTM without ice/rocks/urban/water. Flammable map with 0 and 1.	NA
ignitionFitRTM	SpatRaster	A (template) raster with information with regards to the spatial resolution and geographical extent of `fireSense_ignitionCovariates`. Used to pass this information onto `fireSense_ignitionFitted` Needs to have number of non-NA cells as attribute: (`ignitionFitRTM@data@attributes$nonNAs`), and optionally, `ignitionFitRTM@data@attributes$meanForestB`	NA
fireSense_ignitionFormula	character	formula - as a character - describing the model to be fitted.	NA

Summary of user-visible parameters (Table @ref(tab:moduleParams-fireSense-IgnitionFit))

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

paramName	paramClass	default	min	max	paramDesc
family	function....	poisson,....	NA	NA	a family function (must be wrapped with `quote()`) or a character string naming a family function. Only the negative binomial has been implemented For additional details see `?family`. This was formerly `quote(MASS::negative.binomial(theta = 1, link = 'identity'))`.
plot_fuelBiomassPerPrediction	numeric		1	10	when generating plots of climate x fuel class, the log of biomass (g/m2) for which to generate predictions across a gradient of climate values. If supplied, it will override any values in `sim$ignitionFitRTM$meanForestB`
rescaleVars	logical	TRUE	NA	NA	Attempt to rescale variables? If `rescalers` is defined, use it to rescale variables as `var / rescalers['var']`. Otherwise, `scale()` will be used to rescale variables to `[0,1]`, if they are not already within this range.
.plots	character	screen	NA	NA	See ?Plots. There are a few plots that are made within this module, if set.
.plotInitialTime	numeric		NA	NA	when to do plot
.runInitialTime	numeric	0	NA	NA	when to start this module? By default, the start time of the simulation.
.runInterval	numeric	NA	NA	NA	optional. Interval between two runs of this module, expressed in units of simulation time. By default, NA, which means that this module only runs once per simulation.
.saveInitialTime	numeric	NA	NA	NA	optional. When to start saving output to a file.
.saveInterval	numeric	NA	NA	NA	optional. Interval between save events.
.seed	list		NA	NA	Named list of seeds to use for each event (names). E.g., `list('init' = 123)` will `set.seed(123)` at the start of the init event and unset it at the end. Defaults to `NULL`, meaning that no seeds will be set.
.studyAreaName	character	NA	NA	NA	Human-readable name for the study area used. If NA, a hash of `studyAreaLarge` will be used.
.useCache	logical	FALSE	NA	NA	Should this entire module be run with caching activated? This is generally intended for data-type modules, where stochasticity and time are not relevant.

Events

Describe what happens for each event type.

Plotting

Write what is plotted.

Saving

Write what is saved.

Module outputs

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

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

objectName	objectClass	desc
covMinMax_ignition	data.table	Table of the original ranges (min and max) of covariates
fireSense_IgnitionFitted	fireSense_IgnitionFit	A fitted model object of class `fireSense_IgnitionFit`.
ignitionRescalers	integer	scaling vector if rescaling variables to 0-10 range

Links to other modules

This model can be used to parameterize the fire ignition component of landscape fire models such as fireSense.

Getting help

• https://github.com/PredictiveEcology/fireSense_IgnitionFit/issues

References