Fire-History Analysis in R

Basic tools to analyze forest fire history data (e.g. FHX) in R.


Travis-CI Build Status Coverage Status Research software impact

Basic tools to analyze forest fire history data (e.g. FHX) in R. This is designed for power users and projects with special needs.

The project is under heavy development. Hic sunt dracones.

A quick example

library(burnr)
 
data(lgr2)
 
plot(lgr2)

This gives you a basic plot. There are more advanced options. For example, we can color our plot by sample species.

data(lgr2_meta)
 
plot(lgr2, color_group = lgr2_meta$SpeciesID, color_id = lgr2_meta$TreeID,
     plot_legend = TRUE)

Cool, eh?

See help(plot_demograph) for more plot options. You can read and write your own FHX files with read_fhx() and write_fhx().

Installation

You can install a relatively stable version of this package from CRAN by opening an R session and running:

install.packages('burnr')

You can also install the development version of the package from Github. First, be sure you have the devtools package installed in R. Install burnr with:

devtools::install_github("ltrr-arizona-edu/burnr")

Support

Documentation is included in the code. If you're new to burnr, we have an introduction. And more information can be found on the project's wiki. Note, this is still under construction.

We also have a Google Group for questions, announcements, and discussion.

Development

Want to contribute? Great! We're following Hadley's packaging workflow and code style. Fork away.

Please file bugs in the bug tracker.

News

burnr v0.2.2

Changes in this patch:

  • Added warnings and errors to catch bad input on seas() (#112).

  • Added warning if using series_mean_interval() on fhx object with multiple series (#113).

  • Fixed bad numbers in print() for SEAs objects (#111).

  • Fixed typos in warning messages (#114).

burnr v0.2.1

Changes in this patch:

  • intervals objects' KS test for distribution test is now two sided (Issue #108).

  • Printed intervals objects now report the Weibull median, regardless of fit chosen (Issue #109).

burnr v0.2.0

Changes in this minor release:

  • Renamed run_sea() to sea() and enhanced speed, and changed the time_span parameter to event_range, key argument is now event, and years_before and years_after are now nbefore and nafter, respectively. The function now returns a proper sea object with special plot() and print() methods. The plot() generic method uses the new plot_sealags(). You can still use the old run_sea(), but it is deprecated and will be removed in future releases. We're happy with the general interfaces to sea() but its internal structure may change over the next few minor releases, so beware.

  • Added intervals() to handle interval analysis. These are a whole new object. mean_interval() has been renamed series_mean_interval() to avoid confusion. We also have a generic plot() function that uses plot_intervals_dist(). It plots a little histogram with a rug along the x-axis.

  • Added pgm_pdsi data to run with sea. Load it with data("pgm_pdsi").

  • Added make_rec_type(). I hope this will make it easier to create rec_type factors used by fhx().

  • Added event_count_position(), which gives the number of events found in different positions or seasons.

  • Added year_range() to give (min, max) years for an fhx object.

  • Updated composite() to include a filter for number of events. This necesitates fixes in other functions (e.g. plot_demograph()).

  • Added summary() function for fhx and intervals objects.

  • count_fire() renamed count_scar()

  • Added quantile() function for intervals.

burnr v0.1.2

Changes in this patch:

  • Fixed additional bug in read_fhx() caused by "FHX2 format" in FHX file header.

  • Fixed bug #71, causing read_fhx() to fail when FHX has empty lastline.

  • Added text option to read_fhx().

  • Corrected error message for series arg in fhx(). Fixes #73.

  • Fixed write_fhx() reversing order of series names in output file.

burnr v0.1.1

Changes in this patch:

  • Added option to sort series by their last (or most recent) year with sort().

  • Updated run_sea() to better replicate EVENT Fortran program. Addresses #58. Added detailed description and an example page with graphics. Also fixed issue with percentage CIs in the departure table. Mind you, run_sea() is still super experimental.

  • Several minor changes to documentation and meta data.

burnr v0.1.0

Changes in this minor release:

  • Added a vignette!

  • get_ggplot() is being depreciated. Please use plot_demograph().

  • Changed design of fhx objects. They are now data.frame and not lists (nobody used the 'meta', list member anyways). This means that if x is your fhx object and you previously used x$rings, you can now just use x.

  • Added function is.fhx().

  • Updated pgm example data.

  • composite() now returns an fhx object.

  • Added function get_event_years() to find fire and fire injury years in fhx objects. This is especially helpful for composites.

  • concatenate() and combine() were reverted back to '+' at the request of beloved users. This means code like lgr2 + pgm will combine these objects together into a single fhx object!

  • Added examples to all function documentation.

  • resolve_duplicates() is now hidden (i.e. burnr:::check_duplicates()).

  • Added function sample_depth() to get sample depth.

  • Added run_sea function to begin to address issue #58. Has pretty table output. This is still very experimental.

  • Bug fix in series_stats to maintain series IDs for those with no features

  • Changed composite() behavior. Now more similar to FHAES. Can choose to count injuries as "fire events" with the injury_event argument.

  • Added count_recording() function.

  • Fixed minor bugs in series_stats.

  • Removed sorting by default on read_fhx() and '+.fhx'

  • Fixed sort()s non-responsive decreasing argument.

  • Fixed poor sorting function for FHX objects.

  • Added several small utility functions: get_year(), get_series(), series_names(), delete().

  • Improved documentation!

  • Adding series_stats function, closes issue #44.

burnr v0.0.2

Changes in this patch:

  • plot() and get_ggplot() should no longer allow the user to plot facets and composite rugs in the same plot. This closes bug #25.

  • Ring types (the rec_type column in x$rings) has "." in all levels replaced with a "_". For example, 'dormant.fs' is now 'dormant_fs.' Closes #45.

  • In get_ggplot() the legend argument is now plot_legend to avoid clash with common functions.

  • In fhx$rings and all functions, type arugment is now rec_type to avoid clash with type function. rec_type is short for "record_type".

  • Can now read FHX files with a single series (closes bug #43).

  • lgr2 and pgm are available fire-history datasets when you load this package. The metadata for each of these sets is lgr2_meta and pgm_meta. Load the data with data().

burnr v0.0.1

  • First github release

  • Added NEWS.md file. Existing users should check back here for changes.

  • rug.filter function is renamed composite.

  • ggplot.fhx is now get_ggplot. This is more descriptive. The following arguments for this function have been changed as a part of this fix: plot.rug is now composite_rug, filter.min is now filter_min, filter.prop is now filter_prop, event.size is now event_size, rugbuffer.size is now rugbuffer_size, rugdivide.pos is now rugdivide_pos. spp argument is renamed to color_group. sppid is now color_id. cluster is now facet_group. clusterid is now cluster_id.

  • read.fhx function is renamed read_fhx.

  • write.fhx function is renamed write_fhx.

  • order.fhx is now sort (see method sort.fhx). Also, added a boolean argument decreasing, which defaults to FALSE. Previously this has been TRUE..

  • + with fhx objects, (+.fhx) is now concatenate. So, a + b should now be concatenate(a, b).

  • Fixed bug that disappeared a series which started or ended with fire scars.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("burnr")

0.2.2 by Steven Malevich, 2 months ago


https://github.com/ltrr-arizona-edu/burnr/


Report a bug at https://github.com/ltrr-arizona-edu/burnr/issues


Browse source code at https://github.com/cran/burnr


Authors: Steven Malevich [aut, cre], Christopher Guiterman [ctb], Ellis Margolis [ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports MASS, stats, ggplot2, reshape2, plyr

Suggests testthat, knitr, rmarkdown


See at CRAN