msi_tool: Multi-Species Indicator tool

In BiologicalRecordsCentre/BRCindicators: Creating multispecies biodiversity indicators

Multi-Species Indicator tool

Description

A functionalised version of code developed by Statistics Netherlands (see source). See 'msi' for a wrapper that removes the need to write files to a folder first. Multi-Species Indicators (MSI) are biodiversity indicators that combine the population development of species into a single indicator. The MSI-tool calculates an MSI, confidence intervals for the MSIs and linear and flexible (smoothed) trends. The trends are classified in terms like "moderate increase", "strong decrease" or "stable". A number of additional analyses can be performed like testing for changepoints, comparison of trends before and after a changepoint and the calculation and testing of the total change in a time series.

Usage

msi_tool(
  wd = getwd(),
  inputFile,
  jobname = "MSI_job",
  nsim = 1000,
  SEbaseyear = NULL,
  plotbaseyear = NULL,
  index_smooth = "SMOOTH",
  span = 0.75,
  lastyears = 10,
  maxCV = 3,
  changepoint = NULL,
  truncfac = 10,
  TRUNC = 1,
  plot = TRUE
)

Arguments

wd	The path for input and ouput files
inputFile	The name of the input file. This must have columns species, year, index, se in that order. The index value in the base year (which need not be the first year), should be set to 100 with se of 0.
jobname	Generic name for output files
nsim	Number of Monte Carlo simulations
SEbaseyear	Desired year to set MSI to 100 and SE to 0; usually the first year of the time series
plotbaseyear	desired year to set to 100 in plots
index_smooth	A character, either 'INDEX' or 'SMOOTH'. "INDEX" will cause the index in plotbaseyear set to 100; "SMOOTH" will set the smoothed trend value in the plotbaseyear to 100.
span	Span is the proportion of points to use in the weighted estimation of the smoothed line. Values close to 1 are more smoothed than values close to 0
lastyears	last X years of time series for which separate trend (short-term trends) should be calculated
maxCV	maximum allowed mean Coefficient of Variation (CV) of species indices (0.5 = 50 Species with higher mean CV are excluded.
changepoint	compare trends before and after this year
truncfac	truncation factor (=max year-to-year index ratio). Default for Living Planet Index = 10.
TRUNC	set all indices below TRUNC to this value and their SE to 0. TRUNC = 0 means no truncation.
plot	logical, should plots be created

Source

https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends–trim–/msi-tool

BiologicalRecordsCentre/BRCindicators documentation built on April 22, 2024, 2:32 p.m.