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Multi-Species Indicator tool

Source: R/msi_tool.R
msi_tool.Rd

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
)

Source

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

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