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