humpfit {vegan} | R Documentation |
Function humpfit
fits a no-interaction model for species
richness vs. biomass data (Oksanen 1996). This is a null model that
produces a hump-backed response as an artifact of plant size and
density.
humpfit(mass, spno, family = poisson) ## S3 method for class 'humpfit': summary(object, ...) ## S3 method for class 'humpfit': predict(object, newdata = NULL, ...) ## S3 method for class 'humpfit': plot(x, xlab = "Biomass", ylab = "Species Richness", lwd = 2, l.col = "blue", p.col = 1, type = "b", ...) ## S3 method for class 'humpfit': points(x, ...) ## S3 method for class 'humpfit': lines(x, segments=101, ...)
mass |
Biomass. |
spno |
Species richness. |
family |
Family of error distribution. Any family
can be used, but the link function is always Fisher's diversity
model, and other link functions are silently ignored. |
x, object |
Result object of humpfit |
newdata |
Values of mass used in predict . The
original data values are used if missing. |
xlab,ylab |
Axis labels in plot |
lwd |
Line width |
l.col, p.col |
Line and point colour in plot |
type |
Type of plot : "p" for observed points,
"l" for fitted lines, "b" for both, and "n" for
only setting axes. |
segments |
Number of segments used for fitted lines. |
... |
Other parameters to functions. |
The no-interaction model assumes that the humped species richness
pattern along biomass gradient is an artifact of plant size and
density (Oksanen 1996). For low-biomass sites, it assumes that plants
have a fixed size, and biomass increases with increasing number of
plants. When the sites becomes crowded, the number of plants and
species richness reaches the maximum. Higher biomass is reached by
increasing the plant size, and then the number of plants and species
richness will decrease. At biomasses below the hump, plant number and
biomass are linearly related, and above the hump, plant number is
proportional to inverse squared biomass. The number of plants is
related to the number of species by the relationship (link
function) from Fisher's log-series (Fisher et al. 1943).
The parameters of the model are:
hump
: the location of the hump on the biomass gradient.
scale
: an arbitrary multiplier to translate the biomass
into virtual number of plants.
alpha
: Fisher's alpha to translate the
virtual number of plants into number of species.
The parameters scale
and alpha
are intermingled and this
function should not be used for estimating Fisher's
alpha. Probably the only meaningful and interesting
parameter is the location of the hump
.
The original model intended to show that there is no need to speculate about `competition' and `stress' (Al-Mufti et al. 1977), but humped response can be produced as an artifact of using fixed plot size for varying plant sizes and densities.
The function returns an object of class "humpfit"
inheriting
from class "glm"
. The result object has specific
summary
, predict
, plot
, points
and
lines
methods. In addition, it can be accessed by the following
methods for glm
objects: AIC
,
extractAIC
, deviance
, coef
,
residuals.glm
(except type = "partial"
),
fitted
, and perhaps some others.
The function is a replacement for the original GLIM4
function
at the archive of Journal of Ecology. There the function was
represented as a mixed glm
with one non-linear
parameter (hump
) and a special one-parameter link function from
Fisher's log-series. The current function directly applies non-linear
maximum likelihood fitting using function nlm
. Some
expected problems with the current approach are:
hump
and may be
difficult to optimize in some cases (the lines will always join, but
the derivative jumps).
scale
and
alpha
should always be positive. Perhaps they should be
fitted as logarithmic (which could improve the symmetry of
confidence limits, too, but this needs research, and a
profile
function). Fitting Gamma
family
models might become easier, too.
Jari Oksanen
Al-Mufti, M.M., Sykes, C.L, Furness, S.B., Grime, J.P & Band, S.R. (1977) A quantitative analysis of shoot phenology and dominance in herbaceous vegetation. Journal of Ecology 65,759–791.
Fisher, R.A., Corbet, A.S. & Williams, C.B. (1943) The relation between the number of species and the number of individuals in a random sample of of an animal population. Journal of Animal Ecology 12, 42–58.
Oksanen, J. (1996) Is the humped relationship between species richness and biomass an artefact due to plot size? Journal of Ecology 84, 293–295.
## ## Data approximated from Al-Mufti et al. (1977) ## mass <- c(140,230,310,310,400,510,610,670,860,900,1050,1160,1900,2480) spno <- c(1, 4, 3, 9, 18, 30, 20, 14, 3, 2, 3, 2, 5, 2) sol <- humpfit(mass, spno) summary(sol) # Almost infinite alpha... plot(sol)