Description Usage Arguments Details Value Authors Examples
MDMnMod
1 |
MDMn.form |
an object of class "formula" (or one that can be coerced to that class):a symbolic description of the model to be fitted. Must include both the response and covariates |
data |
a data frame containing the variables in the formula. Must contain a column with the ordered (most to least) abundances for each site. Covariates must be repeated for each row belonging to a site. |
ID |
Vector of site identifiers for all observations. For every abundance (row) that comes from a site, the same identifier must be used. The length of ID must equal nrows(data) |
dist |
one of either multinomial "Mn" or Dirichlet Multinomial "DMN" or Modified Dirichlet Multinomial "MDMn" (default) |
scale.covar |
Should the model matrix be scaled (TRUE/FALSE)? Useful if models do not converge. Setting this to TRUE will save the column means and sd for later prediction. |
est.var |
estimate the variance-covariance matrix using newton-raphson |
calc.resid |
should residuals be calculated? |
trace |
print model trace |
Fits a selected distribution to the vector of relative abundances. See Foster and Dunstan 2009 for details.
coef |
coefficents |
vcov |
variance-covariance matrix |
logl |
log-likelihood |
AIC |
AIC |
residuals |
model residuals, calculated using PIT |
fitted |
matrix of fitted values (nij and pij) |
mean.X |
column means for model matrix if scale.covar is TRUE |
sd.X |
column sds for model matrix if scale.covar is TRUE |
formula |
model formula |
Piers Dunstan and Scott Foster
1 2 3 4 5 6 7 8 | head(n.data)
## format for the data object
n.data$N.scale <- n.data$N/n.data$area
n.data$S.scale <- n.data$S/n.data$area
nij.form <- nij~1 + N.scale + S.scale + depth + O2_AV + temp_AV
model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)
plot(model.nij$fitted$nij,model.nij$residuals)
plot(log(model.nij$fitted$nij),model.nij$residuals)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.