# Species abundance models  - použijeme data ktera jsou k dispozici v R-ku
# data(BCI) - 50 společenstev a 225 druhů; pro matematicke modely potrebujeme velka spolecenstva


library (vegan)
data(BCI)             
a <- BCI[1, ]
b <- BCI[2, ]
c <- BCI[3, ]
Na <- rowSums(a)
Nb <- rowSums(b)
Nc <- rowSums(c)
Sa <- specnumber(a)
Sb <- specnumber(b)
Sc <- specnumber(c)
Na
Nb
Nc
Sa
Sb
Sc

# Functions rad.null, rad.preempt, rad.lognormal, rad.zipf and zipfbrot fit the individual models for a single vector 
# (row of data frame), and function radfit fits all models.# The argument of the function radfit can be either a vector for a single community
# or a data frame where # each row represents a distinct community.

model.preempt_a <- rad.preempt(a)         # geometric series   
model.preempt_a
plot(model.preempt_a)

model.lognormal_a <- rad.lognormal(a)     # lognormal
model.lognormal_a
plot(model.lognormal_a)

model.null_a <- rad.null(a)               # brocken stick
model.null_a
plot(model.null_a)

# podle hodnoty AIC a BIC muzeme shodnotit ktery model lepe vystihuje pozorovana data


models_a <- radfit(a)
                  # vsechny modely
plot(models_a)

## Lattice graphics separately for each model

radlattice(models_a)