Description Usage Arguments Details Value Author(s)
cscore_site
to calculate C-score for each site.
1 2 | cscore_site(df, method = "c0", nsimul = 1000, rarefy = FALSE, n = 1000,
q = 20)
|
df |
data frame of vegtation data. Should have site, quad, sp columns. This function will call wide_by_site function inside. |
method |
methods for building null models. Check oecosium from vegan package for more options. 'c0' for fixed species incidence and equalprobalility for site (site species richness can vary); 'quasiswap' for fixed sp - fixed site, suppose to be faster; 'tswap' also for fixed-fixed but slower. Default is 'c0'. |
nsimul |
how many null communities to use for simulation? Default is 1000. |
rarefy |
Do you want to rarefy sites or not? Default is FALSE. |
n |
used only if rarefy=TRUE. n times of ramdom sampling from quadrats of 2000s data for each site. |
q |
used only if rarefy=TRUE. How many quadrats to sample out for 2000s data for all sites. |
If no rarefy, this function uses wide_by_site() function to change long veg table into wide table for each site (returned a list), then for each site of the list, calculate the standardized effect size z = (X_obs - X_meanSim) / sd_sim using null models. If rarefy=TRUE, it calls wide_by_site_rarefy() function to change long veg table into wide table for each site n times
If no rarefy, it returns a dataframe. It has 'z', 'means_sim', 'pval', 'cs_obs', 'site' columns. If rarefy=TRUE, it returns a list: detail and summary for all sites.
Daijiang Li
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