borealbirds/qpad

Calibrating indices of avian density from non-standardized survey data

qpad's Issues

Problem with edr matrix....

I'm experiencing an issue with the localBAMcorrections function in QPAD version 3. It seems to be related to incorporating LCC values into the detection probability (q). The error references "Xr" and occurs only when the edr model specified is >1. It does not occur for model.edr=2 in QPAD version 2.

Update: It seems to be a leveling issue within the LCC variable - either unrecognized categories or missing levels, I was still getting errors in version 2 for my own data until I added empty factor levels so that levels 1-5 were present; I'm still having issues in version 3...

For example, using the ovenbird data (with LCC and pforest derived as in the supplement of Solymos et al. 2013):

bm <- bestmodelBAMspecies("OVEN", type = "BIC")
bc <- with(oven, localBAMcorrections("OVEN", t = dur, r = dist,
jday = JDAY, tssr = TSSR, tree = pforest, lcc = LCC, model.sra = bm$sra,
model.edr = bm$edr))

#Error in Xr %*% coefBAMspecies(species, model.sra, model.edr)$edr : requires
numeric/complex matrix/vector arguments

Add option for AIc

Weights in selectmodelBAMspecies: only AIC reported

weights should be calculated for AIC, BIC (and AICc for v3)