Created
February 22, 2015 14:38
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| library(dplyr) | |
| # install.packages("rgeos", type="source") | |
| # install.packages("rgbif", type="source") | |
| # library(rgbif) | |
| # d <- occ_search(orderKey=797, datasetKey="a8d08280-1def-11de-be11-b8a03c50a862", year="2013", limit=2000) | |
| library(RJSONIO) | |
| gen.template <- "http://hyonteiset.luomus.fi/insects/json?op=%s&order=Lep&%s" | |
| kuhmo.url <- sprintf(gen.template, "search", "&county=Kuhmo&startYear=2013&endYear=2013&select=all") | |
| jsobj <- readLines(kuhmo.url) | |
| Encoding(jsobj) <- "latin1" | |
| d.orig <- plyr::ldply(fromJSON(jsobj), identity) %>% | |
| filter(grepl("[0-9]+W|valorysä", method) & grepl("Marko Tähtinen|Hannu Saarenmaa", observer)) %>% | |
| mutate(name=paste(genus, species, sep=" "), count=as.integer(totalCount)) | |
| d <- d %>% | |
| select(name, count) %>% | |
| group_by(name) %>% | |
| summarise(count=sum(count)) | |
| plot(log(-sort(-d$count))) | |
| m.ls <- sads::fitsad(d$count, "ls") | |
| m.ls | |
| sqrt(m.ls@vcov[1, 1]) # approximate posterior sd of alpha | |
| m.mzsm <- sads::fitsad(d$count, "mzsm") | |
| m.mzsm | |
| sqrt(m.mzsm@vcov[1, 1]) # approximate posterior sd of theta | |
| data.frame(n.speciments=1:10, | |
| real.count=table(d$count)[1:10], | |
| pred.ls=nrow(d)*sads::dls(1:10, sum(d$count), m.ls@coef), | |
| pred.mzsm=nrow(d)*sads::dmzsm(1:10, sum(d$count), m.mzsm@coef)) | |
| # Per yday there's too little data to get proper estimates for theta or alpha. | |
| # (Also the gaussian approximation for the posterior breaks up.) | |
| d2 <- d.orig %>% | |
| select(name, count, startDay, startMonth) %>% | |
| mutate(yday=30*as.integer(startMonth)+as.integer(startDay)) %>% | |
| group_by(yday, name) %>% | |
| summarise(count=sum(count)) | |
| library(ggplot2) | |
| d2 %>% do({ m <- sads::fitsad(.$count, "ls"); data.frame(alpha=m@coef, sd=m@vcov[1, 1])}) %>% | |
| ggplot(., aes(x=yday, y=alpha, ymin=alpha-sd, ymax=alpha+sd)) + geom_line() + geom_ribbon(alpha=.2) | |
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