knitr::opts_chunk$set(echo = TRUE, eval = FALSE)
library(dplyrOracle) library(mar) db <- src_oracle("mar") Station <- husky::STODVAR %>% bind_rows() %>% filter(tognumer %in% 1:39) %>% select(id = synis.id, year = ar, towlength = toglengd, strata = newstrata, reitur, tognumer, lon, lat) %>% mutate(towlength = pax:::trim_towlength(towlength), mult = 1) %>% arrange(id) %>% mutate(sid = paste(reitur, tognumer)) %>% select(-c(reitur, tognumer)) # Use same strata for 2017 stations as last year x <- Station %>% filter(year == 2016) %>% select(sid, strata) st <- lesa_stodvar(db) %>% mutate(lon = ifelse(!is.na(hift_v_lengd), (kastad_v_lengd + hift_v_lengd)/2, kastad_v_lengd), lat = ifelse(!is.na(hift_n_breidd), (kastad_n_breidd + hift_n_breidd)/2, kastad_n_breidd)) %>% filter(veidarfaeri %in % 73, ar == 2017, tognumer %in% 1:39) %>% select(id = synis_id, year = ar, towlength = toglengd, reitur, tognumer, lon, lat) %>% collect(n = Inf) %>% mutate(towlength = pax:::trim_towlength(towlength), mult = 1, sid = paste(reitur, tognumer)) %>% select(-c(reitur, tognumer)) %>% left_join(x) %>% filter(!is.na(strata)) table(!is.na(st$strata)) st %>% ggplot(aes(lon, lat)) + geom_point() + coord_quickmap() Station <- Station %>% filter(sid %in% st$sid) %>% bind_rows(st) %>% select(id, year, towlength, strata, lon, lat) %>% mutate(mult = 1) Stratas <- husky::stratas_df %>% select(strata, area = rall.area) res <- calc_length_indices(Station, Stratas, SPECIES = 1, oracle = TRUE) tidy_fixed <- res$aggr %>% filter(length == 5) %>% mutate(source = "tidy") tidy_fixed %>% select(year, cb, cb.cv) %>% ggplot(aes(year, cb)) + geom_pointrange(aes(ymin = cb * (1 - cb.cv), ymax = cb * (1 + cb.cv)), colour = "red", lwd = 1) + geom_line(colour = "red", lwd = 1) + scale_colour_brewer(palette = "Set1") res$aggr %>% filter(year %in% c(2005:2017)) %>% ggplot(aes(length, n)) + geom_line() + facet_wrap(~ year) x <- res$aggr %>% filter(year %in% c(2014:2017)) %>% group_by(length) %>% mutate(n.mean = mean(n), b.mean = mean(b)) x %>% ggplot(aes(length)) + theme_bw() + geom_polygon(aes(y = n.mean), fill = "grey") + geom_ribbon(aes(ymin = n * (1 - n.cv), ymax = n * (1 + n.cv)), fill = "pink", alpha = 0.6) + geom_line(aes(y = n), colour = "red") + facet_grid(year ~ .) + labs(x = NULL, y = NULL, title = "Abundance indices", subtitle = "All years: only tows that have so far been taken in 2017") x %>% ggplot(aes(length)) + theme_bw() + geom_polygon(aes(y = b.mean), fill = "grey") + geom_ribbon(aes(ymin = b * (1 - b.cv), ymax = b * (1 + b.cv)), fill = "pink", alpha = 0.6) + geom_line(aes(y = b), colour = "red") + facet_grid(year ~ .) cpue <- catch_by_station(1, Station, std = "towlength", oracle = TRUE) cpue %>% filter(length == 5, year %in% 2014:2017) %>% ggplot(aes(lon, lat, size = cb)) + theme_bw() + geom_point(col = "red", alpha = 0.4) + facet_wrap(~ year) + scale_size_area(max_size = 15)
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