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chl_pinellas.R
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chl_pinellas.R
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# setup -------------------------------------------------------------------
library(tidyverse)
library(tbeptools)
library(sf)
library(lubridate)
library(patchwork)
library(readxl)
library(gridExtra)
prj <- 4326
# otb wq data, stations, segments -----------------------------------------
# OTB pts
otbsta <- stations %>%
filter(bay_segment %in% 'OTB') %>%
st_as_sf(coords = c('Longitude', 'Latitude'), crs = prj)
epcdata <- read_importwq('epcdata.xlsx', download_latest = T)
# sf object of chl in otb, subset to date range for modis data
otbepc <- epcdata %>%
filter(bay_segment %in% 'OTB') %>%
dplyr::select(SampleTime, bay_segment, epchc_station, chla) %>%
mutate(date = as.Date(SampleTime)) %>%
dplyr::group_by(date, bay_segment, epchc_station) %>%
dplyr::summarise(chla = mean(chla, na.rm = T), .groups = 'drop') %>%
na.omit %>%
mutate(
mo = month(date),
yr = year(date)
) %>%
left_join(stations, by = c('epchc_station', 'bay_segment')) %>%
st_as_sf(coords = c('Longitude', 'Latitude'), crs = prj) %>%
filter(date >= min(otbpic$date) & date <= max(otbpic$date))
# otb segment polygon
otbseg <- tbseg %>%
dplyr::filter(bay_segment %in% 'OTB')
# otb segment averages
otbavg <- epcdata %>%
anlz_avedat %>%
.$mos %>%
dplyr::filter(bay_segment %in% 'OTB') %>%
spread(var, val) %>%
dplyr::select(-mean_la)
# pinellas co data --------------------------------------------------------
# data from query here https://www.tampabay.wateratlas.usf.edu/datadownload/Filters.aspx
picdata <- read_excel('pinellascowq.xlsx')
# raw data as sf, otb clip
otbpic <- picdata %>%
.[, 1:21] %>%
dplyr::filter(Parameter %in% 'Chla_ugl') %>%
select(StationName, StationID = Actual_StationID, Longitude = Actual_Longitude, Latitude = Actual_Latitude, date = SampleDate, chla = Result_Value) %>%
mutate(
date = as.Date(date),
mo = month(date),
yr = year(date),
Longitude = ifelse(Longitude > 0, -1 * Longitude, Longitude)
) %>%
st_as_sf(coords = c('Longitude', 'Latitude'), crs = prj) %>%
.[otbseg, ]
# extract pinellas county by proximity ------------------------------------
dst <- 0.01
bffotbsta <- st_buffer(otbsta, dist = dst)
mapview(otbpic[bffotbsta, ]) + mapview(bffotbsta, col.regions = 'red')
otbpicavg <- otbpic %>%
.[bffotbsta, ] %>%
st_set_geometry(NULL) %>%
group_by(yr, mo) %>%
summarise(mean_chla = mean(chla, na.rm = T), .groups = 'drop')
out1 <- otbpicavg %>%
inner_join(otbavg, by = c("mo", "yr")) %>%
rename(
pic_chla = mean_chla.x,
epc_chla = mean_chla.y
)
# OTB segment averages ----------------------------------------------------
otbpicavg <- otbpic %>%
st_set_geometry(NULL) %>%
group_by(yr, mo) %>%
summarise(mean_chla = mean(chla, na.rm = T), .groups = 'drop')
out2 <- otbpicavg %>%
inner_join(otbavg, by = c("mo", "yr")) %>%
rename(
pic_chla = mean_chla.x,
epc_chla = mean_chla.y
)
# some plots --------------------------------------------------------------
toplo1 <- out1
toplo2 <- out1 %>%
filter(mo %in% c(4, 5))
toplo3 <- out2
toplo4 <- out2 %>%
filter(mo %in% c(4, 5))
xlb <- "Pinellas co. chl-a"
ylb <- "EPC chl-a"
ttl1 <- 'OTB station, EPC chl matched to monthly ave of Pinellas stations with spatial buffer'
ttl2 <- 'OTB segment ave, EPC chl matched to monthly ave of all Pinellas stations'
p1 <- ggplot(toplo1, aes(x = pic_chla, y = epc_chla)) +
geom_point() +
theme_bw() +
scale_y_log10() +
scale_x_log10() +
geom_smooth(method = 'lm', se = F) +
geom_abline(aes(intercept = 0, slope = 1)) +
labs(
x = xlb,
y = ylb,
subtitle = 'All months'
)
p2 <- ggplot(toplo2, aes(x = pic_chla, y = epc_chla)) +
geom_point() +
theme_bw() +
scale_y_log10() +
scale_x_log10() +
geom_smooth(method = 'lm', se = F) +
geom_abline(aes(intercept = 0, slope = 1)) +
labs(
x = xlb,
y = ylb,
subtitle = 'April, May only'
)
p3 <- ggplot(toplo3, aes(x = pic_chla, y = epc_chla)) +
geom_point() +
theme_bw() +
scale_y_log10() +
scale_x_log10() +
geom_smooth(method = 'lm', se = F) +
geom_abline(aes(intercept = 0, slope = 1)) +
labs(
x = xlb,
y = ylb,
subtitle = 'All months'
)
p4 <- ggplot(toplo4, aes(x = pic_chla, y = epc_chla)) +
geom_point() +
theme_bw() +
scale_y_log10() +
scale_x_log10() +
# facet_wrap(~epchc_station) +
geom_smooth(method = 'lm', se = F) +
geom_abline(aes(intercept = 0, slope = 1)) +
labs(
x = xlb,
y = ylb,
subtitle = 'April, May only'
)
p <- grid.arrange(
arrangeGrob(p1, p2, top = grid::textGrob(ttl1), ncol = 2),
arrangeGrob(p3, p4, top = grid::textGrob(ttl2), ncol = 2),
ncol = 1
)
png('figures/epcvpinchl.png', height = 8, width = 8, units = 'in', res = 300)
plot(p)
dev.off()