2. Real-time Fish Detections
library(leaflet)
library(maps)
library(htmlwidgets)
library(leaflet.extras)
library(dplyr)
library(dbplyr)
library(DBI)
library(odbc)
library(data.table)
# Create connection with cloud database
con <- dbConnect(odbc(),
Driver = "SQL Server",
Server = "calfishtrack-server.database.windows.net",
Database = "realtime_detections",
UID = "realtime_user",
PWD = "Pass@123",
Port = 1433)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
## THIS CODE CHUNK WILL NOT WORK IF USING ONLY ERDDAP DATA, REQUIRES ACCESS TO LOCAL FILES
if (nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) == 0){
cat("No detections yet")
# Use dbplyr to load realtime_locs and qryHexCodes sql table
gen_locs <- tbl(con, "realtime_locs") %>% collect()
# gen_locs <- read.csv("realtime_locs.csv", stringsAsFactors = F) %>% filter(is.na(stop))
leaflet(data = gen_locs[is.na(gen_locs$stop),]) %>%
# setView(-72.14600, 43.82977, zoom = 8) %>%
addProviderTiles("Esri.WorldStreetMap", group = "Map") %>%
addProviderTiles("Esri.WorldImagery", group = "Satellite") %>%
addProviderTiles("Esri.WorldShadedRelief", group = "Relief") %>%
# Marker data are from the sites data frame. We need the ~ symbols
# to indicate the columns of the data frame.
addMarkers(~longitude, ~latitude, label = ~general_location, group = "Receiver Sites", popup = ~location) %>%
# addAwesomeMarkers(~lon_dd, ~lat_dd, label = ~locality, group = "Sites", icon=icons) %>%
addScaleBar(position = "bottomleft") %>%
addLayersControl(
baseGroups = c("Street Map", "Satellite", "Relief"),
overlayGroups = c("Receiver Sites"),
options = layersControlOptions(collapsed = FALSE)) %>%
addSearchFeatures(targetGroups = c("Receiver Sites"))
} else {
# Use dbplyr to load realtime_locs and qryHexCodes sql table
gen_locs <- tbl(con, "realtime_locs") %>% collect()
# gen_locs <- read.csv("realtime_locs.csv", stringsAsFactors = F)
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life)*1.5)))
beacon_by_day <- fread("beacon_by_day.csv", stringsAsFactors = F) %>%
mutate(day = as.Date(day)) %>%
# Subset to only look at data for the correct beacon for that day
filter(TagCode == beacon) %>%
# Only keep beacon by day for days since fish were released
filter(day >= as.Date(min(study_tagcodes$release_time)) & day <= endtime) %>%
dplyr::left_join(., gen_locs[,c("location", "general_location","rkm")], by = "location")
arrivals_per_day <- detects_study %>%
group_by(general_location, TagCode) %>%
summarise(DateTime_PST = min(DateTime_PST, na.rm = T)) %>%
arrange(TagCode, general_location) %>%
mutate(day = as.Date(DateTime_PST, "%Y-%m-%d", tz = "Etc/GMT+8")) %>%
group_by(day, general_location) %>%
summarise(New_arrivals = length(TagCode)) %>%
na.omit() %>%
mutate(day = as.Date(day)) %>%
dplyr::left_join(unique(beacon_by_day[,c("general_location", "day", "rkm")]), .,
by = c("general_location", "day")) %>%
arrange(general_location, day) %>%
mutate(day = as.factor(day)) %>%
filter(general_location != "Bench_test") %>% # Remove bench test
filter(!(is.na(general_location))) # Remove NA locations
## Remove sites that were not operation the whole time
#### FOR THE SEASONAL SURVIVAL PAGE, KEEP ALL SITES SINCE PEOPLE WANT TO SEE DETECTIONS OF LATER FISH AT NEWLY
#### DEPLOYED SPOTS
gen_locs_days_in_oper <- arrivals_per_day %>%
group_by(general_location) %>%
summarise(days_in_oper = length(day))
#gen_locs_days_in_oper <- gen_locs_days_in_oper[gen_locs_days_in_oper$days_in_oper ==
# max(gen_locs_days_in_oper$days_in_oper),]
arrivals_per_day_in_oper <- arrivals_per_day %>%
filter(general_location %in% gen_locs_days_in_oper$general_location)
fish_per_site <- arrivals_per_day_in_oper %>%
group_by(general_location) %>%
summarise(fish_count = sum(New_arrivals, na.rm=T))
gen_locs_mean_coords <- gen_locs %>%
filter(is.na(stop) & general_location %in% fish_per_site$general_location) %>%
group_by(general_location) %>%
summarise(latitude = mean(latitude), # estimate mean lat and lons for each genloc
longitude = mean(longitude))
fish_per_site <- merge(fish_per_site, gen_locs_mean_coords)
release_stats_agg <- aggregate(cbind(Release_lon, Release_lat) ~ Release_location, data = release_stats[release_stats$Release != "ALL",], FUN = mean)
release_stats_agg <- merge(release_stats_agg, aggregate(Number_fish_released ~ Release_location, data = release_stats[release_stats$Release != "ALL",], FUN = sum))
if(!is.na(release_stats$Release_lat[1])){
leaflet(data = fish_per_site) %>%
addProviderTiles("Esri.WorldStreetMap", group = "Map") %>%
addProviderTiles("Esri.WorldImagery", group = "Satellite") %>%
addProviderTiles("Esri.WorldShadedRelief", group = "Relief") %>%
# Marker data are from the sites data frame. We need the ~ symbols
# to indicate the columns of the data frame.
addPulseMarkers(data = fish_per_site[seq(from = 1, to = nrow(fish_per_site), by = 2),], lng = ~longitude, lat = ~latitude, label = ~fish_count,
labelOptions = labelOptions(noHide = T, direction = "left", textsize = "15px"), group = "Receiver Sites",
popup = ~general_location, icon = makePulseIcon(heartbeat = 1.3)) %>%
addPulseMarkers(data = fish_per_site[seq(from = 2, to = nrow(fish_per_site), by = 2),], lng = ~longitude, lat = ~latitude, label = ~fish_count,
labelOptions = labelOptions(noHide = T, direction = "right", textsize = "15px"), group = "Receiver Sites",
popup = ~general_location, icon = makePulseIcon(heartbeat = 1.3)) %>%
addCircleMarkers(data = release_stats_agg, ~Release_lon, ~Release_lat, label = ~Number_fish_released, stroke = F, color = "blue", fillOpacity = 1,
group = "Release Sites", popup = ~Release_location, labelOptions = labelOptions(noHide = T, textsize = "15px")) %>%
addScaleBar(position = "bottomleft") %>%
addLegend("bottomright", labels = c("Receivers", "Release locations"), colors = c("red","blue")) %>%
addLayersControl(baseGroups = c("Street Map", "Satellite", "Relief"), options = layersControlOptions(collapsed = FALSE))
} else {
leaflet(data = fish_per_site) %>%
addProviderTiles("Esri.WorldStreetMap", group = "Map") %>%
addProviderTiles("Esri.WorldImagery", group = "Satellite") %>%
addProviderTiles("Esri.WorldShadedRelief", group = "Relief") %>%
# Marker data are from the sites data frame. We need the ~ symbols
# to indicate the columns of the data frame.
addPulseMarkers(lng = fish_per_site$longitude, lat = fish_per_site$latitude, label = ~fish_count,
labelOptions = labelOptions(noHide = T, textsize = "15px"), group = "Receiver Sites",
popup = ~general_location, icon = makePulseIcon(heartbeat = 1.3)) %>%
addScaleBar(position = "bottomleft") %>%
addLayersControl(baseGroups = c("Street Map", "Satellite", "Relief"),
options = layersControlOptions(collapsed = FALSE))
}
}
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
if (nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) > 0){
detects_study <- detects_study[order(detects_study$TagCode, detects_study$DateTime_PST),]
## Now estimate the time in hours between the previous and next detection, for each detection.
detects_study$prev_genloc <- shift(detects_study$general_location, fill = NA, type = "lag")
#detects_study$prev_genloc <- shift(detects_study$General_Location, fill = NA, type = "lag")
## Now make NA the time diff values when it's between 2 different tagcodes or genlocs
detects_study[which(detects_study$TagCode != shift(detects_study$TagCode, fill = NA, type = "lag")), "prev_genloc"] <- NA
detects_study[which(detects_study$general_location != detects_study$prev_genloc), "prev_genloc"] <- NA
detects_study$mov_score <- 0
detects_study[is.na(detects_study$prev_genloc), "mov_score"] <- 1
detects_study$mov_counter <- cumsum(detects_study$mov_score)
detects_summary <- aggregate(list(first_detect = detects_study$DateTime_PST), by = list(TagCode = detects_study$TagCode, release_time = detects_study$release_time, mov_counter = detects_study$mov_counter ,general_location = detects_study$general_location, river_km = detects_study$river_km, release_rkm = detects_study$release_rkm), min)
detects_summary <- detects_summary[is.na(detects_summary$first_detect) == F,]
releases <- aggregate(list(first_detect = detects_study$release_time), by = list(TagCode = detects_study$TagCode, release_time = detects_study$release_time, release_location=detects_study$release_location, release_rkm = detects_study$release_rkm), min)
releases$river_km <- releases$release_rkm
releases$mov_counter <- NA
releases$general_location <- paste(releases$release_location,"_RELEASE", sep = "")
releases$release_location <- NULL
detects_summary <- rbindlist(list(detects_summary, releases), use.names = T)
detects_summary <- detects_summary[order(detects_summary$TagCode, detects_summary$first_detect),]
starttime <- as.Date(min(detects_study$release_time), "Etc/GMT+8")
## Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d"))+1, max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
#par(mar=c(6, 5, 2, 5) + 0.1)
plot_ly(detects_summary, x = ~first_detect, y = ~river_km, color = ~TagCode, width = 900, height = 600, dynamicTicks = TRUE, connectgaps = TRUE, mode = "lines+markers", type = "scatter",hoverinfo = "text",
text = ~paste("</br> TagCode: ", TagCode,
"</br> Arrival: ", first_detect,
"</br> Location: ", general_location)) %>%
layout(showlegend = T,
xaxis = list(title = "<b> Date <b>", mirror=T,ticks="outside",showline=T, range=c(starttime,endtime)),
yaxis = list(title = "<b> Kilometers upstream of the Golden Gate <b>", mirror=T,ticks="outside",showline=T, range=c(max(detects_study$Rel_rkm)+10, min(gen_locs[is.na(gen_locs$stop),"rkm"])-10)),
legend = list(title=list(text='<b> Tag Code </b>')),
margin=list(l = 50,r = 100,b = 50,t = 50)
)
}else{
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Kilometers upstream of the Golden Gate")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
}
_______________________________________________________________________________________________________
library(tidyr)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_3 <- detects_study %>% filter(general_location == "Stan_Valley_Oak")
if(nrow(detects_3) == 0){
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else {
detects_3 <- detects_3 %>%
dplyr::left_join(., detects_3 %>%
group_by(TagCode) %>%
summarise(first_detect = min(DateTime_PST))) %>%
mutate(Day = as.Date(as.Date(first_detect, "Etc/GMT+8")))
starttime <- as.Date(min(detects_3$release_time), "Etc/GMT+8")
# Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_3$Release))])
tagcount1 <- detects_3 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
# Download flow data
flow_day <- readNWISuv(siteNumbers = "11303000", parameterCd="00060", startDate = starttime,
endDate = endtime+1) %>%
mutate(Day = as.Date(format(dateTime, "%Y-%m-%d"))) %>%
group_by(Day) %>%
summarise(parameter_value = mean(X_00060_00000))
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange2 <- daterange1[,order(colnames(daterange1))] %>%
dplyr::left_join(., flow_day, by = "Day")
rownames(daterange2) <- daterange2$Day
daterange2$Date <- daterange2$Day
daterange2$Day <- NULL
daterange2_flow <- daterange2 %>% select(Date, parameter_value)
daterange3 <- melt(daterange2[,!(names(daterange2) %in% c("parameter_value"))],
id.vars = "Date", variable.name = ".")
daterange3$. <- factor(daterange3$., levels = sort(unique(daterange3$.), decreasing = T))
par(mar=c(6, 5, 2, 5) + 0.1)
ay <- list(
overlaying = "y",
nticks = 5,
color = "#947FFF",
side = "right",
title = "Flow (cfs) at Ripon",
automargin = TRUE
)
plot_ly(daterange3, width = 900, height = 600, dynamicTicks = TRUE) %>%
add_bars(x = ~Date, y = ~value, color = ~.) %>%
add_annotations(text="Release (click on legend items to isolate)", xref="paper", yref="paper",
x=0.01, xanchor="left",
y=1.056, yanchor="top", # Same y as legend below
legendtitle=TRUE, showarrow=FALSE ) %>%
add_lines(x=~daterange2_flow$Date,
y=~daterange2_flow$parameter_value,
line = list(color = alpha("#947FFF", alpha = 0.5)), yaxis="y2", showlegend=FALSE,
inherit=FALSE) %>%
layout(yaxis2 = ay,showlegend = T,
barmode = "stack",
xaxis = list(title = "Date", mirror=T,ticks="outside",showline=T),
yaxis = list(title = "Number of fish arrivals per day", mirror=T,ticks="outside",showline=T),
legend = list(orientation = "h",x = 0.34, y = 1.066),
margin=list(l = 50,r = 100,b = 50,t = 50))
}
_______________________________________________________________________________________________________
library(tidyr)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_3 <- detects_study %>% filter(general_location == "Stan_Caswell")
if(nrow(detects_3) == 0){
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else {
detects_3 <- detects_3 %>%
dplyr::left_join(., detects_3 %>%
group_by(TagCode) %>%
summarise(first_detect = min(DateTime_PST))) %>%
mutate(Day = as.Date(as.Date(first_detect, "Etc/GMT+8")))
starttime <- as.Date(min(detects_3$release_time), "Etc/GMT+8")
# Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_3$Release))])
tagcount1 <- detects_3 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
# Download flow data
flow_day <- readNWISuv(siteNumbers = "11303000", parameterCd="00060", startDate = starttime,
endDate = endtime+1) %>%
mutate(Day = as.Date(format(dateTime, "%Y-%m-%d"))) %>%
group_by(Day) %>%
summarise(parameter_value = mean(X_00060_00000))
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange2 <- daterange1[,order(colnames(daterange1))] %>%
dplyr::left_join(., flow_day, by = "Day")
rownames(daterange2) <- daterange2$Day
daterange2$Date <- daterange2$Day
daterange2$Day <- NULL
daterange2_flow <- daterange2 %>% select(Date, parameter_value)
daterange3 <- melt(daterange2[,!(names(daterange2) %in% c("parameter_value"))],
id.vars = "Date", variable.name = ".")
daterange3$. <- factor(daterange3$., levels = sort(unique(daterange3$.), decreasing = T))
par(mar=c(6, 5, 2, 5) + 0.1)
ay <- list(
overlaying = "y",
nticks = 5,
color = "#947FFF",
side = "right",
title = "Flow (cfs) at Ripon",
automargin = TRUE
)
plot_ly(daterange3, width = 900, height = 600, dynamicTicks = TRUE) %>%
add_bars(x = ~Date, y = ~value, color = ~.) %>%
add_annotations(text="Release (click on legend items to isolate)", xref="paper", yref="paper",
x=0.01, xanchor="left",
y=1.056, yanchor="top", # Same y as legend below
legendtitle=TRUE, showarrow=FALSE ) %>%
add_lines(x=~daterange2_flow$Date,
y=~daterange2_flow$parameter_value,
line = list(color = alpha("#947FFF", alpha = 0.5)), yaxis="y2", showlegend=FALSE,
inherit=FALSE) %>%
layout(yaxis2 = ay,showlegend = T,
barmode = "stack",
xaxis = list(title = "Date", mirror=T,ticks="outside",showline=T),
yaxis = list(title = "Number of fish arrivals per day", mirror=T,ticks="outside",showline=T),
legend = list(orientation = "h",x = 0.34, y = 1.066),
margin=list(l = 50,r = 100,b = 50,t = 50))
}
_______________________________________________________________________________________________________
library(dplyr)
library(cder)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
recv_locs <- gen_locs
detects_3 <- detects_study %>% filter(general_location %in% c("Old_River_Quimby", "Holland_Cut_Quimby", "Old River", "MiddleRiver", "Clifton_Court_US_Radial_Gates", "SWP_radial_gates_DS", "SWP_radial_gates_US", "CVP_Trash_Rack_1", "CVP_Tank", "SWP_intake", "Clifton_Court_Intake_Canal"))
if(nrow(detects_3) > 0){
# Save the last detection at each location
detects_3 <- detects_3 %>%
dplyr::left_join(., detects_3 %>%
group_by(TagCode, general_location) %>%
summarise(last_detect = max(DateTime_PST))) %>%
mutate(Day = as.Date(last_detect, "Etc/GMT+8")) # Convert last detection to day
starttime <- as.Date(min(detects_3$release_time), "Etc/GMT+8")
## Endtime should be either now or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
daterange <- data.frame(Date = seq.Date(from = starttime, to = endtime, by = "day"))
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_3$Release))])
tagcount1 <- detects_3 %>%
group_by(Day, general_location) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
rename(., Date = Day, Location = general_location) %>%
mutate(Location = factor(Location, levels = c("Old_River_Quimby", "Holland_Cut_Quimby", "Old River",
"MiddleRiver", "Clifton_Court_US_Radial_Gates",
"SWP_radial_gates_DS", "SWP_radial_gates_US",
"CVP_Trash_Rack_1", "CVP_Tank", "SWP_intake",
"Clifton_Court_Intake_Canal")))
tagcount1 <- reshape2::dcast(tagcount1, Date ~ Location, drop = FALSE)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
daterange2 <- daterange1
rownames(daterange2) <- daterange2$Date
par(mar=c(6, 5, 2, 5) + 0.1)
daterange3 <- melt(daterange2, id.vars = "Date", variable.name = ".", )
# Add latitude to daterange df
locs <- data.frame(general_location = unique(daterange3$.)) %>%
left_join(., recv_locs, by = "general_location") %>% filter(is.na(stop) | stop > min(detects_3$RelDT)) %>%
select(location, general_location, latitude) %>% group_by(general_location) %>%
summarise(latitude = mean(latitude))
locs <- locs[order(locs$latitude, decreasing = FALSE),]
locs$loc_num <- seq.int(nrow(locs))
daterange4 <- daterange3 %>% left_join(., locs, by = c("." = "general_location"))
# Get flow data from CDEC
flow <- cdec_query("OMR", "20", "H", starttime, endtime)
# Fish movement
move_df <- detects_3 %>%
distinct(., TagCode, last_detect, general_location,
.keep_all = TRUE) # find last detection and remove duplicate value for that column
dup_codes <- move_df$TagCode[which(duplicated(move_df$TagCode))] # then get the tag codes that were detected at multiple locations
move_df <- move_df[(move_df$TagCode %in% dup_codes),] # save only the fish that were detected at multiple locations
if(nrow(move_df)>1){
move_df$Day <- as.Date(move_df$last_detect, "Etc/GMT+8")
new_move_df <- NULL
for(i in 1:length(unique(move_df$TagCode))){
tmp_code <- unique(move_df$TagCode)[i]
tmp_move_df <- move_df %>% filter(TagCode == tmp_code) # subset data
tmp_move_df <- tmp_move_df[order(tmp_move_df$last_detect, decreasing = FALSE),] # order data
for(j in 1:(length(tmp_move_df$TagCode) - 1)){
tmp_new_move_df <- data.frame(TagCode = tmp_code, location1 = tmp_move_df$general_location[j],
day1 = tmp_move_df$Day[j], location2 = tmp_move_df$general_location[j+1],
day2 = tmp_move_df$Day[j+1])
tmp_new_move_df$loc_num1 <- locs$loc_num[which(locs$general_location == tmp_new_move_df$location1)]
tmp_new_move_df$loc_num2 <- locs$loc_num[which(locs$general_location == tmp_new_move_df$location2)]
new_move_df <- rbind(new_move_df, tmp_new_move_df)
}
}
fig1 <- plot_ly(data = daterange4, type = "scatter", mode = "markers",
marker = list(color = ~ value, size = ~value*5,
colorbar = list(title = "Num. of arrivals", len = 0.35, x = 1.06, y = 0.73),
colorscale = "Viridis", line = list(width = 0)),
hoverinfo = "text", text = ~paste("Date:", Date,"<br># of arrivals:", value),
x = ~Date, y = ~loc_num) %>%
add_annotations(x = new_move_df$day2, y = new_move_df$loc_num2, axref="x", ayref="y", text="", showarrow=TRUE,
ax = new_move_df$day1, ay = new_move_df$loc_num1, arrowcolor = "darkgrey",
opacity = 0.5, standoff = 5, startstandoff = 5) %>%
layout(xaxis = list(range = c(min(daterange$Date) - 1, max(daterange$Date) + 1), showgrid = FALSE, showline = TRUE),
yaxis = list(range = c(min(locs$loc_num) - 1, max(locs$loc_num) + 1), showline = TRUE,
title = "", ticktext = locs$general_location, tickvals = locs$loc_num), showlegend = FALSE) %>%
add_annotations(text = sprintf("<b>North<b>"), xref = "paper", yref = "paper", x = -0.13, xanchor = "left",
y = 1.05, yanchor = "top", showarrow = FALSE, font = list(size = 20)) %>%
add_annotations(text = sprintf("<b>South<b>"), xref = "paper", yref = "paper", x = -0.13, xanchor = "left",
y = 0.04, yanchor = "top", showarrow = FALSE, font = list(size = 20))
fig2 <- plot_ly(data = flow, type = "scatter", mode = "lines") %>%
add_trace(x = ~DateTime, y = ~Value) %>%
layout(xaxis = list(range = c(min(daterange$Date) - 1, max(daterange$Date) + 1), showgrid = FALSE, showline = TRUE),
yaxis = list(title = "Flow (cfs) at OMR"))
subplot(fig1, fig2, nrows = 2, margin = 0.04, heights = c(0.7, 0.3), titleY = TRUE)
}else{
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NOT ENOUGH DETECTIONS", cex = 2)
}
} else {
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
}
_______________________________________________________________________________________________________
library(tidyr)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_4 <- detects_study %>% filter(general_location == "Benicia_west" | general_location == "Benicia_east")
if(nrow(detects_4) == 0){
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else {
detects_4 <- detects_4 %>%
dplyr::left_join(., detects_4 %>%
group_by(TagCode) %>%
summarise(first_detect = min(DateTime_PST))) %>%
mutate(Day = as.Date(as.Date(first_detect, "Etc/GMT+8")))
starttime <- as.Date(min(detects_4$release_time), "Etc/GMT+8")
# Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_4$Release))])
tagcount1 <- detects_4 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange1 <- daterange1[,order(colnames(daterange1))]
daterange2 <- daterange1
rownames(daterange2) <- daterange2$Day
daterange2$Day <- NULL
par(mar=c(6, 5, 2, 5) + 0.1)
daterange2$Date <- as.Date(row.names(daterange2))
daterange3 <- melt(daterange2, id.vars = "Date", variable.name = ".", )
daterange3$. <- factor(daterange3$., levels = sort(unique(daterange3$.), decreasing = T))
plot_ly(daterange3, width = 900, height = 600, dynamicTicks = TRUE) %>%
add_bars(x = ~Date, y = ~value, color = ~.) %>%
add_annotations(text="Release (click on legend<br> items to isolate)", xref="paper", yref="paper",
x=0.01, xanchor="left",
y=1.02, yanchor="bottom", # Same y as legend below
legendtitle=TRUE, showarrow=FALSE ) %>%
layout(yaxis2 = ay,showlegend = T,
barmode = "stack",
xaxis = list(title = "Date", mirror=T,ticks="outside",showline=T),
yaxis = list(title = "Number of fish arrivals per day", mirror=T,ticks="outside",showline=T),
legend = list(orientation = "h",x = 0.34, y = 1.01, yanchor="bottom", xanchor="left"),
margin=list(l = 50,r = 100,b = 50,t = 50))
}
3. Survival and Routing Probability
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
try(benicia <- read.csv("benicia_surv.csv", stringsAsFactors = F))
detects_benicia <- detects_study[detects_study$general_location %in% c("Benicia_west", "Benicia_east"),]
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")), max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life))))
if(nrow(detects_benicia) == 0){
if(as.numeric(difftime(Sys.time(), min(detects_study$RelDT), units = "days"))>30){
WR.surv <- data.frame("Release"="ALL", "estimate"=0, "se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
} else {
WR.surv <- data.frame("Release"=NA, "estimate"="NO DETECTIONS YET", "se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
}
WR.surv1 <- WR.surv
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.1 Minimum survival to Benicia Bridge East Span (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else if(length(table(detects_benicia$general_location)) == 1){
if(as.numeric(difftime(Sys.time(), min(detects_study$RelDT), units = "days"))>30){
WR.surv <- data.frame("Release"="ALL", "estimate"=round(length(unique(detects_benicia$TagCode))/length(unique(detects_study$TagCode))*100,1),
"se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
} else {
WR.surv <- data.frame("Release" = NA, "estimate" = "NOT ENOUGH DETECTIONS", "se" = NA, "lcl" = NA, "ucl" = NA, "Detection_efficiency" = NA)
}
WR.surv1 <- WR.surv
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.1 Minimum survival to Benicia Bridge East Span (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
# Only do survival to Benicia here
test3 <- detects_study[which(detects_study$river_km < 53),]
# calculate mean and SD travel time
travel <- aggregate(list(first_detect = test3$DateTime_PST), by = list(Release = test3$Release, TagCode = test3$TagCode, RelDT = test3$RelDT), min)
travel$days <- as.numeric(difftime(travel$first_detect, travel$RelDT, units = "days"))
travel_final <- aggregate(list(mean_travel_time = travel$days), by = list(Release = travel$Release), mean)
travel_final <- merge(travel_final, aggregate(list(sd_travel_time = travel$days), by = list(Release = travel$Release), sd))
travel_final <- merge(travel_final, aggregate(list(n = travel$days), by = list(Release = travel$Release), length))
travel_final <- rbind(travel_final, data.frame(Release = "ALL", mean_travel_time = mean(travel$days), sd_travel_time = sd(travel$days), n = nrow(travel)))
# Create inp for survival estimation
inp <- as.data.frame(reshape2::dcast(test3, TagCode ~ river_km, fun.aggregate = length))
# Sort columns by river km in descending order
# Count number of genlocs
gen_loc_sites <- ncol(inp)-1
inp <- inp[,c(1,order(names(inp[,2:(gen_loc_sites+1)]), decreasing = T)+1)]
inp <- merge(study_tagcodes, inp, by = "TagCode", all.x = T)
inp2 <- inp[,(ncol(inp)-gen_loc_sites+1):ncol(inp)]
inp2[is.na(inp2)] <- 0
inp2[inp2 > 0] <- 1
inp <- cbind(inp, inp2)
groups <- as.character(sort(unique(inp$Release)))
groups_w_detects <- names(table(test3$Release))
inp[,groups] <- 0
for(i in groups){
inp[as.character(inp$Release) == i, i] <- 1
}
inp$inp_final <- paste("1",apply(inp2, 1, paste, collapse=""),sep="")
if(length(groups) > 1){
# make sure factor levels have a release that has detections first. if first release in factor order has zero #detectins, model goes haywire
inp.df <- data.frame(ch = as.character(inp$inp_final), freq = 1, rel = inp$Release, stringsAsFactors = F)
WR.process <- process.data(inp.df, model="CJS", begin.time=1)
WR.ddl <- make.design.data(WR.process)
WR.mark.all <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
inp.df <- inp.df[inp.df$rel %in% groups_w_detects,]
inp.df$rel <- factor(inp.df$rel, levels = groups_w_detects)
if(length(groups_w_detects) > 1){
WR.process <- process.data(inp.df, model="CJS", begin.time=1, groups = "rel")
WR.ddl <- make.design.data(WR.process)
WR.mark.rel <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time*rel),p=list(formula=~time)), silent = T, output = F)
} else {
WR.process <- process.data(inp.df, model="CJS", begin.time=1)
WR.ddl <- make.design.data(WR.process)
WR.mark.rel <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
}
WR.surv <- cbind(Release = "ALL",round(WR.mark.all$results$real[1,c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv.rel <- cbind(Release = groups_w_detects, round(WR.mark.rel$results$real[seq(from=1,to=length(groups_w_detects)*2,by = 2),
c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv.rel <- merge(WR.surv.rel, data.frame(Release = groups), all.y = T)
WR.surv.rel[is.na(WR.surv.rel$estimate),"estimate"] <- 0
WR.surv <- rbind(WR.surv, WR.surv.rel)
} else {
inp.df <- data.frame(ch = as.character(inp$inp_final), freq = 1, stringsAsFactors = F)
WR.process <- process.data(inp.df, model="CJS", begin.time=1)
WR.ddl <- make.design.data(WR.process)
WR.mark.all <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
WR.surv <- cbind(Release = c("ALL", groups),round(WR.mark.all$results$real[1,c("estimate", "se", "lcl", "ucl")] * 100,1))
}
WR.surv$Detection_efficiency <- NA
WR.surv[1,"Detection_efficiency"] <- round(WR.mark.all$results$real[gen_loc_sites+1,"estimate"] * 100,1)
WR.surv1 <- WR.surv
colnames(WR.surv1)[1] <- "Release"
WR.surv1 <- merge(WR.surv1, travel_final, by = "Release", all.x = T)
WR.surv1$mean_travel_time <- round(WR.surv1$mean_travel_time,1)
WR.surv1$sd_travel_time <- round(WR.surv1$sd_travel_time,1)
colnames(WR.surv1) <- c("Release", "Survival (%)", "SE", "95% lower C.I.",
"95% upper C.I.", "Detection efficiency (%)", "Mean time to Benicia (days)", "SD of time to Benicia (days)", "Count")
#colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.3 Minimum survival to Benicia Bridge East Span (using CJS survival model), and travel time") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
}
3.3 Minimum survival to Benicia Bridge East Span (using CJS survival model), and travel time
|
Release
|
Survival (%)
|
SE
|
95% lower C.I.
|
95% upper C.I.
|
Detection efficiency (%)
|
Mean time to Benicia (days)
|
SD of time to Benicia (days)
|
Count
|
|
Abv_Buttonbush_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Abv_Horseshoe_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Abv_Orange_Blossom_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
ALL
|
0.8
|
0.8
|
0.1
|
5.3
|
100
|
121.9
|
NA
|
1
|
|
Blw_Honolulu_Bar_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Blw_Orange_Blossom_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Blw_Russian_Rapids_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Goodwin_Dam_Rel
|
3.7
|
3.6
|
0.5
|
22.1
|
NA
|
121.9
|
NA
|
1
|
|
Honolulu_Bar_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Lovers_Leap_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Orange_Blossom_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Russian_Rapids_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
The_Hole_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Two_Mile_Bar_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Valley_Oak_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
|
Wildcat_Creek_Rel
|
0.0
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
if(exists("benicia")==T & is.numeric(WR.surv1[1,2])){
# Find mean release time per release group, and ALL
reltimes <- aggregate(list(RelDT = study_tagcodes$release_time), by = list(Release = study_tagcodes$Release), FUN = mean)
reltimes <- rbind(reltimes, data.frame(Release = "ALL", RelDT = mean(study_tagcodes$release_time)))
# Assign whether the results are tentative or final
quality <- "tentative"
if(endtime < as.Date(format(Sys.time(), "%Y-%m-%d"))){
quality <- "final"
}
WR.surv <- merge(WR.surv, reltimes, by = "Release", all.x = T)
WR.surv$RelDT <- as.POSIXct(WR.surv$RelDT, origin = "1970-01-01")
benicia$RelDT <- as.POSIXct(benicia$RelDT)
# remove old benicia record for this studyID
benicia <- benicia[!benicia$StudyID == unique(detects_study$Study_ID),]
benicia <- rbind(benicia, data.frame(WR.surv, StudyID = unique(detects_study$Study_ID), data_quality = quality))
write.csv(benicia, "benicia_surv.csv", row.names = F, quote = F)
}
