CalFishTrack
Central Valley Enhanced
Acoustic Tagging Project
Hatchery-origin Chinook salmon Seasonal Survival Study
1. Project Status
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
library(knitr)
library(kableExtra)
library(lubridate)
library(data.table)
library(ggplot2)
library(RMark)
library(scales)
library(viridis)
library(forcats)
library(reshape2)
library(png)
library(dataRetrieval)
library(rerddap)
library(plotly)
study <- "Seasonal_Survival_2025"
detects_study <- fread("study_detections.csv", stringsAsFactors = F,
colClasses = c(DateTime_PST = "character", RelDT = "character")) %>%
filter(Study_ID == study) %>%
mutate(DateTime_PST = as.POSIXct(DateTime_PST, format = "%Y-%m-%d %H:%M:%S", tz="Etc/GMT+8"),
release_time = as.POSIXct(RelDT, format = "%Y-%m-%d %H:%M:%S", tz="Etc/GMT+8")) %>%
rename(., weight=Weight, length=Length, release_rkm=Rel_rkm, release_location=Rel_loc, river_km=rkm)
latest <- read.csv("latest_download.csv", stringsAsFactors = F)$x
##################################################################################################################
#### TO RUN THE FOLLOWING CODE CHUNKS FROM HERE ON DOWN USING R ERDDAP, UN-COMMENT THESE NEXT 9 LINES OF CODE ####
##################################################################################################################
# cache_delete_all()
# query = paste('&','Study_ID','="', study, '"', sep = '')
# datafile=URLencode(paste("https://oceanview.pfeg.noaa.gov/erddap/tabledap/","FEDcalFishTrack",".csv?",query,sep = ""))
# options(url.method = "libcurl", download.file.method = "libcurl", timeout = 180)
# detects_study <- data.frame(read.csv(datafile,row.names = NULL, stringsAsFactors = F))
# detects_study <- detects_study[-1,]
# detects_study$DateTime_PST <- as.POSIXct(detects_study$local_time, format = "%Y-%m-%d %H:%M:%S", "Etc/GMT+8")
# detects_study$release_time <- as.POSIXct(detects_study$release_time, format = "%Y-%m-%d %H:%M:%S", "Etc/GMT+8")
# detects_study$river_km <- as.numeric(detects_study$river_km)
##################################################################################################################Study is in progress. Data current as of 2025-04-27 15:00:00. All times in Pacific Standard Time.
if (nrow(detects_study) == 0){
cat("Study has not yet begun ")
} else {
if (min(detects_study$release_time) > Sys.time()){
cat("Study has not yet begun, below data is a placeholder: ")
}
if (min(detects_study$release_time) < Sys.time()){
cat(paste("Study began on ", min(detects_study$release_time), ", see tagging details below:", sep = ""))
}
######################################
#### RELEASE GROUPS ASSIGNED HERE ####
######################################
detects_study$Release <- "Week 1"
detects_study[detects_study$release_time > as.POSIXct("2025-01-01 12:00:00") & detects_study$release_time < as.POSIXct("2025-02-20 12:00:00"), "Release"] <- "Week 2"
detects_study[detects_study$release_time > as.POSIXct("2025-02-20 12:00:00") & detects_study$release_time < as.POSIXct("2025-02-28 12:00:00"), "Release"] <- "Week 3"
detects_study[detects_study$release_time > as.POSIXct("2025-02-28 12:00:00") & detects_study$release_time < as.POSIXct("2025-03-20 12:00:00"), "Release"] <- "Week 4"
detects_study[detects_study$release_time > as.POSIXct("2025-03-20 12:00:00") , "Release"] <- "Week 5"
study_tagcodes <- as.data.frame(unique(detects_study[,c("TagCode", "release_time", "weight", "length", "release_rkm",
"release_location", "Release","Rel_latitude","Rel_longitude")]))
release_stats <- study_tagcodes %>%
group_by(Release) %>%
summarise(First_release_time = min(release_time),
Last_release_time = max(release_time),
Number_fish_released = length(unique(TagCode)),
Release_location = head(release_location, 1),
Release_rkm = head(release_rkm,1),
Mean_length = mean(length, na.rm=T),
Mean_weight = mean(weight, na.rm=T),
Release_lat = head(Rel_latitude,1),
Release_lon = head(Rel_longitude,1)) %>%
mutate(Mean_length = round(Mean_length, 1),
Mean_weight = round(Mean_weight, 1),
First_release_time = format(First_release_time, tz = "Etc/GMT+8"),
Last_release_time = format(Last_release_time, tz = "Etc/GMT+8")) %>%
arrange(First_release_time)
release_stats_all <- study_tagcodes %>%
summarise(First_release_time = min(release_time),
Last_release_time = max(release_time),
Number_fish_released = length(unique(TagCode)),
Release_location = NA,
Release_rkm = mean(release_rkm,na.rm = T),
Mean_length = mean(length, na.rm=T),
Mean_weight = mean(weight, na.rm=T),
Release_lat = head(Rel_latitude,1),
Release_lon = head(Rel_longitude,1)) %>%
mutate(Mean_length = round(Mean_length, 1),
Mean_weight = round(Mean_weight, 1),
Release_rkm = round(Release_rkm,1),
First_release_time = format(First_release_time, tz = "Etc/GMT+8"),
Last_release_time = format(Last_release_time, tz = "Etc/GMT+8"))
release_stats <- rbind(release_stats, data.frame(Release = "ALL", release_stats_all))
kable(release_stats[,!names(release_stats)%in% c("Release_lon","Release_lat","release_location")], format = "html", row.names = F) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left")
}| Release | First_release_time | Last_release_time | Number_fish_released | Release_location | Release_rkm | Mean_length | Mean_weight |
|---|---|---|---|---|---|---|---|
| Week 1 | 2024-12-10 09:45:00 | 2024-12-11 08:39:00 | 200 | RBDD_Rel | 461.579 | 148.2 | 35.7 |
| Week 2 | 2025-02-05 09:00:00 | 2025-02-06 09:45:00 | 200 | RBRiverPark_Rel | 463.700 | 87.9 | 7.5 |
| Week 3 | 2025-02-25 10:20:00 | 2025-02-26 10:00:00 | 200 | RBDD_Rel | 461.579 | 87.7 | 7.5 |
| Week 4 | 2025-03-18 07:50:00 | 2025-03-19 07:58:00 | 199 | RBDD_Rel | 461.579 | 91.9 | 8.7 |
| Week 5 | 2025-04-08 08:45:00 | 2025-04-09 09:20:00 | 200 | RBDD_Rel | 461.579 | 78.0 | 5.3 |
| ALL | 2024-12-10 09:45:00 | 2025-04-09 09:20:00 | 999 | NA | 461.800 | 98.7 | 13.0 |
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))
}
}2.1 Map of unique fish detections at operational realtime detection locations
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
library(cder)
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$tag_life))))
#par(mar=c(6, 5, 2, 5) + 0.1)
MLW <- data.frame()
CLW <- data.frame()
TIS <- data.frame()
FRE <- data.frame()
## download weir data only if release loc is above at least fremont
if(max(detects_study$release_rkm) > 209.5){
MLW <- try(cdec_query(stations = c("MLW"), sensors = 20, durations = "H", start.date = starttime, end.date = endtime))
CLW <- try(cdec_query(stations = c("CLW"), sensors = 20, durations = "H", start.date = starttime, end.date = endtime))
TIS <- try(cdec_query(stations = c("TIS"), sensors = 20, durations = "H", start.date = starttime, end.date = endtime))
FRE <- try(cdec_query(stations = c("FRE"), sensors = 20, durations = "H", start.date = starttime, end.date = endtime))
}
if(inherits(MLW, "try-error")|
inherits(CLW, "try-error")|
inherits(TIS, "try-error")|
inherits(FRE, "try-error")|
nrow(MLW)==0|
nrow(CLW)==0|
nrow(TIS)==0|
nrow(FRE)==0){
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{
CLW[which(CLW$Value == 0),"Value"] <- NA
MLW[is.na(MLW$Value)==F, "rkm"] <- 326.3
CLW[is.na(CLW$Value)==F, "rkm"] <- 310.2
TIS[is.na(TIS$Value)==F, "rkm"] <- 267.7
FRE[is.na(FRE$Value)==F, "rkm"]<- 209.5
MLW[1,"rkm"] <- 1000 ## this ensures it shows up on legend even when weirs arent overtopping
CLW[1,"rkm"] <- 1000 ## this ensures it shows up on legend even when weirs arent overtopping
TIS[1,"rkm"] <- 1000 ## this ensures it shows up on legend even when weirs arent overtopping
FRE[1,"rkm"] <- 1000 ## this ensures it shows up on legend even when weirs arent overtopping
plot_ly(width = 900, height = 600) %>%
add_trace(x=~MLW$DateTime, y=~MLW$rkm, type = "scatter", mode = "markers", name = "Moulton spill", marker=list(symbol="square-open", color="red")) %>%
add_trace(x=~CLW$DateTime, y=~CLW$rkm, type = "scatter", mode = "markers", name = "Colusa spill", marker=list(symbol="square-open", color="blue")) %>%
add_trace(x=~TIS$DateTime, y=~TIS$rkm, type = "scatter", mode = "markers", name = "Tisdale spill", marker=list(symbol="square-open", color="orange")) %>%
add_trace(x=~FRE$DateTime, y=~FRE$rkm, type = "scatter", mode = "markers", name = "Fremont spill", marker=list(symbol="square-open", color="green")) %>%
add_trace(data=detects_summary, x = ~first_detect, y = ~river_km, color = ~TagCode, dynamicTicks = TRUE, connectgaps = TRUE, mode = "lines+markers", type = "scatter",hoverinfo = "text",
text = ~paste("</br> TagCode: ", detects_summary$TagCode,"</br> Arrival: ", detects_summary$first_detect,"</br> Location: ", detects_summary$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(min(gen_locs[is.na(gen_locs$stop),"rkm"], na.rm = T)-10, max(detects_study$release_rkm, na.rm = T)+10)),legend = list(title=list(text="<b> Weir Spill and Tag Codes </b>")),
#legend2 = 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)
}2.2 Waterfall Detection Plot
_______________________________________________________________________________________________________
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 == "MeridianBr")
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$Release))])
tagcount1 <- detects_4 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
# Download flow data
flow_day <- readNWISuv(siteNumbers = "11390500", parameterCd="00060", startDate = starttime,
endDate = endtime+1) %>%
mutate(Day = as.Date(format(dateTime, "%Y-%m-%d"))) %>%
group_by(Day) %>%
summarise(parameter_value = mean(X_00060_00000))
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange2 <- daterange1[,order(colnames(daterange1))] %>%
dplyr::left_join(., flow_day, by = "Day")
rownames(daterange2) <- daterange2$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 Wilkins Slough",
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<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 ) %>%
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 = 1.01, yanchor="bottom", xanchor="left"),
margin=list(l = 50,r = 100,b = 50,t = 50))
}2.3 Detections at Meridian Bridge versus Sacramento River flows at Wilkins Slough for duration of tag life
_______________________________________________________________________________________________________
library(tidyr)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_5 <- detects_study %>% filter(general_location == "TowerBridge")
if(nrow(detects_5) == 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_5 <- detects_5 %>%
dplyr::left_join(., detects_5 %>%
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_5$release_time), "Etc/GMT+8")
# Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$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_5$Release))])
tagcount1 <- detects_5 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
# Download flow data
flow_day <- readNWISuv(siteNumbers = "11425500", parameterCd="00060", startDate = starttime,
endDate = endtime+1) %>%
mutate(Day = as.Date(format(dateTime, "%Y-%m-%d"))) %>%
group_by(Day) %>%
summarise(parameter_value = mean(X_00060_00000))
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange2 <- daterange1[,order(colnames(daterange1))] %>%
dplyr::left_join(., flow_day, by = "Day")
rownames(daterange2) <- daterange2$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 Verona",
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<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 ) %>%
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 = 1.01, yanchor="bottom", xanchor="left"),
margin=list(l = 50,r = 100,b = 50,t = 50))
}2.4 Detections at Tower Bridge (downtown Sacramento) versus Sacramento River flows at Verona for duration of tag life
_______________________________________________________________________________________________________
library(tidyr)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_6 <- detects_study %>% filter(general_location == "Benicia_west" | general_location == "Benicia_east")
if(nrow(detects_6) == 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_6 <- detects_6 %>%
dplyr::left_join(., detects_6 %>%
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_6$release_time), "Etc/GMT+8")
# Endtime should be either now, or end of predicted tag life, whichever comes first
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$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_6$Release))])
tagcount1 <- detects_6 %>%
group_by(Day, Release) %>%
summarise(unique_tags = length(unique(TagCode))) %>%
spread(Release, unique_tags)
daterange1 <- merge(daterange, tagcount1, all.x=T)
daterange1[is.na(daterange1)] <- 0
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == "x"] <- paste(i)
}
}
## reorder columns in alphabetical order so its coloring in barplots is consistent
daterange1 <- daterange1[,order(colnames(daterange1))]
daterange2 <- daterange1
rownames(daterange2) <- daterange2$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$.), decreasing = T))
plot_ly(daterange3, width = 900, height = 600, dynamicTicks = TRUE) %>%
add_bars(x = ~Date, y = ~value, color = ~.) %>%
add_annotations(text="Release (click on legend<br> items to isolate)", xref="paper", yref="paper",
x=0.01, xanchor="left",
y=1.02, yanchor="bottom", # Same y as legend below
legendtitle=TRUE, showarrow=FALSE ) %>%
layout(yaxis2 = ay,showlegend = T,
barmode = "stack",
xaxis = list(title = "Date", mirror=T,ticks="outside",showline=T),
yaxis = list(title = "Number of fish arrivals per day", mirror=T,ticks="outside",showline=T),
legend = list(orientation = "h",x = 0.34, y = 1.01, yanchor="bottom", xanchor="left"),
margin=list(l = 50,r = 100,b = 50,t = 50))
}2.5 Detections at Benicia Bridge for duration of tag life
3. Survival and Routing Probability
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_tower <- detects_study %>% filter(general_location == "TowerBridge")
if(nrow(detects_tower) == 0){
WR.surv <- data.frame("Release"=NA, "Survival (%)"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA,
"95% upper C.I."=NA, "Detection efficiency (%)"=NA)
colnames(WR.surv) <- c("Release", "Survival (%)", "SE", "95% lower C.I.",
"95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv, row.names = F, "html", caption = "3.1 Minimum survival to Tower Bridge (using CJS
survival model). If Yolo Bypass Weirs are overtopping during migration, fish may have taken
that route, and therefore this is a minimum estimate of survival") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"),
full_width = F, position = "left"))
} else {
study_count <- nrow(study_tagcodes)
# Only do survival to Sac for now
surv <- detects_study %>% filter(river_km > 168 & river_km < 175)
# calculate mean and SD travel time
travel <- aggregate(list(first_detect = surv$DateTime_PST), by = list(Release = surv$Release, TagCode = surv$TagCode, RelDT = surv$RelDT), min)
travel$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(surv, TagCode ~ river_km, fun.aggregate = length))
# Sort columns by river km in descending order
gen_loc_sites <- ncol(inp)-1 # Count number of genlocs
if(gen_loc_sites < 2){
WR.surv <- data.frame("Release"=NA, "Survival (%)"="NOT ENOUGH DETECTIONS", "SE"=NA, "95% lower C.I."=NA,
"95% upper C.I."=NA, "Detection efficiency (%)"=NA)
colnames(WR.surv) <- c("Release", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.",
"Detection efficiency (%)")
print(kable(WR.surv, row.names = F, "html", caption = "3.1 Minimum survival to Tower Bridge (using CJS
survival model). If Yolo Bypass Weirs are overtopping during migration, fish may
have taken that route, and therefore this is a minimum estimate of survival") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"),
full_width = F,position = "left"))
} else {
inp <- inp[,c(1,order(names(inp[,2:(gen_loc_sites+1)]), decreasing = T)+1)] %>%
dplyr::left_join(study_tagcodes, ., by = "TagCode")
inp2 <- inp[,(ncol(inp)-gen_loc_sites+1):ncol(inp)] %>%
replace(is.na(.), 0) %>%
replace(., . > 0, 1)
inp <- cbind(inp, inp2)
groups <- as.character(sort(unique(inp$Release)))
surv$Release <- factor(surv$Release, levels = groups)
inp[,groups] <- 0
for (i in groups) {
inp[as.character(inp$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 = factor(inp$Release, levels = names(sort(table(surv$Release),decreasing = T))),
stringsAsFactors = F)
WR.process <- process.data(inp.df, model="CJS", begin.time=1, groups = "rel")
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.mark.rel <- mark(WR.process, WR.ddl,
model.parameters=list(Phi=list(formula=~time*rel),p=list(formula=~time*rel)),
silent = T, output = F)
WR.surv <- round(WR.mark.all$results$real[1,c("estimate", "se", "lcl", "ucl")] * 100,1)
WR.surv <- rbind(WR.surv, round(WR.mark.rel$results$real[seq(from=1,to=length(groups)*2,by = 2),
c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv$Detection_efficiency <- NA
WR.surv[1,"Detection_efficiency"] <- round(WR.mark.all$results$real[gen_loc_sites+1,"estimate"] * 100,1)
WR.surv <- cbind(c("ALL", names(sort(table(surv$Release),decreasing = T))), WR.surv)
}
if(length(intersect(colnames(inp),groups)) < 2){
inp$inp_final <- paste("1",apply(inp2, 1, paste, collapse=""), " ", 1,sep = "")
write.table(inp$inp_final,"WRinp.inp",row.names = F, col.names = F, quote = F)
WRinp <- convert.inp("WRinp.inp")
WR.process <- process.data(WRinp, 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.mark.rel <- mark(WR.process, WR.ddl,
model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)),
silent = T, output = F)
WR.surv <- round(WR.mark.all$results$real[1,c("estimate", "se", "lcl", "ucl")] * 100,1)
WR.surv <- rbind(WR.surv, round(WR.mark.rel$results$real[seq(from=1,to=length(groups)*2,by = 2),
c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv$Detection_efficiency <- NA
WR.surv[1,"Detection_efficiency"] <- round(WR.mark.all$results$real[gen_loc_sites+1,"estimate"] * 100,1)
WR.surv <- cbind(c("ALL", groups), WR.surv)
}
colnames(WR.surv)[1] <- "Release"
WR.surv <- merge(WR.surv, travel_final, by = "Release", all.x = T)
WR.surv$mean_travel_time <- round(WR.surv$mean_travel_time,1)
WR.surv$sd_travel_time <- round(WR.surv$sd_travel_time,1)
colnames(WR.surv) <- c("Release", "Survival (%)", "SE", "95% lower C.I.",
"95% upper C.I.", "Detection efficiency (%)", "Mean time to Tower (days)", "SD of time to Tower (days)","Count")
WR.surv <- WR.surv %>% arrange(., Release)
print(kable(WR.surv, row.names = F, "html", caption = "3.1 Minimum survival to Tower Bridge (using CJS
survival model), and travel time. If Yolo Bypass Weirs are overtopping during migration, fish may have taken
that route, and therefore this is a minimum estimate of survival") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"),
full_width = F, position = "left"))
}
}| Release | Survival (%) | SE | 95% lower C.I. | 95% upper C.I. | Detection efficiency (%) | Mean time to Tower (days) | SD of time to Tower (days) | Count |
|---|---|---|---|---|---|---|---|---|
| ALL | 32.4 | 1.5 | 29.5 | 35.4 | 82.6 | 19.0 | 10.1 | 316 |
| Week 1 | 16.5 | 2.6 | 12.0 | 22.3 | NA | 5.9 | 5.6 | 33 |
| Week 2 | 37.3 | 3.5 | 30.7 | 44.3 | NA | 30.4 | 7.4 | 73 |
| Week 3 | 40.6 | 3.6 | 33.8 | 47.8 | NA | 23.3 | 5.9 | 79 |
| Week 4 | 43.7 | 3.6 | 36.8 | 50.9 | NA | 14.5 | 6.2 | 85 |
| Week 5 | 23.7 | 3.1 | 18.2 | 30.3 | NA | 11.5 | 2.1 | 46 |
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
route_results_possible <- FALSE
if(nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) == 0){
results_short <- data.frame("Measure"=NA, "Estimate"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA,
"95% upper C.I."=NA)
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.2 Reach-specific survival and probability
of entering Georgiana Slough") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"),
full_width = F, position = "left"))
} else {
# Only do survival to Georg split for now
test2 <- detects_study %>%
filter(general_location %in% c("TowerBridge", "I80-50_Br","SacRiverWalnutGrove_2", "Sac_BlwGeorgiana",
"Sac_BlwGeorgiana2", "Georg_Sl_1", "Georgiana_Slough2"))
# We can only do a multi-state model if there is at least one detection in each route
if(nrow(test2[test2$general_location %in% c("Sac_BlwGeorgiana", "Sac_BlwGeorgiana2"),]) == 0 |
nrow(test2[test2$general_location %in% c("Georg_Sl_1", "Georgiana_Slough2"),]) == 0){
results_short <- data.frame("Measure"=NA, "Estimate"="NOT ENOUGH DETECTIONS", "SE"=NA, "95% lower C.I."=NA,
"95% upper C.I."=NA)
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.2 Reach-specific survival and probability of
entering Georgiana Slough") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"),
full_width = F, position = "left"))
} else {
# Make tagcode character
study_tagcodes$TagCode <- as.character(study_tagcodes$TagCode)
# Make a crosstab query with frequencies for all tag/location combination
test2$general_location <- factor(test2$general_location,
levels = c("TowerBridge", "I80-50_Br","SacRiverWalnutGrove_2", "Sac_BlwGeorgiana",
"Sac_BlwGeorgiana2", "Georg_Sl_1", "Georgiana_Slough2"))
test2$TagCode <- factor(test2$TagCode, levels = study_tagcodes$TagCode)
mytable <- table(test2$TagCode, test2$general_location) # A will be rows, B will be columns
# Change all frequencies bigger than 1 to 1. Here you could change your minimum cutoff to 2 detections,
# and then make another command that changes all detections=1 to 0
mytable[mytable>0] <- "A"
# Order in order of rkm
mytable2 <- mytable[, c("TowerBridge", "I80-50_Br","SacRiverWalnutGrove_2", "Sac_BlwGeorgiana", "Sac_BlwGeorgiana2",
"Georg_Sl_1", "Georgiana_Slough2")]
# Now sort the crosstab rows alphabetically
mytable2 <- mytable2[order(row.names(mytable2)),]
mytable2[which(mytable2[, "Sac_BlwGeorgiana"]=="A"), "Sac_BlwGeorgiana"] <- "A"
mytable2[which(mytable2[, "Sac_BlwGeorgiana2"]=="A"), "Sac_BlwGeorgiana2"] <- "A"
mytable2[which(mytable2[, "Georg_Sl_1"]=="A"), "Georg_Sl_1"] <- "B"
mytable2[which(mytable2[, "Georgiana_Slough2"]=="A"), "Georgiana_Slough2"] <- "B"
# Now order the study_tagcodes table the same way
study_tagcodes <- study_tagcodes[order(study_tagcodes$TagCode),]
# Paste together (concatenate) the data from each column of the crosstab into one string per row, add to tagging_meta.
# For this step, make sure both are sorted by FishID
study_tagcodes$inp_part1 <- apply(mytable2[,1:3],1,paste,collapse="")
study_tagcodes$inp_partA <- apply(mytable2[,4:5],1,paste,collapse="")
study_tagcodes$inp_partB <- apply(mytable2[,6:7],1,paste,collapse="")
# find last detection at each genloc
departure <- aggregate(list(depart = test2$DateTime_PST), by = list(TagCode = test2$TagCode, last_location = test2$general_location), FUN = max)
# subset for just juncture locations
departure <- departure[departure$last_location %in% c("Sac_BlwGeorgiana", "Sac_BlwGeorgiana2", "Georg_Sl_1", "Georgiana_Slough2"),]
# Find genloc of last known detection per tag
last_depart <- aggregate(list(depart = departure$depart), by = list(TagCode = departure$TagCode), FUN = max)
last_depart1 <- merge(last_depart, departure)
study_tagcodes <- merge(study_tagcodes, last_depart1[,c("TagCode", "last_location")], by = "TagCode", all.x = T)
# Assume that the Sac is default pathway, and for fish that were detected in neither route, it would get a "00" in inp so does not matter anyway
study_tagcodes$inp_final <- paste("A",study_tagcodes$inp_part1, study_tagcodes$inp_partA," 1 ;", sep = "")
# now put in exceptions...fish that were seen in georgiana last
study_tagcodes[study_tagcodes$last_location %in% c("Georg_Sl_1", "Georgiana_Slough2"), "inp_final"] <-
paste("A",
study_tagcodes[study_tagcodes$last_location %in% c("Georg_Sl_1", "Georgiana_Slough2"), "inp_part1"],
study_tagcodes[study_tagcodes$last_location %in% c("Georg_Sl_1", "Georgiana_Slough2"), "inp_partB"],
" 1 ;",
sep = "")
# At this point, some fish might not have been deemed to ever take a route based on last visit analysis. If so, model cannot be run
if(any(grepl(pattern = "A", study_tagcodes$inp_final)==T) & any(grepl(pattern = "B", study_tagcodes$inp_final)==T)){
write.table(study_tagcodes$inp_final,"WRinp_multistate.inp",row.names = F, col.names = F, quote = F)
WRinp <- convert.inp("WRinp_multistate.inp")
dp <- process.data(WRinp, model="Multistrata")
ddl <- make.design.data(dp)
#### p ####
# Cannott be seen at 2B or 3B or 4B (tower or I80 or walnut grove) and currently second georg is missing so set to 0 as well and to 1 for first line
ddl$p$fix = NA
ddl$p$fix[ddl$p$stratum == "B" & ddl$p$time %in% c(2,3,4,6)] = 0
ddl$p$fix[ddl$p$stratum == "B" & ddl$p$time %in% c(5)] = 1
#### Psi ####
# Only 1 transition allowed:
# from A to B at time interval 4 to 5
ddl$Psi$fix = 0
# A to B can only happen for interval 3-4
ddl$Psi$fix[ddl$Psi$stratum == "A"&
ddl$Psi$tostratum == "B" &
ddl$Psi$time == 4] = NA
#### Phi a.k.a. S ####
ddl$S$fix = NA
# None in B for reaches 1,2,3,4 and fixing it to 1 for 5 (between two georg lines). All getting fixed to 1
ddl$S$fix[ddl$S$stratum == "B" & ddl$S$time %in% c(1,2,3,4,5)] = 1
# For route A, fixing it to 1 for 5 (between two blw_georg lines)
ddl$S$fix[ddl$S$stratum == "A" & ddl$S$time == 5] = 1
# We use -1 at beginning of formula to remove intercept. This is because different routes probably should not share the same intercept
p.timexstratum = list(formula=~-1+stratum:time)
Psi.stratumxtime = list(formula=~-1+stratum:time)
S.stratumxtime = list(formula=~-1+stratum:time)
# Run model a first time
S.timexstratum.p.timexstratum.Psi.timexstratum = mark(dp, ddl,
model.parameters = list(S = S.stratumxtime,p = p.timexstratum,Psi = Psi.stratumxtime),
realvcv = T, silent = T, output = F)
# Identify any parameter estimates at 1, which would likely have bad SE estimates.
profile.intervals <- which(S.timexstratum.p.timexstratum.Psi.timexstratum$results$real$estimate %in% c(0,1) &
!S.timexstratum.p.timexstratum.Psi.timexstratum$results$real$fixed == "Fixed")
# Rerun model using profile interval estimation for the tricky parameters
S.timexstratum.p.timexstratum.Psi.timexstratum = mark(dp, ddl,
model.parameters=list(S=S.stratumxtime,p= p.timexstratum,Psi=Psi.stratumxtime),
realvcv = T, profile.int = profile.intervals, silent = T, output = F)
results <- S.timexstratum.p.timexstratum.Psi.timexstratum$results$real
results_short <- results[rownames(results) %in% c("S sA g1 c1 a0 o1 t1",
"S sA g1 c1 a1 o2 t2",
"S sA g1 c1 a2 o3 t3",
"S sA g1 c1 a3 o4 t4",
"p sA g1 c1 a1 o1 t2",
"p sA g1 c1 a2 o2 t3",
"p sA g1 c1 a3 o3 t4",
"p sA g1 c1 a4 o4 t5",
"p sB g1 c1 a4 o4 t5",
"Psi sA toB g1 c1 a3 o4 t4"),]
results_short <- round(results_short[,c("estimate", "se", "lcl", "ucl")] * 100,1)
# Now find estimate and CIs for AtoA route at junction
Psilist = get.real(S.timexstratum.p.timexstratum.Psi.timexstratum,"Psi",vcv=TRUE)
Psivalues = Psilist$estimates
routes <- TransitionMatrix(Psivalues[Psivalues$time==4 & Psivalues$cohort==1,],vcv.real=Psilist$vcv.real)
results_short$Measure <- c("Survival from Release to TowerBridge (minimum estimate since fish may have taken Yolo
Bypass)", "Survival from TowerBridge to I80-50_Br", "% arrived from I80-50_Br to Walnut Grove (not survival because
fish may have taken Sutter/Steam)","Survival from Walnut Grove to Georgiana Slough confluence","Detection probability at TowerBridge",
"Detection probability at I80-50_Br", "Detection probability at Walnut Grove", "Detection probability at Blw_Georgiana",
#"Detection probability at Georgiana Slough (fixed at 1)",
"Routing probability into Georgiana Slough (Conditional on fish arriving to junction)")
results_short <- results_short[,c("Measure", "estimate", "se", "lcl", "ucl")]
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.2 Reach-specific survival and probability of entering Georgiana Slough") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
route_results_possible <- TRUE
} else {
results_short <- data.frame("Measure"=NA, "Estimate"="NOT ENOUGH DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA)
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.2 Reach-specific survival and probability of entering Georgiana Slough") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
}
}
}| Measure | Estimate | SE | 95% lower C.I. | 95% upper C.I. |
|---|---|---|---|---|
| Survival from Release to TowerBridge (minimum estimate since fish may have taken Yolo Bypass) | 33.1 | 1.5 | 30.2 | 36.1 |
| Survival from TowerBridge to I80-50_Br | 99.6 | 1.5 | 8.9 | 100.0 |
| % arrived from I80-50_Br to Walnut Grove (not survival because fish may have taken Sutter/Steam) | 74.4 | 2.6 | 69.0 | 79.1 |
| Survival from Walnut Grove to Georgiana Slough confluence | 99.6 | 0.4 | 97.2 | 99.9 |
| Detection probability at TowerBridge | 80.8 | 2.2 | 76.0 | 84.7 |
| Detection probability at I80-50_Br | 85.3 | 2.3 | 80.3 | 89.2 |
| Detection probability at Walnut Grove | 100.0 | 0.0 | 99.2 | 100.0 |
| Detection probability at Blw_Georgiana | 100.0 | 0.0 | 100.0 | 100.0 |
| Routing probability into Georgiana Slough (Conditional on fish arriving to junction) | 16.8 | 2.4 | 12.6 | 22.0 |
# If you do not have access to local files, uncomment and run next lines of code
#download.file("https://raw.githubusercontent.com/CalFishTrack/real-time/master/data/georg.png",destfile = "georg.png", quiet = T, mode = "wb")
georg <- readPNG("georg.png")
par(mar = c(2,0,0,0))
# Set up the plot area
plot(1:2, type="n", xlab="", ylab="", xaxt = "n", yaxt = "n")
# Get the plot information so the image will fill the plot box, and draw it
lim <- par()
rasterImage(georg, lim$usr[1], lim$usr[3], lim$usr[2], lim$usr[4])
if(nrow(detects_study[is.na(detects_study$DateTime_PST) == F,]) == 0){
legend(x = 1.55,y = 1.6,legend = "No detections yet",col = "white", box.col = "light gray", bg = "light gray")
legend(x = 1.55,y = 1.45,legend = "No detections yet",col = "white", box.col = "light gray", bg = "light gray")
} else if (route_results_possible == F){
legend(x = 1.55,y = 1.6,legend = "Too few detections",col = "white", box.col = "light gray", bg = "light gray")
legend(x = 1.55,y = 1.45,legend = "Too few detections",col = "white", box.col = "light gray", bg = "light gray")
} else {
legend(x = 1.55,y = 1.6,legend = paste(round(routes$TransitionMat["A","A"],3)*100,
"% (", round(routes$lcl.TransitionMat["A","A"],3)*100, "-",
round(routes$ucl.TransitionMat["A","A"],3)*100,")", sep =""),
col = "white", box.col = "light gray", bg = "light gray")
legend(1.55,1.45, legend = paste(round(routes$TransitionMat["A","B"],3)*100,
"% (", round(routes$lcl.TransitionMat["A","B"],3)*100, "-",
round(routes$ucl.TransitionMat["A","B"],3)*100,")", sep =""),
box.col = "light gray", bg = "light gray")
}
mtext(text = "3.3 Routing Probabilities at Georgiana Slough Junction (with 95% C.I.s)", cex = 1.3, side = 1, line = 0.2, adj = 0)
if (nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) == 0){
plot(1:2, type = "n",xaxt = "n", yaxt = "n",
xlab = "Range of days study fish were present at Georgiana Sl Junction",
ylab = "Routing probability into Georgiana Slough at the junction")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else if(route_results_possible == F){
plot(1:2, type = "n",xaxt = "n", yaxt = "n",
xlab = "Range of days study fish were present at Georgiana Sl Junction",
ylab = "Routing probability into Georgiana Slough at the junction")
text(1.5,1.5, labels = "TOO FEW DETECTIONS", cex = 2)
} else {
library(repmis)
trytest <- try(source_data("https://code.usgs.gov/crrl_qfes/Enhanced_Acoustic_Telemetry_Project/raw/master/EAT_data_2024.Rdata?raw=True"))
if (inherits(trytest, "try-error")){
plot(1:2, type = "n",xaxt = "n", yaxt = "n",
xlab = "Range of days study fish were present at Georgiana Sl Junction",
ylab = "Routing probability into Georgiana Slough at the junction")
text(1.5,1.5, labels = "ERROR DOWNLOADING STARS", cex = 2)
} else {
detects_5 <- detects_study %>% filter(general_location == "SacRiverWalnutGrove_2")
detects_5 <- detects_5 %>%
dplyr::left_join(., detects_5 %>%
group_by(TagCode) %>%
summarise(first_detect = min(DateTime_PST))) %>%
mutate(Day = as.Date(as.Date(first_detect, "Etc/GMT+8")))
tagcount5 <- detects_5 %>%
group_by(Day) %>%
summarise(unique_tags = length(unique(TagCode)))
tagcount5$density <- tagcount5$unique_tags / sum(tagcount5$unique_tags)
test2 <- as.data.frame(test2)
# first, find min and max arrivals at georg for a study
min_georg <- as.Date(format(min(test2[test2$general_location %in% c("Sac_BlwGeorgiana", "Sac_BlwGeorgiana2","Georg_Sl_1",
"Georgiana_Slough2"),"DateTime_PST"]), "%Y-%m-%d"))
max_georg <- as.Date(format(max(test2[test2$general_location %in% c("Sac_BlwGeorgiana", "Sac_BlwGeorgiana2","Georg_Sl_1",
"Georgiana_Slough2"),"DateTime_PST"]), "%Y-%m-%d"))
psi_study <- psi_GeoCond[psi_GeoCond$Date <= max_georg & psi_GeoCond$Date >=min_georg-1,]
ggplot()+
geom_bar(data = tagcount5, aes(x = Day, y = density), alpha = 0.4, stat = "identity", fill = "red") +
geom_ribbon(data = psi_study, aes(x=Date, ymin = psi_geo.10, ymax = psi_geo.90), alpha = 0.3) +
geom_line(data = psi_study, aes(x=Date, y=psi_geo.50), size = 1.2) +
geom_point(aes(x = median(rep(tagcount5$Day, tagcount5$unique_tags)), y = tail(results_short$Estimate,1)/100), size = 4)+
geom_errorbar(width = 0.2, size = 1.2, aes(ymin = tail(results_short$`95% lower C.I.`,1)/100, ymax = tail(results_short$`95% upper C.I.`,1)/100, x = median(rep(tagcount5$Day, tagcount5$unique_tags))))+
xlim(c(min_georg, max_georg))+
xlab("Range of days study fish were present at Georgiana Sl Junction") +
geom_hline(yintercept=0, linetype="dashed") +
geom_segment(aes(x=median(rep(tagcount5$Day, tagcount5$unique_tags)),y =-0.01,xend=median(rep(tagcount5$Day, tagcount5$unique_tags)),yend =0.01)) +
geom_text(aes(x=median(rep(tagcount5$Day, tagcount5$unique_tags)),y =-0.02, label = "median"), color = "red")+
scale_y_continuous(name = "Routing probability into Georgiana Slough at the junction",limits = c(-0.02,1), sec.axis = dup_axis(name="Histogram of arrivals to junction")) +
theme_bw()+
theme(axis.text.y.right = element_text(color = "red"), axis.title.y.right = element_text(color = "red"))
}
}
3.4 STARS prediction (ribbon) vs. empirical (point) estimate of Routing Probability at Georgiana Slough Junction
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
try(Delta <- read.csv("Delta_surv.csv", stringsAsFactors = F))
if(nrow(detects_study[is.na(detects_study$DateTime_PST) == F,]) == 0){
WR.surv1 <- data.frame("Measure"=NA, "Estimate"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA)
colnames(WR.surv1) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(WR.surv1, row.names = F, "html", caption = "3.5 Minimum through-Delta survival: City of Sacramento to Benicia (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
test4 <- detects_study[detects_study$general_location %in% c("TowerBridge", "I80-50_Br", "Benicia_west", "Benicia_east"),]
if(nrow(test4[test4$general_location =="Benicia_west",]) == 0 | nrow(test4[test4$general_location =="Benicia_east",]) == 0){
WR.surv1 <- data.frame("Measure"=NA, "Estimate"="NOT ENOUGH DETECTIONS", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA)
colnames(WR.surv1) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(WR.surv1, row.names = F, "html", caption = "3.5 Minimum through-Delta survival: City of Sacramento to Benicia (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
# calculate mean and SD travel time
sac <- test4[test4$general_location %in% c("TowerBridge", "I80-50_Br"),]
ben <- test4[test4$general_location %in% c("Benicia_west", "Benicia_east"),]
travel_sac <- aggregate(list(first_detect_sac = sac$DateTime_PST), by = list(Release = sac$Release, TagCode = sac$TagCode), min)
travel_ben <- aggregate(list(first_detect_ben = ben$DateTime_PST), by = list(Release = ben$Release, TagCode = ben$TagCode), min)
travel <- merge(travel_sac, travel_ben, by = c("Release","TagCode"))
travel$days <- as.numeric(difftime(travel$first_detect_ben, travel$first_detect_sac, units = "days"))
if(nrow(travel)>0){
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)))
}else{
travel_final <- data.frame(Release = c(unique(detects_study$Release),"ALL"), mean_travel_time = NA, sd_travel_time = NA, n = NA)
}
travel_final <- aggregate(list(mean_travel_time = travel$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$days), n = nrow(travel)))
inp <- as.data.frame(reshape2::dcast(test4, TagCode ~ general_location, fun.aggregate = length))
# add together detections at Tower and I80 to ensure good detection entering Delta
if("I80-50_Br" %in% colnames(inp) & "TowerBridge" %in% colnames(inp)){
inp$`I80-50_Br` <- inp$`I80-50_Br` + inp$TowerBridge
} else if("TowerBridge" %in% colnames(inp)){
inp$`I80-50_Br` <- inp$TowerBridge
}
# Sort columns by river km in descending order, this also removes TowerBridge, no longer needed
inp <- inp[,c("TagCode","I80-50_Br", "Benicia_east", "Benicia_west")]
# 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$Release)))
groups_w_detects <- names(table(detects_study[which(detects_study$river_km < 53),"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$real[2,c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv.rel <- cbind(Release = groups_w_detects,
round(WR.mark.rel$results$real[seq(from=2,to=length(groups_w_detects)*3,by = 3),
c("estimate", "se", "lcl", "ucl")] * 100,1))
WR.surv.rel <- merge(WR.surv.rel, data.frame(Release = groups), all.y = T)
WR.surv.rel[is.na(WR.surv.rel$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$real[2,c("estimate", "se", "lcl", "ucl")] * 100,1))
}
WR.surv1 <- WR.surv
colnames(WR.surv1)[1] <- "Release"
WR.surv1 <- merge(WR.surv1, travel_final, by = "Release", all.x = T)
WR.surv1$mean_travel_time <- round(WR.surv1$mean_travel_time,1)
WR.surv1$sd_travel_time <- round(WR.surv1$sd_travel_time,1)
colnames(WR.surv1) <- c("Release", "Survival (%)", "SE", "95% lower C.I.",
"95% upper C.I.", "Mean Delta passage (days)", "SD of Delta Passage (days)","Count")
#colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(WR.surv1, row.names = F, "html", caption = "3.2 Minimum through-Delta survival, and travel time: City of Sacramento to Benicia (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
if(exists("Delta")==T & is.numeric(WR.surv1[1,2])){
reltimes <- aggregate(list(RelDT = study_tagcodes$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")
Delta$RelDT <- as.POSIXct(Delta$RelDT)
# remove old benicia record for this studyID
Delta <- Delta[!Delta$StudyID %in% unique(detects_study$Study_ID),]
Delta <- rbind(Delta, data.frame(WR.surv, StudyID = unique(detects_study$Study_ID), data_quality = quality))
write.csv(Delta, "Delta_surv.csv", row.names = F, quote = F)
}
}
}| Release | Survival (%) | SE | 95% lower C.I. | 95% upper C.I. | Mean Delta passage (days) | SD of Delta Passage (days) | Count |
|---|---|---|---|---|---|---|---|
| ALL | 57.7 | 2.8 | 52.1 | 63.0 | 5.7 | 3.1 | 181 |
| Week 1 | 44.9 | 8.7 | 29.0 | 62.0 | 7.6 | 4.1 | 15 |
| Week 2 | 58.4 | 5.9 | 46.6 | 69.2 | 8.8 | 3.9 | 43 |
| Week 3 | 62.3 | 5.4 | 51.2 | 72.2 | 4.8 | 1.4 | 48 |
| Week 4 | 72.1 | 4.9 | 61.6 | 80.7 | 4.2 | 1.1 | 61 |
| Week 5 | 31.1 | 6.7 | 19.6 | 45.5 | 3.5 | 0.8 | 14 |
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
try(benicia <- read.csv("benicia_surv.csv", stringsAsFactors = F))
detects_benicia <- detects_study[detects_study$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$RelDT), units = "days"))>30){
WR.surv <- data.frame("Release"="ALL", "estimate"=0, "se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
} else {
WR.surv <- data.frame("Release"=NA, "estimate"="NO DETECTIONS YET", "se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
}
WR.surv1 <- WR.surv
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.6 Minimum survival to Benicia Bridge East Span (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else if(length(table(detects_benicia$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$TagCode))*100,1),
"se"=NA, "lcl"=NA, "ucl"=NA, "Detection_efficiency"=NA)
} else {
WR.surv <- data.frame("Release" = NA, "estimate" = "NOT ENOUGH DETECTIONS", "se" = NA, "lcl" = NA, "ucl" = NA, "Detection_efficiency" = NA)
}
WR.surv1 <- WR.surv
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.6 Minimum survival to Benicia Bridge East Span (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
# Only do survival to Benicia here
test3 <- detects_study[which(detects_study$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$sd_travel_time,1)
colnames(WR.surv1) <- c("Release", "Survival (%)", "SE", "95% lower C.I.",
"95% upper C.I.", "Detection efficiency (%)", "Mean time to Benicia (days)", "SD of time to Benicia (days)", "Count")
#colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.3 Minimum survival to Benicia Bridge East Span (using CJS survival model), and travel time") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
}| Release | Survival (%) | SE | 95% lower C.I. | 95% upper C.I. | Detection efficiency (%) | Mean time to Benicia (days) | SD of time to Benicia (days) | Count |
|---|---|---|---|---|---|---|---|---|
| ALL | 18.9 | 1.2 | 16.6 | 21.5 | 94.6 | 25.7 | 10.5 | 188 |
| Week 1 | 7.5 | 1.9 | 4.6 | 12.1 | NA | 12.2 | 4.4 | 15 |
| Week 2 | 21.6 | 2.9 | 16.5 | 27.9 | NA | 40.1 | 5.5 | 43 |
| Week 3 | 26.2 | 3.1 | 20.5 | 32.7 | NA | 27.9 | 4.5 | 52 |
| Week 4 | 31.9 | 3.3 | 25.8 | 38.8 | NA | 19.9 | 5.6 | 63 |
| Week 5 | 7.5 | 1.9 | 4.6 | 12.1 | NA | 14.4 | 1.9 | 15 |
if(exists("benicia")==T & is.numeric(WR.surv1[1,2])){
# Find mean release time per release group, and ALL
reltimes <- aggregate(list(RelDT = study_tagcodes$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$Study_ID), data_quality = quality))
write.csv(benicia, "benicia_surv.csv", row.names = F, quote = F)
}4. Detections statistics at all realtime receivers
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
if(nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) == 0){
"No detections yet"
} else {
arrivals <- detects_study %>%
group_by(general_location, TagCode) %>%
summarise(DateTime_PST = min(DateTime_PST)) %>%
arrange(TagCode)
tag_stats <- arrivals %>%
group_by(general_location) %>%
summarise(First_arrival = min(DateTime_PST),
Mean_arrival = mean(DateTime_PST),
Last_arrival = max(DateTime_PST),
Fish_count = length(unique(TagCode))) %>%
mutate(Percent_arrived = round(Fish_count/nrow(study_tagcodes) * 100,2)) %>%
dplyr::left_join(., unique(detects_study[,c("general_location", "river_km")])) %>%
arrange(desc(river_km)) %>%
mutate(First_arrival = format(First_arrival, tz = "Etc/GMT+8"),
Mean_arrival = format(Mean_arrival, tz = "Etc/GMT+8"),
Last_arrival = format(Last_arrival, tz = "Etc/GMT+8")) %>%
na.omit()
print(kable(tag_stats, row.names = F,
caption = "4.1 Detections for all releases combined",
"html") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
count <- 0
for(j in sort(unique(study_tagcodes$Release))){
if(nrow(detects_study[detects_study$Release == j,]) > 0){
count <- count + 1
arrivals1 <- detects_study %>%
filter(Release == j) %>%
group_by(general_location, TagCode) %>%
summarise(DateTime_PST = min(DateTime_PST)) %>%
arrange(TagCode)
rel_count <- nrow(study_tagcodes[study_tagcodes$Release == j,])
tag_stats1 <- arrivals1 %>%
group_by(general_location) %>%
summarise(First_arrival = min(DateTime_PST),
Mean_arrival = mean(DateTime_PST),
Last_arrival = max(DateTime_PST),
Fish_count = length(unique(TagCode))) %>%
mutate(Percent_arrived = round(Fish_count/rel_count * 100,2)) %>%
dplyr::left_join(., unique(detects_study[,c("general_location", "river_km")])) %>%
arrange(desc(river_km)) %>%
mutate(First_arrival = format(First_arrival, tz = "Etc/GMT+8"),
Mean_arrival = format(Mean_arrival, tz = "Etc/GMT+8"),
Last_arrival = format(Last_arrival, tz = "Etc/GMT+8")) %>%
na.omit()
final_stats <- kable(tag_stats1, row.names = F,
caption = paste("4.2.", count, " Detections for ", j, " release groups", sep = ""),
"html")
print(kable_styling(final_stats, bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
cat("\n\n\\pagebreak\n")
print(paste("No detections for",j,"release group yet", sep=" "), quote = F)
cat("\n\n\\pagebreak\n")
}
}
}| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| Blw_Salt_RT | 2024-12-10 11:45:11 | 2025-01-01 13:08:14 | 2025-04-22 13:15:40 | 193 | 19.32 | 457.000 |
| MeridianBr | 2024-12-13 03:50:23 | 2025-03-13 08:04:35 | 2025-04-26 05:15:03 | 410 | 41.04 | 290.848 |
| TowerBridge | 2024-12-14 20:47:36 | 2025-03-13 11:56:49 | 2025-04-24 18:51:04 | 267 | 26.73 | 172.000 |
| I80-50_Br | 2024-12-14 21:22:22 | 2025-03-16 06:48:34 | 2025-04-24 19:10:12 | 281 | 28.13 | 170.748 |
| MiddleRiver | 2025-03-17 07:13:42 | 2025-03-17 07:13:42 | 2025-03-17 07:13:42 | 1 | 0.10 | 150.000 |
| Old_River_Quimby | 2024-12-24 13:00:30 | 2025-02-22 08:13:24 | 2025-03-27 15:16:46 | 3 | 0.30 | 141.000 |
| SanJoaquinMcDonald | 2025-03-06 06:17:04 | 2025-03-15 03:10:13 | 2025-03-24 00:03:22 | 2 | 0.20 | 126.000 |
| SanJoaquinMcDonald_2 | 2025-03-05 21:33:56 | 2025-03-14 23:07:46 | 2025-03-24 00:41:37 | 2 | 0.20 | 125.420 |
| SacRiverWalnutGrove_2 | 2024-12-15 18:14:23 | 2025-03-19 16:54:31 | 2025-04-25 13:50:34 | 245 | 24.52 | 120.300 |
| Georg_Sl_1 | 2024-12-15 17:38:24 | 2025-03-16 15:02:23 | 2025-04-25 14:15:11 | 41 | 4.10 | 119.600 |
| Sac_BlwGeorgiana | 2024-12-16 08:15:50 | 2025-03-20 07:35:07 | 2025-04-22 17:12:18 | 203 | 20.32 | 119.058 |
| Sac_BlwGeorgiana2 | 2024-12-16 08:33:42 | 2025-03-20 07:49:06 | 2025-04-22 17:20:08 | 203 | 20.32 | 118.398 |
| Benicia_east | 2024-12-17 22:05:43 | 2025-03-23 12:39:55 | 2025-04-24 16:44:36 | 179 | 17.92 | 52.240 |
| Benicia_west | 2024-12-17 22:08:33 | 2025-03-22 06:02:27 | 2025-04-25 02:33:00 | 166 | 16.62 | 52.040 |
| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| Blw_Salt_RT | 2024-12-10 11:45:11 | 2024-12-11 06:51:17 | 2025-01-03 02:38:44 | 161 | 80.5 | 457.000 |
| MeridianBr | 2024-12-13 03:50:23 | 2024-12-14 07:31:30 | 2024-12-15 12:44:39 | 39 | 19.5 | 290.848 |
| TowerBridge | 2024-12-14 20:47:36 | 2024-12-16 18:42:59 | 2025-01-16 22:01:31 | 33 | 16.5 | 172.000 |
| I80-50_Br | 2024-12-14 21:22:22 | 2024-12-16 21:28:56 | 2025-01-16 22:33:51 | 30 | 15.0 | 170.748 |
| Old_River_Quimby | 2024-12-24 13:00:30 | 2024-12-24 13:00:30 | 2024-12-24 13:00:30 | 1 | 0.5 | 141.000 |
| SacRiverWalnutGrove_2 | 2024-12-15 18:14:23 | 2024-12-18 04:45:11 | 2025-01-17 19:49:32 | 20 | 10.0 | 120.300 |
| Georg_Sl_1 | 2024-12-15 17:38:24 | 2024-12-16 13:40:01 | 2024-12-17 11:53:10 | 6 | 3.0 | 119.600 |
| Sac_BlwGeorgiana | 2024-12-16 08:15:50 | 2024-12-18 21:52:17 | 2025-01-17 20:28:30 | 14 | 7.0 | 119.058 |
| Sac_BlwGeorgiana2 | 2024-12-16 08:33:42 | 2024-12-18 22:09:04 | 2025-01-17 20:45:25 | 14 | 7.0 | 118.398 |
| Benicia_east | 2024-12-17 22:05:43 | 2024-12-23 04:13:36 | 2025-01-03 23:32:14 | 14 | 7.0 | 52.240 |
| Benicia_west | 2024-12-17 22:08:33 | 2024-12-23 05:41:19 | 2025-01-03 23:41:08 | 15 | 7.5 | 52.040 |
| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| MeridianBr | 2025-02-13 09:16:05 | 2025-02-28 16:05:52 | 2025-03-26 10:06:01 | 99 | 49.5 | 290.848 |
| TowerBridge | 2025-02-22 10:03:01 | 2025-03-08 13:41:58 | 2025-03-27 22:14:43 | 66 | 33.0 | 172.000 |
| I80-50_Br | 2025-02-26 03:31:15 | 2025-03-09 13:53:03 | 2025-03-27 22:36:41 | 61 | 30.5 | 170.748 |
| MiddleRiver | 2025-03-17 07:13:42 | 2025-03-17 07:13:42 | 2025-03-17 07:13:42 | 1 | 0.5 | 150.000 |
| SanJoaquinMcDonald | 2025-03-06 06:17:04 | 2025-03-06 06:17:04 | 2025-03-06 06:17:04 | 1 | 0.5 | 126.000 |
| SanJoaquinMcDonald_2 | 2025-03-05 21:33:56 | 2025-03-05 21:33:56 | 2025-03-05 21:33:56 | 1 | 0.5 | 125.420 |
| SacRiverWalnutGrove_2 | 2025-02-23 14:43:43 | 2025-03-08 23:11:21 | 2025-03-28 13:49:19 | 49 | 24.5 | 120.300 |
| Georg_Sl_1 | 2025-02-28 09:14:18 | 2025-03-06 06:40:55 | 2025-03-18 11:52:26 | 6 | 3.0 | 119.600 |
| Sac_BlwGeorgiana | 2025-02-23 14:56:03 | 2025-03-09 08:42:54 | 2025-03-28 14:14:31 | 43 | 21.5 | 119.058 |
| Sac_BlwGeorgiana2 | 2025-02-23 15:02:56 | 2025-03-09 08:59:53 | 2025-03-28 14:32:06 | 43 | 21.5 | 118.398 |
| Benicia_east | 2025-03-01 14:00:24 | 2025-03-18 05:46:06 | 2025-03-31 10:41:06 | 41 | 20.5 | 52.240 |
| Benicia_west | 2025-03-01 08:20:53 | 2025-03-18 04:44:05 | 2025-03-31 10:42:18 | 38 | 19.0 | 52.040 |
| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| Blw_Salt_RT | 2025-04-20 06:34:04 | 2025-04-20 06:34:04 | 2025-04-20 06:34:04 | 1 | 0.5 | 457.000 |
| MeridianBr | 2025-02-28 06:41:53 | 2025-03-15 23:34:46 | 2025-04-04 04:30:49 | 102 | 51.0 | 290.848 |
| TowerBridge | 2025-03-05 09:51:13 | 2025-03-20 10:28:21 | 2025-04-06 00:10:56 | 62 | 31.0 | 172.000 |
| I80-50_Br | 2025-03-05 10:17:25 | 2025-03-21 02:53:46 | 2025-04-12 04:55:48 | 72 | 36.0 | 170.748 |
| Old_River_Quimby | 2025-03-20 20:22:57 | 2025-03-24 05:49:51 | 2025-03-27 15:16:46 | 2 | 1.0 | 141.000 |
| SanJoaquinMcDonald | 2025-03-24 00:03:22 | 2025-03-24 00:03:22 | 2025-03-24 00:03:22 | 1 | 0.5 | 126.000 |
| SanJoaquinMcDonald_2 | 2025-03-24 00:41:37 | 2025-03-24 00:41:37 | 2025-03-24 00:41:37 | 1 | 0.5 | 125.420 |
| SacRiverWalnutGrove_2 | 2025-03-08 08:51:29 | 2025-03-21 21:10:23 | 2025-04-12 19:23:10 | 66 | 33.0 | 120.300 |
| Georg_Sl_1 | 2025-03-12 23:16:09 | 2025-03-21 02:06:18 | 2025-03-29 06:51:24 | 9 | 4.5 | 119.600 |
| Sac_BlwGeorgiana | 2025-03-08 09:37:46 | 2025-03-22 00:45:19 | 2025-04-12 19:48:52 | 57 | 28.5 | 119.058 |
| Sac_BlwGeorgiana2 | 2025-03-08 09:57:17 | 2025-03-22 00:58:49 | 2025-04-12 20:00:24 | 57 | 28.5 | 118.398 |
| Benicia_east | 2025-03-18 11:34:06 | 2025-03-25 10:11:38 | 2025-04-01 22:20:23 | 49 | 24.5 | 52.240 |
| Benicia_west | 2025-03-18 11:39:37 | 2025-03-26 00:44:40 | 2025-04-15 06:17:53 | 46 | 23.0 | 52.040 |
| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| Blw_Salt_RT | 2025-04-22 13:15:40 | 2025-04-22 13:15:40 | 2025-04-22 13:15:40 | 1 | 0.50 | 457.000 |
| MeridianBr | 2025-03-21 03:05:15 | 2025-03-30 15:41:00 | 2025-04-15 12:12:03 | 94 | 47.24 | 290.848 |
| TowerBridge | 2025-03-23 12:34:23 | 2025-04-02 15:45:08 | 2025-04-17 01:47:20 | 71 | 35.68 | 172.000 |
| I80-50_Br | 2025-03-23 12:54:24 | 2025-04-02 01:28:09 | 2025-04-17 02:12:57 | 76 | 38.19 | 170.748 |
| SacRiverWalnutGrove_2 | 2025-03-24 03:47:35 | 2025-04-02 23:53:53 | 2025-04-17 16:15:42 | 74 | 37.19 | 120.300 |
| Georg_Sl_1 | 2025-03-28 11:52:37 | 2025-04-05 10:01:54 | 2025-04-14 18:18:32 | 10 | 5.03 | 119.600 |
| Sac_BlwGeorgiana | 2025-03-24 04:07:12 | 2025-04-02 18:09:54 | 2025-04-17 16:33:36 | 63 | 31.66 | 119.058 |
| Sac_BlwGeorgiana2 | 2025-03-24 04:17:51 | 2025-04-02 18:22:07 | 2025-04-17 16:43:07 | 63 | 31.66 | 118.398 |
| Benicia_east | 2025-03-29 17:37:11 | 2025-04-08 00:42:09 | 2025-04-20 10:55:46 | 60 | 30.15 | 52.240 |
| Benicia_west | 2025-03-29 17:39:41 | 2025-04-07 15:38:12 | 2025-04-20 11:00:20 | 53 | 26.63 | 52.040 |
| general_location | First_arrival | Mean_arrival | Last_arrival | Fish_count | Percent_arrived | river_km |
|---|---|---|---|---|---|---|
| Blw_Salt_RT | 2025-04-17 03:05:38 | 2025-04-18 07:52:06 | 2025-04-20 11:34:27 | 30 | 15.0 | 457.000 |
| MeridianBr | 2025-04-11 18:10:57 | 2025-04-19 13:10:06 | 2025-04-26 05:15:03 | 76 | 38.0 | 290.848 |
| TowerBridge | 2025-04-13 05:27:10 | 2025-04-20 08:48:35 | 2025-04-24 18:51:04 | 35 | 17.5 | 172.000 |
| I80-50_Br | 2025-04-13 05:48:03 | 2025-04-20 05:16:57 | 2025-04-24 19:10:12 | 42 | 21.0 | 170.748 |
| SacRiverWalnutGrove_2 | 2025-04-13 21:56:22 | 2025-04-20 18:55:42 | 2025-04-25 13:50:34 | 36 | 18.0 | 120.300 |
| Georg_Sl_1 | 2025-04-20 14:40:37 | 2025-04-22 01:31:36 | 2025-04-25 14:15:11 | 10 | 5.0 | 119.600 |
| Sac_BlwGeorgiana | 2025-04-13 22:15:40 | 2025-04-20 07:40:10 | 2025-04-22 17:12:18 | 26 | 13.0 | 119.058 |
| Sac_BlwGeorgiana2 | 2025-04-13 22:26:35 | 2025-04-20 07:53:04 | 2025-04-22 17:20:08 | 26 | 13.0 | 118.398 |
| Benicia_east | 2025-04-18 12:34:44 | 2025-04-23 02:30:59 | 2025-04-24 16:44:36 | 15 | 7.5 | 52.240 |
| Benicia_west | 2025-04-18 16:25:50 | 2025-04-23 03:02:20 | 2025-04-25 02:33:00 | 14 | 7.0 | 52.040 |
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){
"No detections yet"
} else {
arrivals <- detects_study %>%
group_by(general_location, TagCode) %>%
summarise(DateTime_PST = min(DateTime_PST)) %>%
mutate(day = as.Date(DateTime_PST, "%Y-%m-%d", tz = "Etc/GMT+8"))
# 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)
beacon_by_day <- fread("beacon_by_day.csv", stringsAsFactors = F) %>%
mutate(day = as.Date(day)) %>%
filter(TagCode == beacon) %>% # Now subset to only look at data for the correct beacon for that day
filter(day >= as.Date(min(study_tagcodes$release_time)) &
day <= endtime) %>% # Now only keep beacon by day for days since fish were released
dplyr::left_join(., gen_locs[,c("location", "general_location","rkm")], by = "location")
arrivals_per_day <- arrivals %>%
group_by(day, general_location) %>%
summarise(New_arrivals = length(TagCode)) %>%
arrange(general_location) %>% na.omit() %>%
mutate(day = as.Date(day)) %>%
dplyr::left_join(unique(beacon_by_day[,c("general_location", "day", "rkm")]),
., by = c("general_location", "day")) %>%
arrange(general_location, day) %>%
mutate(day = factor(day)) %>%
filter(general_location != "Bench_test") %>% # Remove bench test and other NA locations
filter(!(is.na(general_location))) %>%
arrange(desc(rkm)) %>% # Change order of data to plot decreasing river_km
mutate(general_location = factor(general_location, unique(general_location)))
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")),
max(as.Date(detects_study$release_time)+(as.numeric(detects_study$tag_life)*1.5)))
crosstab <- xtabs(formula = arrivals_per_day$New_arrivals ~ arrivals_per_day$day + arrivals_per_day$general_location,
addNA =T)
crosstab[is.na(crosstab)] <- ""
crosstab[crosstab==0] <- NA
crosstab <- as.data.frame.matrix(crosstab)
kable(crosstab, align = "c", caption = "4.3 Fish arrivals per day (\"NA\" means receivers were non-operational)") %>%
kable_styling(c("striped", "condensed"), font_size = 11, full_width = F, position = "left", fixed_thead = TRUE) %>%
column_spec(column = 1:ncol(crosstab),width_min = "50px",border_left = T, border_right = T) %>%
column_spec(1, bold = T, width_min = "75px")%>%
scroll_box(height = "700px")
}| Blw_Salt_RT | Sac_OrdFerry | MeridianBr | Stan_Valley_Oak | Stan_Caswell | SJ_Vernalis | TowerBridge | I80-50_Br | MiddleRiver | Clifton_Court_US_Radial_Gates | Holland_Cut_Quimby | CVP_Tank | CVP_Trash_Rack_1 | Clifton_Court_Intake_Canal | Old_River_Quimby | SanJoaquinMcDonald | SanJoaquinMcDonald_2 | SacRiverWalnutGrove_2 | Georg_Sl_1 | Sac_BlwGeorgiana | Sac_BlwGeorgiana2 | Benicia_east | Benicia_west | |
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| 2024-12-10 | 82 | NA | NA | NA | |||||||||||||||||||
| 2024-12-11 | 77 | NA | NA | NA | |||||||||||||||||||
| 2024-12-12 | 1 | NA | NA | NA | |||||||||||||||||||
| 2024-12-13 | NA | 6 | NA | NA | |||||||||||||||||||
| 2024-12-14 | NA | 30 | NA | 2 | 2 | NA | |||||||||||||||||
| 2024-12-15 | NA | 3 | NA | 23 | 21 | NA | 1 | 1 | |||||||||||||||
| 2024-12-16 | NA | NA | 6 | 5 | NA | 14 | 3 | 11 | 11 | ||||||||||||||
| 2024-12-17 | NA | NA | 4 | 2 | 2 | 2 | 1 | 1 | |||||||||||||||
| 2024-12-18 | NA | NA | 1 | 1 | 1 | 1 | |||||||||||||||||
| 2024-12-19 | NA | NA | 1 | ||||||||||||||||||||
| 2024-12-20 | NA | NA | 2 | 1 | |||||||||||||||||||
| 2024-12-21 | NA | NA | 2 | 3 | |||||||||||||||||||
| 2024-12-22 | NA | NA | 2 | 1 | |||||||||||||||||||
| 2024-12-23 | NA | NA | 3 | 3 | |||||||||||||||||||
| 2024-12-24 | NA | NA | 1 | 1 | |||||||||||||||||||
| 2024-12-25 | NA | NA | 1 | 1 | |||||||||||||||||||
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| 2024-12-28 | NA | NA | 1 | 1 | |||||||||||||||||||
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| 2025-01-16 | NA | NA | 1 | 1 | |||||||||||||||||||
| 2025-01-17 | NA | NA | 1 | 1 | 1 | ||||||||||||||||||
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| 2025-02-12 | NA | NA | |||||||||||||||||||||
| 2025-02-13 | NA | NA | 1 | ||||||||||||||||||||
| 2025-02-14 | NA | NA | |||||||||||||||||||||
| 2025-02-15 | NA | NA | |||||||||||||||||||||
| 2025-02-16 | NA | NA | 1 | ||||||||||||||||||||
| 2025-02-17 | NA | NA | 2 | ||||||||||||||||||||
| 2025-02-18 | NA | NA | 2 | ||||||||||||||||||||
| 2025-02-19 | NA | NA | 3 | ||||||||||||||||||||
| 2025-02-20 | NA | NA | 2 | ||||||||||||||||||||
| 2025-02-21 | NA | NA | 5 | ||||||||||||||||||||
| 2025-02-22 | NA | NA | 6 | 1 | |||||||||||||||||||
| 2025-02-23 | NA | NA | 4 | 1 | 1 | 1 | |||||||||||||||||
| 2025-02-24 | NA | NA | 7 | ||||||||||||||||||||
| 2025-02-25 | NA | NA | 9 | ||||||||||||||||||||
| 2025-02-26 | NA | NA | 5 | 1 | 1 | ||||||||||||||||||
| 2025-02-27 | NA | NA | 7 | 4 | 1 | 2 | 2 | 2 | |||||||||||||||
| 2025-02-28 | NA | NA | 8 | 3 | 5 | 2 | 2 | ||||||||||||||||
| 2025-03-01 | NA | NA | 7 | 4 | 3 | 2 | 2 | 2 | 1 | 1 | |||||||||||||
| 2025-03-02 | NA | NA | 10 | 2 | 2 | 3 | 1 | 2 | 2 | ||||||||||||||
| 2025-03-03 | NA | NA | 1 | 5 | 2 | 1 | 1 | 1 | |||||||||||||||
| 2025-03-04 | NA | NA | 8 | 4 | 4 | 3 | 3 | 3 | |||||||||||||||
| 2025-03-05 | NA | NA | 8 | 6 | 5 | 1 | 6 | 1 | 6 | 6 | |||||||||||||
| 2025-03-06 | NA | NA | 4 | 6 | 7 | 1 | 4 | 3 | 3 | ||||||||||||||
| 2025-03-07 | NA | NA | 2 | 2 | 2 | 4 | 4 | 4 | |||||||||||||||
| 2025-03-08 | NA | NA | 7 | 3 | 3 | 2 | 2 | 2 | |||||||||||||||
| 2025-03-09 | NA | NA | 4 | 4 | 4 | 5 | 1 | 4 | 3 | ||||||||||||||
| 2025-03-10 | NA | NA | 6 | 4 | 4 | 2 | 2 | 3 | |||||||||||||||
| 2025-03-11 | NA | NA | 4 | 3 | 3 | 1 | 1 | 1 | 2 | ||||||||||||||
| 2025-03-12 | NA | NA | 5 | 4 | 4 | 2 | 1 | 1 | 1 | 1 | 2 | ||||||||||||
| 2025-03-13 | NA | NA | 2 | 4 | 4 | 4 | 4 | 4 | 4 | 3 | |||||||||||||
| 2025-03-14 | NA | NA | 5 | 5 | 6 | 4 | 1 | 3 | 3 | 3 | 5 | ||||||||||||
| 2025-03-15 | NA | NA | 1 | 1 | 1 | 3 | 3 | 3 | 6 | 5 | |||||||||||||
| 2025-03-16 | NA | NA | 3 | 4 | 4 | 1 | 1 | 1 | 3 | 4 | |||||||||||||
| 2025-03-17 | NA | NA | 3 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 3 | 3 | |||||||||||
| 2025-03-18 | NA | NA | 16 | 4 | 4 | 2 | 1 | 1 | 1 | 4 | 3 | ||||||||||||
| 2025-03-19 | NA | NA | 6 | 11 | 12 | 5 | 1 | 4 | 4 | 5 | 3 | ||||||||||||
| 2025-03-20 | NA | NA | 11 | 7 | 8 | 1 | 10 | 2 | 8 | 8 | 2 | 2 | |||||||||||
| 2025-03-21 | NA | NA | 6 | 7 | 9 | 8 | 8 | 8 | 5 | 6 | |||||||||||||
| 2025-03-22 | NA | NA | 10 | 9 | 9 | 8 | 8 | 7 | 5 | 5 | |||||||||||||
| 2025-03-23 | NA | NA | 8 | 6 | 6 | 5 | 5 | 6 | 6 | 3 | |||||||||||||
| 2025-03-24 | NA | NA | 9 | 3 | 2 | 1 | 1 | 6 | 6 | 6 | 12 | 11 | |||||||||||
| 2025-03-25 | NA | NA | 10 | 9 | 11 | 5 | 5 | 5 | 3 | 3 | |||||||||||||
| 2025-03-26 | NA | NA | 12 | 5 | 9 | 10 | 9 | 9 | 4 | 3 | |||||||||||||
| 2025-03-27 | NA | NA | 11 | 5 | 8 | 1 | 8 | 2 | 6 | 6 | 8 | 7 | |||||||||||
| 2025-03-28 | NA | NA | 8 | 7 | 8 | 8 | 1 | 7 | 7 | 6 | 8 | ||||||||||||
| 2025-03-29 | NA | NA | 5 | 9 | 8 | 8 | 1 | 6 | 6 | 4 | 3 | ||||||||||||
| 2025-03-30 | NA | NA | 1 | 4 | 7 | 8 | 4 | 5 | 5 | 5 | 5 | ||||||||||||
| 2025-03-31 | NA | NA | 3 | 6 | 7 | 6 | 6 | 6 | 4 | 4 | |||||||||||||
| 2025-04-01 | NA | NA | 6 | 2 | 1 | 5 | 4 | 4 | 5 | 5 | |||||||||||||
| 2025-04-02 | NA | NA | 3 | 2 | 3 | 1 | 2 | 2 | 4 | 4 | |||||||||||||
| 2025-04-03 | NA | NA | 2 | 4 | 4 | 3 | 3 | 2 | 4 | 2 | |||||||||||||
| 2025-04-04 | NA | NA | 3 | 1 | 1 | 1 | 1 | 2 | 3 | 3 | |||||||||||||
| 2025-04-05 | NA | NA | 1 | 5 | 4 | 2 | 1 | 1 | 1 | 3 | 3 | ||||||||||||
| 2025-04-06 | NA | NA | 2 | 3 | 3 | 5 | 5 | 5 | 1 | 1 | |||||||||||||
| 2025-04-07 | NA | NA | 7 | 1 | 1 | 2 | 2 | 2 | 3 | 3 | |||||||||||||
| 2025-04-08 | NA | NA | 1 | NA | 1 | 1 | 5 | 4 | |||||||||||||||
| 2025-04-09 | NA | NA | 2 | NA | 5 | 4 | 5 | 1 | 4 | 4 | 3 | 4 | |||||||||||
| 2025-04-10 | NA | NA | 4 | NA | 1 | 2 | 2 | 2 | 2 | 2 | 1 | ||||||||||||
| 2025-04-11 | NA | NA | 3 | NA | 2 | 2 | 1 | 1 | 1 | 3 | 3 | ||||||||||||
| 2025-04-12 | NA | NA | 4 | NA | 5 | 6 | 4 | 4 | 4 | 5 | 4 | ||||||||||||
| 2025-04-13 | NA | NA | 1 | NA | 2 | 2 | 4 | 1 | 3 | 3 | 3 | 3 | |||||||||||
| 2025-04-14 | NA | NA | 1 | NA | 3 | 2 | 4 | 2 | 2 | 2 | 4 | 2 | |||||||||||
| 2025-04-15 | NA | NA | 3 | NA | 1 | 1 | 1 | 2 | |||||||||||||||
| 2025-04-16 | NA | NA | 1 | NA | 1 | 2 | 2 | 2 | 2 | 2 | |||||||||||||
| 2025-04-17 | 12 | NA | NA | 2 | 2 | 1 | 1 | 1 | 1 | ||||||||||||||
| 2025-04-18 | 12 | NA | 29 | NA | 1 | 2 | 1 | 1 | 1 | 2 | 2 | ||||||||||||
| 2025-04-19 | 4 | NA | 19 | NA | 3 | 3 | 1 | 1 | 1 | ||||||||||||||
| 2025-04-20 | 3 | NA | 10 | NA | 11 | 15 | 10 | 2 | 8 | 8 | 2 | 2 | |||||||||||
| 2025-04-21 | NA | 1 | NA | 13 | 14 | 11 | 4 | 7 | 7 | 2 | 2 | ||||||||||||
| 2025-04-22 | 1 | NA | 2 | 2 | 2 | 8 | 3 | 5 | 5 | 1 | 1 | ||||||||||||
| 2025-04-23 | NA | 2 | 5 | 4 | |||||||||||||||||||
| 2025-04-24 | NA | 1 | 1 | 5 | 4 | ||||||||||||||||||
| 2025-04-25 | NA | 4 | 1 | 1 | 1 | ||||||||||||||||||
| 2025-04-26 | NA | 2 | |||||||||||||||||||||
| 2025-04-27 | NA |
rm(list = ls())
cleanup(ask = F)
For questions or comments, please contact cyril.michel@noaa.gov