2. Real-time Fish Detections
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_butte <- detects_study[detects_study$general_location == "ButteBrRT",]
if (nrow(detects_butte) == 0){
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else {
detects_butte <- merge(detects_butte,aggregate(list(first_detect = detects_butte$DateTime_PST), by = list(TagCode= detects_butte$TagCode), FUN = min))
detects_butte$Day <- as.Date(detects_butte$first_detect, "Etc/GMT+8")
starttime <- as.Date(min(detects_butte$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_butte$release_time)+(as.numeric(detects_butte$tag_life)*1.5)))
#BTC_flow <- cdec_query("BTC", "20", "H", starttime, endtime+1)
## download bend bridge flow data
BTC_flow <- readNWISuv(siteNumbers = "11377100", parameterCd="00060", startDate = starttime, endDate = endtime+1)
BTC_flow$datetime <- as.Date(format(BTC_flow$dateTime, "%Y-%m-%d"))
BTC_flow_day <- aggregate(list(parameter_value = BTC_flow$X_00060_00000),
by = list(Day = BTC_flow$datetime),
FUN = mean, na.rm = T)
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
#rels <- unique(study_tagcodes[study_tagcodes$StudyID == unique(detects_butte$StudyID), "Release"])
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_butte$Release))])
tagcount <- aggregate(list(unique_tags = detects_butte$TagCode), by = list(Day = detects_butte$Day, Release = detects_butte$Release), FUN = function(x){length(unique(x))})
tagcount1 <- reshape2::dcast(tagcount, Day ~ Release)
daterange1 <- merge(daterange, tagcount1, all.x=T)
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == 'x'] <- paste(i)
}
}
daterange2 <- merge(daterange1, BTC_flow_day, by = "Day", all.x = T)
rownames(daterange2) <- daterange2$Day
daterange2$Day <- NULL
par(mar=c(6, 5, 2, 5) + 0.1)
barp <- barplot(t(daterange2[,1:ncol(daterange2)-1]), plot = FALSE, beside = T)
barplot(t(daterange2[,1:ncol(daterange2)-1]), beside = T, col=viridis_pal()(rel_num),
xlab = "", ylab = "Number of fish arrivals per day",
ylim = c(0,max(daterange2[,1:ncol(daterange2)-1], na.rm = T)*1.2),
las = 2, xlim=c(0,max(barp)+1), cex.lab = 1.5, yaxt = "n", xaxt ="n")#,
#border=NA
#legend.text = colnames(daterange2[,1:ncol(daterange2)-1]),
#args.legend = list(x ='topright', bty='n', inset=c(-0.2,0)), title = "Release Group")
legend(x ='topleft', legend = colnames(daterange2)[1:ncol(daterange2)-1], fill= viridis_pal()(rel_num), horiz = T, title = "Release")
ybreaks <- if(max(daterange2[,1:ncol(daterange2)-1], na.rm = T) < 4) {max(daterange2[,1:ncol(daterange2)-1], na.rm = T)} else {5}
xbreaks <- if(ncol(barp) > 10) {seq(1, ncol(barp), 2)} else {1:ncol(barp)}
barpmeans <- colMeans(barp)
axis(1, at = barpmeans[xbreaks], labels = rownames(daterange2[xbreaks,]), las = 2)
axis(2, at = pretty(0:max(daterange2[,1:ncol(daterange2)-1], na.rm = T), ybreaks))
par(new=T)
plot(x = barpmeans, daterange2$parameter_value, yaxt = "n", xaxt = "n", ylab = "", xlab = "", col = "blue", type = "l", lwd=2, xlim=c(0,max(barp)+1), ylim = c(min(daterange2$parameter_value, na.rm = T), max(daterange2$parameter_value, na.rm=T)*1.1))#, ylab = "Returning adults", xlab= "Outmigration year", yaxt="n", col="red", pch=20)
axis(side = 4)#, labels = c(2000:2016), at = c(2000:2016))
mtext("Flow (cfs) at Bend Bridge", side=4, line=3, cex=1.5, col="blue")
}
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_tower <- detects_study[detects_study$general_location == "TowerBridge",]
#wlk_flow <- read.csv("wlk.csv")
if (nrow(detects_tower) == 0){
plot(1:2, type = "n", xlab = "",xaxt = "n", yaxt = "n", ylab = "Number of fish arrivals per day")
text(1.5,1.5, labels = "NO DETECTIONS YET", cex = 2)
} else {
detects_tower <- merge(detects_tower,aggregate(list(first_detect = detects_tower$DateTime_PST), by = list(TagCode= detects_tower$TagCode), FUN = min))
detects_tower$Day <- as.Date(detects_tower$first_detect, "Etc/GMT+8")
starttime <- as.Date(min(detects_tower$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_tower$release_time)+(as.numeric(detects_tower$tag_life)*1.5)))
## download wilkins slough flow data
wlk_flow <- readNWISuv(siteNumbers = "11390500", parameterCd="00060", startDate = starttime, endDate = endtime+1)
wlk_flow$datetime <- as.Date(format(wlk_flow$dateTime, "%Y-%m-%d"))
wlk_flow_day <- aggregate(list(parameter_value = wlk_flow$X_00060_00000),
by = list(Day = wlk_flow$datetime),
FUN = mean, na.rm = T)
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
#rels <- unique(study_tagcodes[study_tagcodes$StudyID == unique(detects_tower$StudyID), "Release"])
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_tower$Release))])
tagcount <- aggregate(list(unique_tags = detects_tower$TagCode), by = list(Day = detects_tower$Day, Release = detects_tower$Release ), FUN = function(x){length(unique(x))})
tagcount1 <- reshape2::dcast(tagcount, Day ~ Release)
daterange1 <- merge(daterange, tagcount1, all.x=T)
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == 'x'] <- paste(i)
}
}
daterange2 <- merge(daterange1, wlk_flow_day, by = "Day", all.x = T)
rownames(daterange2) <- daterange2$Day
daterange2$Day <- NULL
par(mar=c(6, 5, 2, 5) + 0.1)
barp <- barplot(t(daterange2[,1:ncol(daterange2)-1]), plot = FALSE, beside = T)
barplot(t(daterange2[,1:ncol(daterange2)-1]), beside = T, col=viridis_pal()(rel_num),
xlab = "", ylab = "Number of fish arrivals per day",
ylim = c(0,max(daterange2[,1:ncol(daterange2)-1], na.rm = T)*1.2),
las = 2, xlim=c(0,max(barp)+1), cex.lab = 1.5, yaxt = "n", xaxt ="n")#,
#border=NA
#legend.text = colnames(daterange2[,1:ncol(daterange2)-1]),
#args.legend = list(x ='topright', bty='n', inset=c(-0.2,0)), title = "Release Group")
legend(x ='topleft', legend = colnames(daterange2)[1:ncol(daterange2)-1], fill= viridis_pal()(rel_num), horiz = T, title = "Release")
ybreaks <- if(max(daterange2[,1:ncol(daterange2)-1], na.rm = T) < 4) {max(daterange2[,1:ncol(daterange2)-1], na.rm = T)} else {5}
xbreaks <- if(ncol(barp) > 10) {seq(1, ncol(barp), 2)} else {1:ncol(barp)}
barpmeans <- colMeans(barp)
axis(1, at = barpmeans[xbreaks], labels = rownames(daterange2[xbreaks,]), las = 2)
axis(2, at = pretty(0:max(daterange2[,1:ncol(daterange2)-1], na.rm = T), ybreaks))
par(new=T)
plot(x = barpmeans, daterange2$parameter_value, yaxt = "n", xaxt = "n", ylab = "", xlab = "", col = "blue", type = "l", lwd=2, xlim=c(0,max(barp)+1), ylim = c(min(daterange2$parameter_value, na.rm = T), max(daterange2$parameter_value, na.rm=T)*1.1))#, ylab = "Returning adults", xlab= "Outmigration year", yaxt="n", col="red", pch=20)
axis(side = 4)#, labels = c(2000:2016), at = c(2000:2016))
mtext("Flow (cfs) at Wilkins Slough", side=4, line=3, cex=1.5, col="blue")
}
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
detects_benicia <- detects_study[detects_study$general_location %in% c("Benicia_west", "Benicia_east"),]
if (nrow(detects_benicia)>0) {
detects_benicia <- merge(detects_benicia,aggregate(list(first_detect = detects_benicia$DateTime_PST), by = list(TagCode= detects_benicia$TagCode), FUN = min))
detects_benicia$Day <- as.Date(detects_benicia$first_detect, "Etc/GMT+8")
starttime <- as.Date(min(detects_benicia$release_time), "Etc/GMT+8")
endtime <- min(as.Date(format(Sys.time(), "%Y-%m-%d")), max(as.Date(detects_benicia$release_time)+(as.numeric(detects_benicia$tag_life)*1.5)))
#wlk_flow <- cdec_query("COL", "20", "H", starttime, endtime+1)
#wlk_flow$datetime <- as.Date(wlk_flow$datetime)
#wlk_flow_day <- aggregate(list(parameter_value = wlk_flow$parameter_value), by = list(Day = wlk_flow$datetime), FUN = mean, na.rm = T)
daterange <- data.frame(Day = seq.Date(from = starttime, to = endtime, by = "day"))
rels <- unique(study_tagcodes$Release)
rel_num <- length(rels)
rels_no_detects <- as.character(rels[!(rels %in% unique(detects_benicia$Release))])
tagcount <- aggregate(list(unique_tags = detects_benicia$TagCode), by = list(Day = detects_benicia$Day, Release = detects_benicia$Release ), FUN = function(x){length(unique(x))})
tagcount1 <- reshape2::dcast(tagcount, Day ~ Release)
daterange1 <- merge(daterange, tagcount1, all.x=T)
if(length(rels_no_detects)>0){
for(i in rels_no_detects){
daterange1 <- cbind(daterange1, x=NA)
names(daterange1)[names(daterange1) == 'x'] <- paste(i)
}
}
#daterange2 <- merge(daterange1, wlk_flow_day, by = "Day", all.x = T)
daterange2 <- daterange1
rownames(daterange2) <- daterange2$Day
daterange2$Day <- NULL
par(mar=c(6, 5, 2, 5) + 0.1)
barp <- barplot(t(daterange2[,1:ncol(daterange2)]), plot = FALSE, beside = T)
barplot(t(daterange2[,1:ncol(daterange2)]), beside = T, col=viridis_pal()(rel_num),
xlab = "", ylab = "Number of fish arrivals per day",
ylim = c(0,max(daterange2[,1:ncol(daterange2)], na.rm = T)*1.2),
las = 2, xlim=c(0,max(barp)+1), cex.lab = 1.5, yaxt = "n", xaxt = "n")#,
#legend.text = colnames(daterange2[,1:ncol(daterange2)-1]),
#args.legend = list(x ='topright', bty='n', inset=c(-0.2,0)), title = "Release Group")
legend(x ='topleft', legend = colnames(daterange2)[1:ncol(daterange2)], fill= viridis_pal()(rel_num), horiz = T, title = "Release")
ybreaks <- if(max(daterange2[,1:ncol(daterange2)], na.rm = T) < 4) {max(daterange2[,1:ncol(daterange2)], na.rm = T)} else {5}
xbreaks <- if(ncol(barp) > 10) {seq(1, ncol(barp), 2)} else {1:ncol(barp)}
barpmeans <- colMeans(barp)
axis(1, at = barpmeans[xbreaks], labels = rownames(daterange2)[xbreaks], las = 2)
axis(2, at = pretty(0:max(daterange2[,1:ncol(daterange2)], na.rm = T), ybreaks))
box()
#par(new=T)
#plot(x = barpmeans, daterange2$parameter_value, yaxt = "n", xaxt = "n", ylab = "", xlab = "", col = "blue", type = "l", lwd=2, xlim=c(0,max(barp)+1), ylim = c(min(daterange2$parameter_value, na.rm = T), max(daterange2$parameter_value, na.rm=T)*1.1))#, ylab = "Returning adults", xlab= "Outmigration year", yaxt="n", col="red", pch=20)
#axis(side = 4)#, labels = c(2000:2016), at = c(2000:2016))
#mtext("Flow (cfs) at Colusa Bridge", side=4, line=3, cex=1.5, col="blue")
}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)
}
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[detects_study$general_location == "TowerBridge",]
if (nrow(detects_tower) == 0){
WR.surv <- data.frame("Release"=NA, "Survival (%)"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA, "Detection efficiency (%)"=NA)
colnames(WR.surv) <- c("Release", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv, row.names = F, "html", caption = "3.1 Minimum survival to Tower Bridge (using CJS survival model). If Yolo Bypass Weirs are overtopping during migration, fish may have taken that route, and therefore this is a minimum estimate of survival") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
study_count <- nrow(study_tagcodes)
## Only do survival to Sac for now
test <- detects_study[which(detects_study$river_km > 168 & detects_study$river_km < 175),]
## Create inp for survival estimation
inp <- as.data.frame(reshape2::dcast(test, TagCode ~ river_km, fun.aggregate = length))
## Sort columns by river km in descending order
# Count number of genlocs
gen_loc_sites <- ncol(inp)-1
if(gen_loc_sites <2){
WR.surv <- data.frame("Release"=NA, "Survival (%)"="NOT ENOUGH DETECTIONS", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA, "Detection efficiency (%)"=NA)
colnames(WR.surv) <- c("Release", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv, row.names = F, "html", caption = "3.1 Minimum survival to Tower Bridge (using CJS survival model). If Yolo Bypass Weirs are overtopping during migration, fish may have taken that route, and therefore this is a minimum estimate of survival") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
}else{
inp <- inp[,c(1,order(names(inp[,2:(gen_loc_sites+1)]), decreasing = T)+1)]
inp <- merge(study_tagcodes, inp, by = "TagCode", all.x = T)
inp2 <- inp[,(ncol(inp)-gen_loc_sites+1):ncol(inp)]
inp2[is.na(inp2)] <- 0
inp2[inp2 > 0] <- 1
inp <- cbind(inp, inp2)
groups <- as.character(sort(unique(inp$Release)))
test$Release <- factor(test$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(test$Release),decreasing = T))), stringsAsFactors = F)
WR.process <- process.data(inp.df, model="CJS", begin.time=1, groups = "rel")
WR.ddl <- make.design.data(WR.process)
WR.mark.all <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
WR.mark.rel <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time*rel),p=list(formula=~time)), silent = T, output = F)
WR.surv <- round(WR.mark.all$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(test$Release),decreasing = T))), WR.surv)
}
if(length(unique(inp[,groups])) < 2){
inp$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) <- 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"))
}
}
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
|
Release
|
Survival (%)
|
SE
|
95% lower C.I.
|
95% upper C.I.
|
Detection efficiency (%)
|
|
NA
|
NO DETECTIONS YET
|
NA
|
NA
|
NA
|
NA
|
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
route_results_possible <- F
if (nrow(detects_study[is.na(detects_study$DateTime_PST)==F,]) == 0){
results_short <- data.frame("Measure"=NA, "Estimate"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA)
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.2 Reach-specific survival and probability of entering Georgiana Slough") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
## Only do survival to Georg split for now
test2 <- detects_study[detects_study$general_location %in% c("ButteBrRT","TowerBridge", "I80-50_Br", "Sac_BlwGeorgiana", "Sac_BlwGeorgiana2", "Georgiana_Slough1", "Georgiana_Slough2"),]
## We can only do multistate 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("Georgiana_Slough1", "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("ButteBrRT","TowerBridge", "I80-50_Br", "Sac_BlwGeorgiana", "Sac_BlwGeorgiana2", "Georgiana_Slough1", "Georgiana_Slough2"))
test2$TagCode <- factor(test2$TagCode, levels = study_tagcodes$TagCode)
mytable <- table(test2$TagCode, test2$general_location) # A will be rows, B will be columns
## Change all frequencies bigger than 1 to 1. Here you could change your minimum cutoff to 2 detections, and then make another command that changes all detections=1 to 0
mytable[mytable>0] <- "A"
## Order in order of rkm
mytable2 <- mytable[, c("ButteBrRT","TowerBridge", "I80-50_Br", "Sac_BlwGeorgiana", "Sac_BlwGeorgiana2", "Georgiana_Slough1", "Georgiana_Slough2")]
## Now sort the crosstab rows alphabetically
mytable2 <- mytable2[order(row.names(mytable2)),]
mytable2[which(mytable2[, "Sac_BlwGeorgiana"]=="A"), "Sac_BlwGeorgiana"] <- "A"
mytable2[which(mytable2[, "Sac_BlwGeorgiana2"]=="A"), "Sac_BlwGeorgiana2"] <- "A"
mytable2[which(mytable2[, "Georgiana_Slough1"]=="A"), "Georgiana_Slough1"] <- "B"
mytable2[which(mytable2[, "Georgiana_Slough2"]=="A"), "Georgiana_Slough2"] <- "B"
## Make a crosstab query with frequencies for all weekly Release groups
#test2$Release <- factor(test2$Release)
#mytable3 <- table(test2$TagCode, test2$Release) # A will be rows, B will be columns
## Change all frequencies bigger than 1 to 1. Here you could change your minimum cutoff to 2 detections, and then make another command that changes all detections=1 to 0
#mytable3[mytable3>0] <- 1
## Order in order of rkm
#mytable4 <- mytable3[, order(colnames(mytable3))]
## Now sort the crosstab rows alphabetically
#mytable4 <- mytable4[order(row.names(mytable4)),]
## Now order the study_tagcodes table the same way
study_tagcodes <- study_tagcodes[order(study_tagcodes$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$inp_partB <- apply(mytable2[,6:7],1,paste,collapse="")
#study_tagcodes$inp_group <- apply(mytable4,1,paste,collapse=" ")
## We need to have a way of picking which route to assign to a fish if it was detected by both georg and blw-georg recvs
## We will say that the last detection at that junction is what determines the route it took
## 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", "Georgiana_Slough1", "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 doesn't 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("Georgiana_Slough1", "Georgiana_Slough2"), "inp_final"] <- paste("A",study_tagcodes[study_tagcodes$last_location %in% c("Georgiana_Slough1", "Georgiana_Slough2"), "inp_part1"], study_tagcodes[study_tagcodes$last_location %in% c("Georgiana_Slough1", "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 can't 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$inp_final,"WRinp_multistate.inp",row.names = F, col.names = F, quote = F)
WRinp <- convert.inp("WRinp_multistate.inp")
dp <- process.data(WRinp, model="Multistrata")
ddl <- make.design.data(dp)
#### p ####
# Can't be seen at 2B or 3B or 4B (butte, tower or I80)
ddl$p$fix=NA
ddl$p$fix[ddl$p$stratum == "B" & ddl$p$time %in% c(2,3,4)]=0
#### Psi ####
# Only 1 transition allowed:
# from A to B at time interval 4 to 5
ddl$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$time==5]=1
## We use -1 at beginning of formula to remove intercept. This is because different routes probably shouldn't share the same intercept
p.timexstratum=list(formula=~-1+stratum:time)
Psi.stratumxtime=list(formula=~-1+stratum:time)
S.stratumxtime=list(formula=~-1+stratum:time)
## Run model a first time
S.timexstratum.p.timexstratum.Psi.timexstratum=mark(dp,ddl, model.parameters=list(S=S.stratumxtime,p= p.timexstratum,Psi=Psi.stratumxtime), realvcv = T, silent = T, output = F)
## Identify any parameter estimates at 1, which would likely have bad SE estimates.
profile.intervals <- which(S.timexstratum.p.timexstratum.Psi.timexstratum$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 Butte City","Survival from Butte City to TowerBridge (minimum estimate since fish may have taken Yolo Bypass)", "Survival from TowerBridge to I80-50_Br", "% arrived from I80-50_Br to Georgiana Slough confluence (not survival because fish may have taken Sutter/Steam)","Detection probability at Butte City",
"Detection probability at TowerBridge", "Detection probability at I80-50_Br", "Detection probability at Blw_Georgiana", "Detection probability at Georgiana Slough",
"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 <- T
} 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"))
}
}
}
3.2 Reach-specific survival and probability of entering Georgiana Slough
|
Measure
|
Estimate
|
SE
|
95% lower C.I.
|
95% upper C.I.
|
|
NA
|
NOT ENOUGH DETECTIONS
|
NA
|
NA
|
NA
|
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$ucl.TransitionMat["A","B"],3)*100,")", sep =""), box.col = "light gray", bg = "light gray")
}
mtext(text = "3.3 Routing Probabilities at Georgiana Slough Junction (with 95% C.I.s)", cex = 1.3, side = 1, line = 0.2, adj = 0)
try(setwd(paste(file.path(Sys.getenv("USERPROFILE"),"Desktop",fsep="\\"), "\\Real-time data massaging\\products", sep = "")))
try(benicia <- read.csv("benicia_surv.csv", stringsAsFactors = F))
detects_benicia <- detects_study[detects_study$general_location %in% c("Benicia_west", "Benicia_east"),]
if (nrow(detects_benicia) == 0){
WR.surv1 <- data.frame("Release Group"=NA, "Survival (%)"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA, "Detection efficiency (%)"=NA)
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 = "3.4 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$general_location)) == 1){
WR.surv1 <- data.frame("Release Group"=NA, "Survival (%)"="NOT ENOUGH DETECTIONS", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA, "Detection efficiency (%)"=NA)
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.4 Minimum survival to Benicia Bridge East Span (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
} else {
## Only do survival to Benicia here
test3 <- detects_study[which(detects_study$river_km < 53),]
## 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) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.", "Detection efficiency (%)")
print(kable(WR.surv1, row.names = F, "html", caption = "3.4 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"))
if(exists("benicia")==T){
## 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_benicia$Study_ID),]
benicia <- rbind(benicia, data.frame(WR.surv, StudyID = unique(detects_benicia$Study_ID), data_quality = quality))
write.csv(benicia, "benicia_surv.csv", row.names = F, quote = F)
}
}
3.4 Minimum survival to Benicia Bridge East Span (using CJS survival model)
|
Release Group
|
Survival (%)
|
SE
|
95% lower C.I.
|
95% upper C.I.
|
Detection efficiency (%)
|
|
NA
|
NO DETECTIONS YET
|
NA
|
NA
|
NA
|
NA
|
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$DateTime_PST)==F,]) == 0){
results_short <- data.frame("Measure"=NA, "Estimate"="NO DETECTIONS YET", "SE"=NA, "95% lower C.I."=NA, "95% upper C.I."=NA)
colnames(results_short) <- c("Measure", "Estimate", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(results_short, row.names = F, "html", caption = "3.5 Minimum through-Delta survival: City of Sacramento to Benicia (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
}else{
## Only do survival to Georg split for now
test4 <- detects_study[detects_study$general_location %in% c("I80-50_Br", "Benicia_west", "Benicia_east"),]
if(nrow(test4[test4$general_location =="Benicia_west",]) == 0 |
nrow(test4[test4$general_location =="Benicia_east",]) == 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 = "3.5 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{
inp <- as.data.frame(reshape2::dcast(test4, TagCode ~ general_location, fun.aggregate = length))
## Sort columns by river km in descending order
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$Release)))
inp[,groups] <- 0
for (i in groups) {
inp[as.character(inp$Release) == i, i] <- 1
}
if(length(groups) > 1){
inp$inp_final <- paste("1",apply(inp2, 1, paste, collapse=""), " ",apply(inp[,groups], 1, paste, collapse=" ")," ;",sep = "")
}else{
inp$inp_final <- paste("1",apply(inp2, 1, paste, collapse=""), " ",inp[,groups]," ;",sep = "")
}
write.table(inp$inp_final,"WRinp.inp",row.names = F, col.names = F, quote = F)
if(length(groups) > 1){
WRinp <- convert.inp("WRinp.inp", group.df=data.frame(rel=groups))
WR.process <- process.data(WRinp, model="CJS", begin.time=1, groups = "rel")
WR.ddl <- make.design.data(WR.process)
WR.mark.all <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
WR.mark.rel <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time*rel),p=list(formula=~time)), silent = T, output = F)
WR.surv <- round(WR.mark.all$results$real[2,c("estimate", "se", "lcl", "ucl")] * 100,1)
WR.surv <- rbind(WR.surv, round(WR.mark.rel$results$real[seq(from=2,to=length(groups)*3,by = 3),c("estimate", "se", "lcl", "ucl")] * 100,1))
}else{
WRinp <- convert.inp("WRinp.inp")
WR.process <- process.data(WRinp, model="CJS", begin.time=1)
WR.ddl <- make.design.data(WR.process)
WR.mark.all <- mark(WR.process, WR.ddl, model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)), silent = T, output = F)
WR.surv <- round(WR.mark.all$results$real[2,c("estimate", "se", "lcl", "ucl")] * 100,1)
}
WR.surv <- cbind(Release = c("ALL", groups), WR.surv)
WR.surv1 <- WR.surv
colnames(WR.surv1) <- c("Release Group", "Survival (%)", "SE", "95% lower C.I.", "95% upper C.I.")
print(kable(WR.surv1, row.names = F, "html", caption = "3.5 Minimum through-Delta survival: City of Sacramento to Benicia (using CJS survival model)") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive", "bordered"), full_width = F, position = "left"))
if(exists("Delta")==T){
reltimes <- aggregate(list(RelDT = study_tagcodes$release_time), by = list(Release = study_tagcodes$Release), FUN = mean)
reltimes <- rbind(reltimes, data.frame(Release = "ALL", RelDT = mean(study_tagcodes$release_time)))
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)
}
}
}
3.5 Minimum through-Delta survival: City of Sacramento to Benicia (using CJS survival model)
|
Measure
|
Estimate
|
SE
|
95% lower C.I.
|
95% upper C.I.
|
|
NA
|
NOT ENOUGH DETECTIONS
|
NA
|
NA
|
NA
|
