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Merged
zoeread merged 1 commit into from
Apr 29, 2026
+228 −22
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Edited checks code #61

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121 changes: 121 additions & 0 deletions ancillary-data/TEMPEST_Redox_Monitoring.xlsx - Tracking.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,121 @@
Plot,Logger,Port,PakBus,Loggernet Channel,Reference_Probe_ID,Sensor_Probe_ID,Depth_cm,Grid_Square,Installation_Date,Last_Checked,Status,Pending_Action,Notes
Control,23,,,RedoxRa(1),Ref 1,1,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(2),Ref 1,1,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(3),Ref 1,1,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(4),Ref 1,1,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(5),Ref 1,2,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(6),Ref 1,2,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(7),Ref 1,2,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(8),Ref 1,2,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(9),Ref 1,3,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(10),Ref 1,3,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(11),Ref 1,3,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(12),Ref 1,3,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(13),Ref 1,4,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(14),Ref 1,4,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(15),Ref 1,4,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(16),Ref 1,4,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(17),Ref 1,5,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(18),Ref 1,5,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(19),Ref 1,5,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(20),Ref 1,5,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(1),Ref 2,1,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(2),Ref 2,1,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(3),Ref 2,1,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(4),Ref 2,1,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(5),Ref 2,2,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(6),Ref 2,2,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(7),Ref 2,2,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(8),Ref 2,2,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(9),Ref 2,3,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(10),Ref 2,3,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(11),Ref 2,3,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(12),Ref 2,3,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(13),Ref 2,4,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(14),Ref 2,4,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(15),Ref 2,4,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(16),Ref 2,4,55,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(17),Ref 2,5,10,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(18),Ref 2,5,20,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRb(19),Ref 2,5,35,C6,3-May-2024,10-Apr-2026,Active,,
Control,23,,,RedoxRa(20),Ref 2,5,55,C6,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(1),Ref 1,1,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(2),Ref 1,1,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(3),Ref 1,1,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(4),Ref 1,1,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(5),Ref 1,2,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(6),Ref 1,2,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(7),Ref 1,2,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(8),Ref 1,2,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(9),Ref 1,3,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(10),Ref 1,3,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(11),Ref 1,3,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(12),Ref 1,3,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(13),Ref 1,4,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(14),Ref 1,4,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(15),Ref 1,4,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(16),Ref 1,4,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(17),Ref 1,5,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(18),Ref 1,5,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(19),Ref 1,5,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(20),Ref 1,5,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(1),Ref 2,1,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(2),Ref 2,1,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(3),Ref 2,1,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(4),Ref 2,1,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(5),Ref 2,2,10,F6,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(6),Ref 2,2,20,F6,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(7),Ref 2,2,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(8),Ref 2,2,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(9),Ref 2,3,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(10),Ref 2,3,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(11),Ref 2,3,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(12),Ref 2,3,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(13),Ref 2,4,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(14),Ref 2,4,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(15),Ref 2,4,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(16),Ref 2,4,55,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(17),Ref 2,5,10,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(18),Ref 2,5,20,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRb(19),Ref 2,5,35,F4,3-May-2024,10-Apr-2026,Active,,
Saltwater,32,,,RedoxRa(20),Ref 2,5,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(1),Ref 1,1,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(2),Ref 1,1,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(3),Ref 1,1,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(4),Ref 1,1,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(5),Ref 1,2,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(6),Ref 1,2,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(7),Ref 1,2,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(8),Ref 1,2,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(9),Ref 1,3,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(10),Ref 1,3,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(11),Ref 1,3,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(12),Ref 1,3,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(13),Ref 1,4,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(14),Ref 1,4,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(15),Ref 1,4,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(16),Ref 1,4,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(17),Ref 1,5,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(18),Ref 1,5,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(19),Ref 1,5,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(20),Ref 1,5,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(1),Ref 2,1,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(2),Ref 2,1,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(3),Ref 2,1,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(4),Ref 2,1,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(5),Ref 2,2,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(6),Ref 2,2,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(7),Ref 2,2,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(8),Ref 2,2,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(9),Ref 2,3,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(10),Ref 2,3,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(11),Ref 2,3,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(12),Ref 2,3,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(13),Ref 2,4,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(14),Ref 2,4,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(15),Ref 2,4,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(16),Ref 2,4,55,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(17),Ref 2,5,10,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(18),Ref 2,5,20,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRb(19),Ref 2,5,35,F4,3-May-2024,10-Apr-2026,Active,,
Freshwater,21,,,RedoxRa(20),Ref 2,5,55,F4,3-May-2024,10-Apr-2026,Active,,
129 changes: 107 additions & 22 deletions current-data-zr.qmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -119,9 +119,25 @@ teros_tmp %>%
Site = if_else(Site == "GCREW", "GCW", Site),
Plot = if_else(Plot == "Swamp", "SWAMP", Plot),
Plot = factor(Plot, levels = PLOT_FACTOR_LEVELS),
##Need to check but these logger numbers seemed to be off
Logger = if_else(Site == "SWH" & Plot == "UP", "424", Logger),
Logger = if_else(Site == "MSM" & Plot == "UP", "403", Logger)) ->
TEROS_METADATA


# Redox information, same deal
REDOX_TMP_FILE <- "ancillary-data/TEMPEST_Redox_Monitoring.xlsx - Tracking.csv"
message("Reading ", REDOX_TMP_FILE)
redox_tmp <- read_csv(REDOX_TMP_FILE, col_types = "cccccccdcccccc")
redox_tmp %>%
mutate(Site = "TMP",
Plot = case_when(Plot == "Freshwater" ~ "F",
Plot == "Saltwater" ~ "S",
Plot == "Control" ~ "C")) %>%
separate(`Loggernet Channel`, into = c("which", "number"), extra = "drop") %>%
mutate(number = as.numeric(number)) ->
REDOX_METADATA #There is no synoptic redox metadata yet

```

Sites: `r paste(SITES, collapse = ", ")`
Expand Down Expand Up @@ -273,7 +289,7 @@ no_data_check(sf, "Sapflow")
```

```{r sf-plots}
#| fig-width: 9
#| fig-height: 9
if(nrow(sf) > 0) {
sf %>%
pivotstep() %>%
Expand All @@ -289,16 +305,42 @@ if(nrow(sf) > 0) {
TIMESTAMP <= Sys.time()
)

for(site in unique(sf_long_current$Site)) {
p <- ggplot(filter(sf_long_current, Site == site),
aes(TIMESTAMP, value, color = Tree)) +
my_palette <- rainbow(length(unique(sf_long_current$Tree)))
random_palette <- sample(my_palette)

# sf_long_current <- subset(sf_long_current, Tree != "C12 (1328)")

##Look at rows where the Tree is NA. If the value is also NA or 0, remove that row. If the value is greater than 0, write out a warning that "A sapflow sensor is not correctly matched with its tree ID".
sf_long_current_NA_Tree <- subset(sf_long_current, is.na(Tree))
sf_long_current_NA_value <- subset(sf_long_current_NA_Tree, is.na(value))


sf_long_current_filtered <-
if((nrow(sf_long_current_NA_Tree) > 0 &
mean(sf_long_current_NA_Tree$value, na.rm = TRUE) == 0) |
nrow(sf_long_current_NA_Tree) == nrow(sf_long_current_NA_value)) {
sf_long_current %>% filter(!is.na(Tree))} else {
sf_long_current }

if(nrow(sf_long_current_filtered) < nrow(sf_long_current)) {
print ("All SF sensor trees accounted for")} else {
print ("A sapflow sensor is not correctly matched with its tree ID") }

for(site in unique(sf_long_current_filtered$Site)) {
p <- ggplot(filter(sf_long_current_filtered, Site == site),
aes(TIMESTAMP, value, color = interaction(Tree, Plot))) +
scale_color_manual(values = random_palette) +
facet_grid(. ~ Plot) +
ylab("Raw sapflow") +
geom_point(na.rm = TRUE) +
ggtitle(site)
print(p)
ggtitle(site) +
theme(legend.position = "bottom")

print(p)
}
}


```

# TEROS
Expand All @@ -310,8 +352,8 @@ no_data_check(teros, "TEROS")
```

```{r teros-plots}
#| fig-width: 9
#| fig-height: 6
#| fig-width: 15
#| fig-height: 15
if(nrow(teros) > 0) {
teros %>%
pivotstep() %>%
Expand Down Expand Up @@ -341,13 +383,30 @@ teros_long_current <- teros_long %>%
TIMESTAMP <= Sys.time()
)

##Look at rows where the Depth is NA. If the value is also NA, remove that row. If the value is not NA, write out a warning that "A TEROS sensor is not correctly matched with its depth ID".
teros_long_current_NA <- subset(teros_long_current, is.na(Depth_cm))

teros_long_current_filtered <-
if(nrow(teros_long_current_NA) > 0 &
mean(teros_long_current_NA$value, na.rm = TRUE) == 0) {
teros_long_current %>% filter(!is.na(Depth_cm))} else {
teros_long_current }

if(nrow(teros_long_current_filtered) < nrow(teros_long_current)) {
print ("All TEROS sensor depths accounted for")} else {
print ("A TEROS sensor is not correctly matched with its depth") }


for(site in unique(teros_long_current$Site)) {
teros_site <- filter(teros_long_current, Site == site)
p <- ggplot(teros_site, aes(TIMESTAMP, value, color = Depth_cm)) +
p <- ggplot(teros_site,
aes(TIMESTAMP, value, color = interaction(Depth_cm, ID))) +
facet_grid(sensor_name ~ Plot, scales = "free") +
geom_point(na.rm = TRUE) +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle(paste(site, "TEROS"))
ggtitle(paste(site, "TEROS")) +
theme(legend.position = "bottom")

print(p)
}
}
Expand Down Expand Up @@ -439,16 +498,33 @@ troll_long %>%
)
}

##Set Instrument ID
troll_long_current <- troll_long_current %>%
mutate(AQID = paste0("AQ", gsub("WaterLevel", "", Table)))


if("TMP" %in% troll_long_current$Site) {
troll_long_current <- troll_long_current %>%
mutate(troll_facet = troll_long_current$Plot,
color_key = troll_long_current$AQID)
} else {
troll_long_current <- troll_long_current %>%
mutate(troll_facet = troll_long_current$Site,
color_key = troll_long_current$Plot)
}

## set color palette
location_colors = PNWColors::pnw_palette("Sunset", length(unique(troll_long_current$Plot)))
location_colors = PNWColors::pnw_palette("Sunset", length(unique(troll_long_current$color_key)))
location_colors = c("UP" = "#20063B",
"TR" = "#FFBC42",
"SWAMP" = "darkgrey",
"W" = "#419973",
"UP" = "#3B1F2B",
"C" = "springgreen2",
"F" = "cyan2",
"S" = "violetred2")
"S" = "violetred2",
"AQ200" = "#20063B",
"AQ600" = "#FFBC42")

## This function creates standardized time-series plots
#flag values where AQ is out of water
Expand All @@ -458,22 +534,26 @@ ts_plot <- function(var, y_lab){

x <- troll_long_current %>% filter(name == var)

ggplot(x, aes(TIMESTAMP, value, color = Plot)) +
geom_line(na.rm = TRUE) +
ggplot(x, aes(TIMESTAMP, value, color = color_key)) +
# geom_line(na.rm = TRUE) +
geom_point(na.rm = TRUE) +
geom_point(na.rm = TRUE, data = x %>% filter(flagged == TRUE), color = "red", alpha = 0.75) +
facet_wrap(~ Site, nrow = 1, scales = "free_y") +
facet_wrap(~ troll_facet, nrow = 1, scales = "free_y") +
labs(x = "", y = y_lab) +
scale_color_manual(values = location_colors) +
scale_x_datetime(date_breaks = "3 days", date_labels = "%m/%d")
}

## Create the time-series plots you want
ts_wl_plot <- ggplot(troll_long_current, aes(TIMESTAMP, water_level_cm, color = Plot)) +
geom_line(na.rm = TRUE) +
ts_wl_plot <- ggplot(troll_long_current, aes(TIMESTAMP, water_level_cm,
color = color_key)) +
#geom_line(na.rm = TRUE) +
geom_point(na.rm = TRUE) +
geom_point(na.rm = TRUE, data = troll_long_current %>% filter(flagged == TRUE), color = "red", alpha = 0.75) +
facet_wrap(~ Site, nrow = 1, scales = "free_y") +
geom_point(na.rm = TRUE,
data = troll_long_current %>%
filter(flagged == TRUE),
color = "red", alpha = 0.75) +
facet_wrap(~ troll_facet, nrow = 1, scales = "free_y") +
labs(x = "", y = "Water Level (cm)\nRed = troll above water") +
scale_color_manual(values = location_colors) +
scale_x_datetime(date_breaks = "3 days", date_labels = "%m/%d")
Expand Down Expand Up @@ -551,7 +631,7 @@ if("TMP" %in% troll_long_current$Site) {
prop_plot_200 <- troll_long_current %>%

filter(name == "Pressure" & !is.na(value) & Table == "WaterLevel200") %>% ##Why are there 3 replicates for each timestamp and only one has a value?
group_by(Site, Plot) %>%
group_by(Site, Plot, Instrument_ID) %>%
count() %>%
bind_rows(anti_join(max_counts, .)) %>%
mutate(n = ifelse(is.na(n), 0, n)) %>%
Expand Down Expand Up @@ -667,6 +747,8 @@ if(nrow(redox) > 0) {
pivotstep() %>%
separate(name, into = c("which", "number"), extra = "drop") %>%
mutate(number = as.numeric(number)) %>%
select(-c(Plot, Logger)) %>%
# left_join(REDOX_METADATA, by = c("Site", "which", "number")) %>% ##add in tmp metadata
left_join(redox_assignments, by = "number") %>%
mutate(Depth = as.factor(Depth)) %>%
mutate(Depth_Rep = as.factor(paste(Depth, Rep, sep = "-"))) ->
Expand All @@ -682,7 +764,7 @@ redox_long_current <- redox_long %>%
for(site in unique(redox_long_current$Site)) {
redox_site <- filter(redox_long_current, Site == site)
p <- ggplot(redox_site, aes(TIMESTAMP, value, color = Depth_Rep)) +
facet_grid(which ~ Plot) +
facet_grid(which ~ Site) +
geom_point(na.rm = TRUE) +
scale_color_manual(values = redox_colors) +
theme(axis.text.x = element_text(angle = 90)) +
Expand All @@ -705,7 +787,7 @@ no_data_check(exo, "Exo")
#| fig-height: 9
if(nrow(exo) > 0) {
exo %>%
select(-Date, -Time, -sn, -snn) %>%
select(-Date, -Time, -sn, -snn, -c(Battery_v, TSS_MgL, Wiper_Current_ma, Wiper_Position_mv, pH_mv, ODO_local, ODO_sat, FDOM_RFU, Conductivity, Turbidity_Raw)) %>%
pivotstep() ->
exo_long

Expand All @@ -715,6 +797,9 @@ exo_long_current <- exo_long %>%
TIMESTAMP <= Sys.time()
)

# exo_long_current_pressure <- exo_long_current %>%
# filter(name == "Pressure_psia")

for(site in unique(exo_long_current$Site)) {
p <- ggplot(filter(exo_long_current, Site == site), aes(TIMESTAMP, value)) +
facet_wrap(. ~ name, scales = "free") +
Expand Down
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