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Merged
zoeread merged 1 commit into from
Mar 31, 2026
Merged

Added zr qmd #51

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Binary file removed CB_checks/TMP_Chk_20260330.pdf
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30 changes: 20 additions & 10 deletions current-data-zr.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
author: "COMPASS workflows team"
params:
DROPBOX: "C:/Users/readz/Smithsonian Dropbox/Zoe Read"
SITES: "CB"
SITES: "TMP"
date: now
date-format: "YYYY-MM-DD HH:mm:ssZ"
execute:
Expand Down Expand Up @@ -34,18 +34,18 @@ SITES <- params$SITES
PATH <- params$DROPBOX

PLOT_FACTOR_LEVELS <- c("C", "F", "S", # TMP plots
"UP", "SWAMP", "TR", "WTE", "W", # synoptic plots
"UP", "SWAMP", "TR", "WTE", "W", "WC", # synoptic plots
"F1", "F2", "F3", "R1", "R2") # DLG plots

# User can specify groups of synoptic sites: CB or LE
if(length(SITES == 1)) {
if(SITES == "CB") {
PLOTS <- c("UP", "SWAMP", "TR", "W")
} else if(SITES == "LE") {
PLOTS <- c("UP", "TR", "WTE", "W")
PLOTS <- c("UP", "TR", "WTE", "W", "WC")
} else if(SITES == "TESTING") {
PLOTS <- c("C", "F", "S", # TMP plots
"UP", "SWAMP", "TR", "WTE", "W", # synoptic plots
"UP", "SWAMP", "TR", "WTE", "W", "WC", # synoptic plots
"F1", "F2", "F3", "R1", "R2")
} else if(SITES == "TMP") {
PLOTS <- c("C", "F", "S")
Expand Down Expand Up @@ -315,7 +315,7 @@ if(nrow(teros) > 0) {
pivotstep() %>%
# NA value is -99999.00
mutate(value = if_else(value == -9999, NA_real_, value),
name = gsub("Teros.+\\(", "", name),
name = gsub("Teros\\(", "", name),
name = gsub(")", "", name)) %>%
separate(name, into = c("Port", "sensor"), convert = FALSE) %>%
left_join(TEROS_METADATA, by = c("Site", "Plot", "Logger", "Port")) %>%
Expand Down Expand Up @@ -440,7 +440,10 @@ location_colors = c("UP" = "#20063B",
"TR" = "#FFBC42",
"SWAMP" = "darkgrey",
"WC" = "#419973",
"UP" = "#3B1F2B")
"UP" = "#3B1F2B",
"C" = "springgreen2",
"F" = "cyan2",
"S" = "violetred2")

## This function creates standardized time-series plots
#flag values where AQ is out of water
Expand Down Expand Up @@ -509,7 +512,14 @@ max_counts <- site_locations %>%
filter(!(Site == "GCW" & Plot == "SWAMP")) %>%
filter(!(Site == "GWI" & Plot == "SWAMP")) %>%
filter(!(Site == "MSM" & Plot == "SWAMP")) %>%
mutate(Plot = fct_relevel(Plot, c("UP", "TR", "WTE", "W", "WC")))
filter(!(site == "OWC" & Plot == "UP")) %>%
filter(!(site == "OWC" & Plot == "W")) %>%
filter(!(site == "CRC" & Plot == "WTE")) %>%
filter(!(site == "CRC" & Plot == "WC")) %>%
filter(!(site == "PTR" & Plot == "WTE")) %>%
filter(!(site == "PTR" & Plot == "WC"))
# %>%
# mutate(Plot = fct_relevel(Plot, c("UP", "TR", "WTE", "W", "WC")))

prop_plot <- troll_long_current %>%
filter(name == "Pressure" & !is.na(value)) %>% ##Why are there 3 replicates for each timestamp and only one has a value?
Expand Down Expand Up @@ -554,9 +564,9 @@ redox_colors <- c("10-1" = "darkgoldenrod1",
"15-1" = "chartreuse2",
"15-2" = "darkolivegreen3",
"15-3" = "green4",
"30-1" = "cyan",
"30-2" = "deepskyblue1",
"30-3" = "dodgerblue3",
"30-1" = "deepskyblue1",
"30-2" = "dodgerblue3",
"30-3" = "blue",
"45-1" = "darkorchid2",
"45-2" = "orchid3",
"45-3" = "mediumpurple4")
Expand Down
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