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Updated file read function to account for differend TMP redox file na… #64

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Merged
zoeread merged 1 commit into from
Apr 29, 2026
+15 −12
Merged

Updated file read function to account for differend TMP redox file na… #64

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Binary file modified CB_checks/CB_Chk_20260429_ZR.pdf
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27 changes: 15 additions & 12 deletions current-data-zr.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -234,11 +234,14 @@ read_files <- function(type, sitelist = SITES, path = PATH) {
} else if(site == "TMP") {
# The TMP data files have logger_raw with format PNNL_{LOGGER}
x %>%
separate(Logger_raw, into = c("Site", "Logger"), remove = TRUE) %>%
separate(Logger_raw, into = c("Site", "Logger", "Plot"), remove = TRUE) %>%
mutate(Site = "TMP",
Plot = case_when(Logger %in% c("11", "12", "13") ~ "C",
Logger %in% c("21", "22", "23") ~ "F",
Logger %in% c("31", "32", "33") ~ "S")) ->
Logger %in% c("31", "32", "33") ~ "S",
Plot %in% c("control") ~ "C",
Plot %in% c("fresh") ~ "F",
Plot %in% c("salt") ~ "S")) ->
x
} else {
# The synoptic sites have format Compass_{SITE}_{PLOT}_{LOGGER}
Expand Down Expand Up @@ -759,8 +762,8 @@ 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
select(-Logger) %>%
# left_join(REDOX_METADATA, by = c("Site", "Plot", "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 @@ -772,18 +775,18 @@ redox_long_current <- redox_long %>%
TIMESTAMP <= Sys.time()
)

if("TMP" %in% redox_long_current$Site) {
redox_long_current <- redox_long_current %>%
mutate(redox_facet = redox_long_current$Site)
} else {
redox_long_current <- redox_long_current %>%
mutate(redox_facet = redox_long_current$Plot)
}
# if("TMP" %in% redox_long_current$Site) {
# redox_long_current <- redox_long_current %>%
# mutate(redox_facet = redox_long_current$Site)
# } else {
# redox_long_current <- redox_long_current %>%
# mutate(redox_facet = redox_long_current$Plot)
# }

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 ~ redox_facet) +
facet_grid(which ~ Plot) +
geom_point(na.rm = TRUE) +
scale_color_manual(values = redox_colors) +
theme(axis.text.x = element_text(angle = 90)) +
Expand Down
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