Updated Well Test AQ600 markdown so it would render

Data/aquifer_well/well_test_202509/TEMPEST_Aquifer_WellTest_202509_Data.Rmd

@@ -2,7 +2,9 @@
 title: "TEMPEST_Aquifer_WellTest_202509"
 author: "Stephanie J. Wilson"
 date: "2025-09-05"
-output: pdf_document
+output:
+  pdf_document:
+    latex_engine: xelatex
 ---
 
 ```{r setup, include=FALSE}
@@ -17,14 +19,16 @@ library(tidyr)
 library(lubridate)
 library(knitr)
 library(tibble)
+library(patchwork)
 ```
-
 ## Aquatroll (AQ600) Well Data
-
 ```{r, echo=FALSE}
+cat("In Situ AQ600 was put in a bucket with the well outflow. 
+    Data was recorded every minute for the duration of the test. 
+    Missing points are from removing the AQ600 from the bucket to check transmission.")
 
 well_dat <- read.csv("COMPASS_TEMPEST_WellTest_AQ600_Data.csv")
-head(well_dat)
+#head(well_dat)
 
 #change column names in well_dat
 colnames(well_dat) <- c("Date_Time","pH", "pH_mV" ,"ORP_mV", "DO_mgL", "DO_Sat", "DO_pp", "Actual_Conductivity_µScm" ,
@@ -43,54 +47,55 @@ well_dat_filtered <- well_dat %>%
     filter(DO_mgL < 1) %>%
     filter(TDS_ppt > 0.10) 
 
+#create a table of average concentrations: 
+summary_stats <- well_dat_filtered %>%
+  summarise(
+    Salinity_psu_mean = mean(Salinity_psu, na.rm = TRUE),
+    Salinity_psu_sd = sd(Salinity_psu, na.rm = TRUE),
+    Sp_Conductivity_µScm_mean = mean(Specific_Conductivity_µScm, na.rm = TRUE),
+    Sp_Conductivity_µScm_sd = sd(Specific_Conductivity_µScm, na.rm = TRUE),
+    DO_mgL_mean = mean(DO_mgL, na.rm = TRUE),
+    DO_mgL_sd = sd(DO_mgL, na.rm = TRUE),
+    TDS_ppt_mean = mean(TDS_ppt, na.rm = TRUE),
+    TDS_ppt_sd = sd(TDS_ppt, na.rm = TRUE)
+  ) %>%
+  pivot_longer(
+    everything(),
+    names_to = c("Measurement", ".value"),
+    names_sep = "_(?=[^_]+$)"  # Split at last underscore
+  ) %>%
+  mutate(mean = round(mean, 3), 
+         sd = round(sd, 3)) 
+
+kable(summary_stats)
+
 
 #plot Salinity 
 sal <- ggplot()+
   geom_point(data=well_dat_filtered, aes(x=Date_Time, y=Salinity_psu), size=2, color="blue")+ 
   theme_bw()+ labs(x="Time", y="Salinity (psu)", title="Aquifer Salinity") + theme(legend.title = element_blank())
-sal
+
 
 #plot Conductivity 
 cond <- ggplot()+
   geom_point(data=well_dat_filtered, aes(x=Date_Time, y=Specific_Conductivity_µScm), size=2, color="darkblue")+ 
   theme_bw()+ labs(x="Time", y="Specific Conductivity (µScm)", title="Aquifer Conductivity") + theme(legend.title = element_blank())
-cond
+
+sal + cond
 
 #plot DO
 do <- ggplot()+
   geom_point(data=well_dat_filtered, aes(x=Date_Time, y=DO_mgL), size=2, color="darkred")+ 
   theme_bw()+ labs(x="Time", y="Dissolved Oxygen (mg/L)", title="Aquifer Dissolved Oxygen") + theme(legend.title = element_blank())
-do
 
 
 #plot TDS 
 tds <- ggplot()+
   geom_point(data=well_dat_filtered, aes(x=Date_Time, y=TDS_ppt), size=2, color="darkgreen")+ 
   theme_bw()+ labs(x="Time", y="Total Dissolved Solids (ppt))", title="Aquifer TDS") + theme(legend.title = element_blank())
-tds
 
+do + tds
 
-#create a table of average concentrations: 
-summary_stats <- well_dat_filtered %>%
-  summarise(
-    Salinity_psu_mean = mean(Salinity_psu, na.rm = TRUE),
-    Salinity_psu_sd = sd(Salinity_psu, na.rm = TRUE),
-    Sp_Conductivity_µScm_mean = mean(Specific_Conductivity_µScm, na.rm = TRUE),
-    Sp_Conductivity_µScm_sd = sd(Specific_Conductivity_µScm, na.rm = TRUE),
-    DO_mgL_mean = mean(DO_mgL, na.rm = TRUE),
-    DO_mgL_sd = sd(DO_mgL, na.rm = TRUE),
-    TDS_ppt_mean = mean(TDS_ppt, na.rm = TRUE),
-    TDS_ppt_sd = sd(TDS_ppt, na.rm = TRUE)
-  ) %>%
-  pivot_longer(
-    everything(),
-    names_to = c("Measurement", ".value"),
-    names_sep = "_(?=[^_]+$)"  # Split at last underscore
-  ) %>%
-  mutate(mean = round(mean, 3), 
-         sd = round(sd, 3)) 
-
-kable(summary_stats)
 
 ```