In WDNR-Water-Use/CSLSchem: CSLS Water Chemistry Analysis

library(CSLSchem)
library(extrafont)
library(dplyr)
library(reshape2)
library(patchwork)
library(ggplot2)
text_size  <- 12
descriptions <- c("PH LAB",
                  "ALKALINITY TOTAL CACO3",
                  "COLOR", 
                  "SECCHI DEPTH - FEET", 
                  "CHLOROPHYLL A, FLUORESCENCE (WELSCHMAYER 1994)", "CHLORIDE", 
                  "CALCIUM TOTAL RECOVERABLE", "MAGNESIUM TOTAL RECOVERABLE", 
                  "TURBIDITY, LAB NEPHELOMETRIC NTU", "NITROGEN TOTAL", 
                  "PHOSPHORUS TOTAL")

p1 <- plot_comparison("PH LAB", 
                      "pH", 
                      text_size)
p2 <- plot_comparison("ALKALINITY TOTAL CACO3", 
                      "Alkalinity (as mg/L CaCO3)", 
                      text_size) + 
      theme(axis.text.y = element_blank(),
            axis.ticks.y = element_blank(),
            axis.title.y = element_blank())
p1 + p2 + plot_layout(guides = "collect") + plot_annotation(tag_levels = 'a') &
  theme(plot.tag = element_text(family = "Segoe UI Semibold",
                                        size = text_size))

p1 <- plot_comparison("CALCIUM TOTAL RECOVERABLE", 
                      "Calcium (mg/L)", 
                      text_size) +
      theme(legend.position = "none")
p2 <- plot_comparison("MAGNESIUM TOTAL RECOVERABLE", 
                      "Magnesium (mg/L)", 
                      text_size) + 
      theme(axis.text.y = element_blank(),
            axis.ticks.y = element_blank(),
            axis.title.y = element_blank(),
            legend.position = "none")
p3 <- plot_comparison("CHLORIDE", 
                      "Chloride (mg/L)", 
                      text_size)
combo = {p1 + p2} / {p3 + plot_spacer() + plot_layout(widths = c(2,1))} 
combo +  
  plot_annotation(tag_levels = 'a') &
  theme(plot.tag = element_text(family = "Segoe UI Semibold",
                                size = text_size))

p1 <- plot_comparison("NITROGEN TOTAL", 
                      "Total Nitrogen (mg/L)", 
                      text_size) +
      theme(legend.position = "none")
p2 <- plot_comparison("PHOSPHORUS TOTAL", 
                      "Total Phosphorus (mg/L)", 
                      text_size) + 
      theme(axis.text.y = element_blank(),
            axis.ticks.y = element_blank(),
            axis.title.y = element_blank(),
            legend.position = "none")
p3 <- plot_comparison("CHLOROPHYLL A, FLUORESCENCE (WELSCHMAYER 1994)", 
                      "Chlorophyll A (ug/L)", 
                      text_size)
combo = {p1 + p2} / {p3 + plot_spacer() + plot_layout(widths = c(2,1))} 
combo +  
  plot_annotation(tag_levels = 'a') &
  theme(plot.tag = element_text(family = "Segoe UI Semibold",
                                size = text_size))

p1 <- plot_comparison("TURBIDITY, LAB NEPHELOMETRIC NTU", 
                      "Turbidity (NTU)", 
                      text_size) +
      theme(legend.position = "none")
p2 <- plot_comparison("COLOR", 
                      "Color (SU)", 
                      text_size) + 
      theme(axis.text.y = element_blank(),
            axis.ticks.y = element_blank(),
            axis.title.y = element_blank(),
            legend.position = "none")
p3 <- plot_comparison("SECCHI DEPTH - FEET", 
                      "Secchi Depth (ft)", 
                      text_size)
combo = {p1 + p2} / {p3 + plot_spacer() + plot_layout(widths = c(2,1))} 
combo +  
  plot_annotation(tag_levels = 'a') &
  theme(plot.tag = element_text(family = "Segoe UI Semibold",
                                size = text_size))

descriptions <- c("PH LAB",
                  "ALKALINITY TOTAL CACO3",
                  "CONDUCTIVITY, UMHOS/CM @ 25C",
                  "CALCIUM TOTAL RECOVERABLE", 
                  "MAGNESIUM TOTAL RECOVERABLE",
                  "POTASSIUM TOTAL RECOVERABLE",
                  "SODIUM TOTAL RECOVERABLE",
                  "SULFATE TOTAL",
                  "CHLORIDE",
                  "ALUMINUM,TOTAL RECOVERABLE",
                  "IRON TOTAL RECOVERABLE",
                  "MANGANESE, TOTAL RECOVERABLE",
                  "SILICA, DISSOLVED (MG/L AS SI02)",
                  "CHLOROPHYLL A, FLUORESCENCE (WELSCHMAYER 1994)",
                  "NITROGEN TOTAL",  
                  "PHOSPHORUS TOTAL",
                  "TURBIDITY, LAB NEPHELOMETRIC NTU",
                  "COLOR", 
                  "SECCHI DEPTH - FEET")
labels         <- c("pH",
                  "Alkalinity (as mg/L CaCO3)",
                  "Specific Conductance",
                  "Calcium", 
                  "Magnesium",
                  "Potassium",
                  "Sodium",
                  "Sulfate",
                  "Chloride",
                  "Aluminum",
                  "Iron",
                  "Manganese",
                  "Silica (mg/L as SiO2)",
                  "Chlorophyll A",
                  "Total Nitrogen",  
                  "Total Phosphorus",
                  "Turbidity",
                  "Color", 
                  "Secchi Depth")

# CSLS lakes observations and stats
df <- filter_parameter(CSLSdata::water_chem, descriptions, 
                       note_lake_bottom = TRUE, 
                       no_bad_sample = TRUE,
                       no_bad_well = TRUE) %>%
      filter(.data$site_type == "lake") %>%
      group_by(.data$lake, .data$description, .data$units) %>%
      summarise(mean = mean(.data$result, na.rm = TRUE),
                std = sd(.data$result, na.rm = TRUE)) %>%
      ungroup() %>%
      mutate_at("units", as.character) %>%
      select(lake = .data$lake, 
             Parameter = .data$description, 
             mean = .data$mean, 
             std = .data$std, 
             Units = .data$units)

df$Parameter <- factor(df$Parameter, levels = descriptions, labels = labels)

df$Units[df$Units == "MG/L"] <- "mg/L"
df$Units[df$Units == "FEET"] <- "ft"

df$character <- sprintf("%0.3f (%0.3f)", df$mean, df$std)
df$character[df$Parameter != "Total Phosphorus"] <- sprintf("%0.1f (%0.1f)", 
                                                              df$mean[df$Parameter != "Total Phosphorus"],
                                                              df$std[df$Parameter != "Total Phosphorus"])
df$character[df$Parameter == "Alkalinity (as mg/L CaCO3)"] <- sprintf("%0.0f (%0.0f)", 
                                                                    df$mean[df$Parameter == "Alkalinity (as mg/L CaCO3)"], 
                                                                    df$std[df$Parameter == "Alkalinity (as mg/L CaCO3)"])

table <- dcast(df, Parameter+Units~lake, value.var = "character")