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

library(knitr)
library(CSLSchem)
library(dplyr)
library(stringr)
library(lubridate)
library(reshape2)
library(extrafont)

text_size  <- 12
lakes      <- c("Pleasant", "Long", "Plainfield")
water_chem <- CSLSdata::water_chem
water_chem <- water_chem %>%
              filter(.data$site_type == "lake")

Overview {#top}

The data used here includes data from both SWIMS and LDES. Duplicates between the two data sources as well as samples labeled as blanks or duplicates are removed.

Chlororophyll A

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parameter     <-"CHLOROPHYLL A, FLUORESCENCE (WELSCHMAYER 1994)"
plotting_name <- "Chlorophyll A"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Secchi Depth

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Note: need to adjust secchi depth plot to flip y-axis and note when touches bottom.

parameter     <-"SECCHI DEPTH - FEET"
plotting_name <- "Secchi Depth"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Calcium, Total Recoverable

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parameter     <-"CALCIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Calcium"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Magnesium, Total Recoverable

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parameter     <- "MAGNESIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverabel Magnesium"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Ca:Mg Ratio

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parameter     <-"CALCIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Calcium"
Ca            <- filter_parameter(water_chem, parameter, plotting_name)
Ca            <- Ca %>%
                 select(.data$lake, .data$site_type, .data$date, .data$result,
                        .data$site_id)

parameter     <- "MAGNESIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverabel Magnesium"
Mg            <- filter_parameter(water_chem, parameter, plotting_name)
Mg            <- Mg %>%
                 select(.data$lake, .data$site_type, .data$date, .data$result,
                        .data$site_id)

Ca_Mg         <- merge(Ca, Mg, by = c("date", "lake", "site_type", "site_id"))
Ca_Mg$result  <- Ca_Mg$result.x/Ca_Mg$result.y
Ca_Mg$lod     <- 0
Ca_Mg$loq     <- 0

# plot_summary(Ca_Mg, text_size = text_size)
plot_timeseries_by_year(Ca_Mg, text_size = text_size)

Alkalinity, Total CaCO3

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parameter     <- c("ALKALINITY TOTAL CACO3", "ALKALINITY TOTAL GRAN AVAL UEQ/L")
plotting_name <- "Alkalinity Total CaCO3"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Hardness, Total Recoverable Calculation

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parameter     <-"HARDNESS TOTAL RECOVERABLE CALCULATION"
plotting_name <- "Total Recoverable Hardness"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Aluminum, Total Recoverable

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parameter     <-"ALUMINUM,TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Aluminum"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Iron, Total Recoverable

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parameter     <-"IRON TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Iron"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Manganese, Total Recoverable

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parameter     <-"MANGANESE, TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Manganese"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Conductivity

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parameter     <-"CONDUCTIVITY, UMHOS/CM @ 25C"
plotting_name <- "Conductivity"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Chloride

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parameter     <-"CHLORIDE"
plotting_name <- "Chloride"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Sodium, Total Recoverable

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parameter     <-"SODIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Sodium"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Nitrogen, NH3-N Dissolved

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parameter     <-"NITROGEN NH3-N DISS"
plotting_name <- "Dissolved Ammonium as Nitrogen"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Nitrogen, NO3 + NO2 Dissolved (as N)

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parameter     <-"NITROGEN NO3+NO2 DISS (AS N)"
plotting_name <- "Dissolved Nitrate/Nitrite as Nitrogen"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Total Nitrogen

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parameter     <-"NITROGEN TOTAL"
plotting_name <- "Total Nitrogen"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Phosphorus, Total

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parameter     <-"PHOSPHORUS TOTAL"
plotting_name <- "Total Phosphorus"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Potassium, Total Recoverable

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parameter     <-"POTASSIUM TOTAL RECOVERABLE"
plotting_name <- "Total Recoverable Potassium"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Silica, Dissolved (as SiO2)

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parameter     <-"SILICA, DISSOLVED (MG/L AS SI02)"
plotting_name <- "Dissolved Silica as SiO2"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

pH

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parameter     <-"PH LAB"
plotting_name <- "pH"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

Sulfate, Total

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parameter     <- c("SULFATE TOTAL", "SULFATE DISS, AS SO4")
plotting_name <- "Total Sulfate"

this_parameter <- filter_parameter(water_chem, parameter, plotting_name)
# plot_summary_by_year(this_parameter, text_size = text_size)
plot_timeseries_by_year(this_parameter, text_size = text_size)

WDNR-Water-Use/CSLSchem documentation built on July 3, 2020, 10:51 a.m.