NSci323 Lesson 10 Examples and Homework Template
Brian Broken Leg
2023-12-21
Overview
This file contains a homework template and in-class examples. When you have completed the homework, click Knit to HTML.
Changes to prior code
- changed equiv_wt_CaCO3_mg_l to mg_l_as_CaCO3
- changed sum_hardness_graph to sum_hardness
- changed sum_hardness_long to sum_hardness
- flipped “type” and “ion” in sum_hardness_long
- added steps to clean up environment
- added code to graph ionic constituents
- added code to calculate Ca and Mg - CH and NCH
Homework
Run the code below to make a final graph with hardness, cations, anions.
Look up ‘pivot_wider()’ in Help. Briefly summarize what it does.
This command increases the number of columns and decreases the number of rows.
- Look up ‘pivot_longer()’ in Help. Briefly summarize what it does.
This command decreases the number of columns and increases the number of rows.
- Go through the “Calculate the calcium noncarbonate hardness” example in the ‘Ch06_Ex06_part05_hardness_calcs’ code chunk. Then, a) calculate the magnesium noncarbonate hardness, b) calculate the alkalinity, c) calculate the TDS.
In-class examples
# This code chunk calculates ion concentrations in mg/L into meq/L and
# equivalents as mg/L as CaCO3
# Notes:
# * Getting the data into R is sometimes the least fun of problem solving.
# * I modified some code from last week to get this table.
# -- the molecular_weight and charge are numeric in the table below
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# make a table of molecular weight, charge and concentration
tab_ions <- tibble::tribble(
~Type, ~hardness, ~Ion, ~Molecular.Weight, ~Charge, ~Conc.mg.L,
"cation", "hard_TH", "Ca", 40.1, 2, 80,
"cation", "hard_TH", "Mg", 24.3, 2, 30,
"cation", NA, "Na", 23.0, 1, 72,
"cation", NA, "K", 39.1, 1, 6,
"anion", NA, "Cl", 35.5, 1, 100,
"anion", NA, "SO4", 96.0, 2, 201,
"anion", "hard_CH", "HCO3", 61.0, 1, 165
)
# use the janitor package and dplyr::rename to clean names
tab_ions <- tab_ions %>%
clean_names() %>% # Cleans names of an object (usually a data.frame)
rename(molec_wt_mmol = molecular_weight)
# calculate milliequivalents using the formula:
# Equivalent weight (EW) = Atomic or molecular weight / charge
tab_ions <- tab_ions %>%
mutate(equiv_wt_mg_meq = round(molec_wt_mmol / charge,
digits = 1)) %>%
relocate(equiv_wt_mg_meq, .before = conc_mg_l)
# calculate equivalent weight as CaCO3----
# make a variable to use below
equiv_wt_CaCO3_var <- 50 # mg/meq; note this is a 1x1 vector
# calculate the equivalents as CaCO3
# mg/L of X as CaCO3 = ( conc of X (mg/L) / EW of X (mg/meq) * 50.0 mg CaCO3/meq )
# Note: the units of X are in "as mg/L CaCO3"
tab_ions <- tab_ions %>%
mutate(
mg_l_as_CaCO3 = conc_mg_l/ equiv_wt_mg_meq * equiv_wt_CaCO3_var
) %>%
mutate(mg_l_as_CaCO3 = round(mg_l_as_CaCO3,
digits = 1
))# This code chunk checks the cation and anion balance as as mg/L as CaCO3
# In water, the sum of the anions = the sum of the cations
# Note: !is.na() means NOT = ! and is.na() checks for an NA value
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# add up all the anions and the cations
sum_ions <- tab_ions %>%
group_by(type) %>%
summarise(sum = sum(mg_l_as_CaCO3)) %>%
ungroup()
# calculate total hardness and carbonate hardness
# Total Hardness = Ca + Mg
# Carbonate hardness = alkality or in this case the HCO3 conc as CaCO3
sum_hardness <- tab_ions %>%
group_by(hardness) %>%
summarise(sum = sum(mg_l_as_CaCO3)) %>%
ungroup() %>%
filter(!is.na(hardness)) %>% # drops all the NA rows
rename(type = hardness) # this is to add things together below
# add the cation sum to hardness long--
# get the cation and anion sums by themselves
sum_cations <- sum_ions %>%
filter(type == "cation")
sum_hardness <- bind_rows(sum_hardness, sum_cations)
# we are going to calculate total hardness and carbonate hardness
# pivot the table
sum_hardness_wide <- sum_hardness %>%
pivot_wider(names_from = type,
values_from = sum) %>%
relocate(hard_TH, .before = hard_CH) %>%
rename(cation_sum = cation)
# calculate total hardness and carbonate hardness
# If the alkalinity exceeds the total hardness, then
# CH = TH and NCH = 0
# If alkalinity is less than the total hardness
# CH = alkalinity and NCH = TH — CH
sum_hardness_wide <- sum_hardness_wide %>%
mutate(hard_NCH = hard_TH - hard_CH) %>%
relocate(hard_TH, .before = hard_CH) %>%
relocate(hard_NCH, .after = hard_CH)
# calculate the cations not contributing to hardness -- and check calculations
sum_hardness_wide <- sum_hardness_wide %>%
mutate(other = cation_sum - hard_TH) %>%
relocate(other, .after = hard_NCH) %>%
mutate(cation_check = hard_CH + hard_NCH + other)
# clean up global environment
rm(sum_cations,
equiv_wt_CaCO3_var)# This code chunk will make a stacked bar chart for hardness
# https://r-graph-gallery.com/48-grouped-barplot-with-ggplot2
# https://www.datanovia.com/en/blog/how-to-create-a-ggplot-horizontal-bar-chart/
# the coord flip() turns the barchart sideways
# Note this is not the final graph -- just a check on our process
sum_hardness <- sum_hardness_wide %>%
pivot_longer(cols = c(hard_CH, hard_NCH, other),
names_to = "ion",
values_to = "mg_l_as_CaCO3") %>%
mutate(type = "hardness") %>% # need to do this to make an x-axis to "stack"
select(-c(hard_TH, cation_sum, cation_check))
sum_hardness %>%
ggplot(aes(x = type, y = mg_l_as_CaCO3))+
geom_col(aes(fill = ion), width = 0.7) +
coord_flip()
Code added after class
# This code chunk will make a stacked bar chart for hardness, cations, anions
# Note this is not the final graph -- just a check on our process
# Next step is to change the plotting order of the items
# make a tibble of ions to add to the summary hardness
tab_ions_hard <- tab_ions %>%
select(type, ion, mg_l_as_CaCO3)
tab_ions_hard <- bind_rows(sum_hardness, tab_ions_hard)
# clean up global environment
rm(list = ls(pattern = "wide"))
# check results
tab_ions_hard %>%
ggplot(aes(x = type, y = mg_l_as_CaCO3))+
geom_col(aes(fill = ion), width = 0.7) +
coord_flip()
# this code chunk plots a graph in the order shown in Fig. 9 on page 308.
# use fct_relevel to order the ions for graphing --
# Note the fct_relevel feels like it is in the opposite order.
tab_ions_hard <- tab_ions_hard %>%
mutate(ion = fct_relevel(ion,
"Cl",
"SO4",
"HCO3",
"K",
"Na",
"Mg",
"Ca",
"other",
"hard_NCH",
"hard_CH"
))
# check progress -- plot the ordered table of ions
tab_ions_hard %>%
ggplot(aes(x = type, y = mg_l_as_CaCO3))+
geom_col(aes(fill = ion), width = 0.7) +
coord_flip()
# make a final plot
tab_ions_hard %>%
ggplot(aes(x = type, y = mg_l_as_CaCO3))+
geom_col(aes(fill = ion), width = 0.7) +
coord_flip() +
ggtitle("Ionic constituents of an example water") +
labs(x = "", # drops the 'type' from the graph - originally x-axis
y = "mg/L as CaCO3") +
theme_classic() +
guides(fill = guide_legend(reverse = TRUE))
# Prepare for hardness calculations
hard_calcs <- tab_ions_hard %>%
filter(type == "hardness" |
type == "cation"
) %>%
select(-type) %>% # want to get the data on the same row after pivoting
filter(ion == "hard_CH" |
ion == "hard_NCH" |
ion == "Ca" |
ion == "Mg"
) %>%
pivot_wider(names_from = ion,
values_from = mg_l_as_CaCO3)
# Calculate the calcium noncarbonate hardness
hard_calcs <- hard_calcs %>%
mutate(Ca_CH = hard_CH) %>%
mutate(Ca_NCH = Ca - Ca_CH) %>%
# Calculate the magnesium noncarbonate hardness
# note you should subtract off the Ca-NCH to get the leftover NCH
mutate(Mg_NCH = (Ca + Mg) - hard_CH - Ca_NCH) %>%
# Calculate the alkalinity
mutate(HCO3 = Ca_CH)
# Calculate the TDS
# note -- might want to use tab_ions
sum(tab_ions$conc_mg_l)## [1] 654