In ismayc/chemistr: Facilitates use of R functions and R Markdown files for Chemistry lab reports
Files with the extension .rmd are known as R markdown files. These files combine the use of markdown, which can convert text into many different formats (html, pdf, Microsoft word, etc.), with the use of R code. This allows you to create documents with pretty text and data analysis all in one. This file will knit without errors and is a resource for you to see how what is written in a .rmd translates when it is knit to a pdf.
In this document the white space contains markdown text while the gray boxes contain R code. In markdown text, spaces between words actually produce spaces. Here are some other examples of how to format your document.
Example: Starting a New Paragraph
I want this to be in paragraph 1.
I want this to be in paragraph 2.
vs
I want this to be in paragraph 1.
I want this to be in paragraph 2.
By putting two line spaces in between text you can break the line.
Example: Bold and Italic Text
This is normal text
This is bold text
This is italicized text
Example: Making Headers
Header size 1
Header size 2
Header size 3
Header size 4
How to Add Links
In [] add the name for the link and in () add the URL for the link
Example: How to Make Pretty Equations!
We can use Latex code in a markdown file to format equations by putting it in between two $ signs
For an in line equation we can use $y = mx + b$
For an stand alone equation we want to be centered on the page we can use $$ y = mx + b $$
Here are some common examples of equations you will use in chemistry.
Beer's law is $A = a b c$ where A is the absorbance, $a$ is the molar absorbtivity in units of $M^{-1} cm^{-1}$ $b$ is the path length in $cm$, and $c$ is the concentration in $M$.
Conversions
$P_{atm} = 29.83\: in\: Hg\: * \frac{2.54\: cm}{1\: in} * \frac{1000\: mm}{1\: cm} * \frac{1\: atm}{760\: mm\: Hg}$
In equations to add spaces, $29.83 in Hg$ must be written as $29.83\: in \: Hg$.
Supercript and Subscript
$P_{atm}$ vs $P^{atm}$, the sub-scripted or super-scripted text must be written within the {}
$1.3 \times 10^{-3}$
$S_{2}O_{8}^{2-}$
Fractions
$\frac{a}{b}$ $\frac{1}{1000}$
You can also do sub scripts and super scripts within fractions...
$K_{a} = \frac{[A^{-}][H_{3}O^{+}]}{[HA]}$
Commonly Used Symbols
Degree Symbol: $^\circ$, e.g. 25 $^\circ$C
Delta Symbol: $\Delta$, e.g. $\Delta{A}$
Less Than/Greater Than: < / > , e.g. 10 < 30
Plus or Minus Sign: $\pm$, e.g. 5.0 $\pm$ 0.2
Percent Sign: %, e.g. 25 %
More Example Equations
$P = \frac{nRT}{V}$
$x = \sqrt{x^{2}}$
$rate = k[I^{-}]^{m}\,[S_{2}O_{8}^{2-}]^{n}$
Arrhenius Equation
$k = Ae^{-E_{a}/RT}$
\clearpage This pushes everything after it to the next page
If you want to get fancy...you can also write reaction equations
Mechanism A:
$S_{2}O_{8}^{2-} \rightarrow SO_{4} + SO_{4}^{2-} \: (slow)$
$SO_{4} + I^{-} \rightarrow SO_{4}^{2-} + I^{+}$
$I^{+} + I^{-} \rightarrow I_{2}$
$I_{2} + I^{-} \rightarrow I_{3}^{-}$
Reactions in Equilibrium
$X_{(l)} \rightleftharpoons X_{(g)}$
$2H_{2}O_{l} \rightleftharpoons H_{3}O^{+}{aq} + OH^{-}{aq}$
Example: Adding Images
Follow this format without the
Now for some R code Examples
R code is written in gray chunks, which start with r and end with (see below)
Comments can be added to the code by adding a # in front of text
x <- 10 + 5 # x is the number 15
print(x) #this function prints what x is
x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It converts X to NA and is warning that this is what is happening
pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2")
new.pkg <- pkg[!(pkg %in% installed.packages())]
if (length(new.pkg)) {
install.packages(new.pkg, repos = "http://cran.rstudio.com")
}
library(dplyr) # Code that produces messages
library(xtable)
We can choose not to show messages from the code in the pdf by adding messages = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15
print(x) #this function prints what x is
x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It converts X to NA and is warning that this is what is happening
pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2")
new.pkg <- pkg[!(pkg %in% installed.packages())]
if (length(new.pkg)) {
install.packages(new.pkg, repos = "http://cran.rstudio.com")
}
library(dplyr) # Code that produces messages
We can control whether or not the code is shown in the pdf by adding echo = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15
print(x) #this function prints what x is
x <- as.numeric(c("1", "2", "X")) # Code that gives a warning.
# It converts X to NA and is warning that this is what is happening
pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2")
new.pkg <- pkg[!(pkg %in% installed.packages())]
if (length(new.pkg)) {
install.packages(new.pkg, repos = "http://cran.rstudio.com")
}
library(dplyr) # Code that produces messages
We can choose not to show warnings from the code in the pdf by adding warning = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15
print(x) #this function prints what x is
x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It
# converts X to NA and is warning that this is what is happening
pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2")
new.pkg <- pkg[!(pkg %in% installed.packages())]
if (length(new.pkg)) {
install.packages(new.pkg, repos = "http://cran.rstudio.com")
}
library(dplyr) # Code that produces messages
\clearpage
The % symbol in LaTex is used for comments. When writing r code (only gray chunks) either avoid using the percent symbol (in captions for tables and such) or use \%.
If when trying to knit to pdf you get an error message in red that reads, ! File ended while scanning use of \textbf, then you have used the percent symbol somewhere in the file where it is being read as a comment in LaTex. To fix the error, try either removing % symbols from r code or using \%.
Example: Creating Plots in R
# Add caption title within quotes above
#Defining values for x and y to plot
x <- c(1, 2.2, 4, 6.3, 8.1)
y <- c(5, 7.2, 8.4, 9.5, 12.3)
#Basic plot of y vs x (2 options)
plot(x, y)
#or
plot(y ~ x)
# The data look pretty linear, so let's fit a straight line (y = mx + b) to it
# and plot with the best fit line
# First, let's put x and y values into a dataframe, much like columns in excel
x.and.y <- data_frame(x, y)
# Take a look at the data frame by typing the name for the data frame
x.and.y
# Let's fit the data to our equation y = mx + b
fit <- nls(y ~ m*x + b, data = x.and.y, start = list(m = 1, b = 4)) # put in
# very rough guesses for slope (m) and y intercept (b)
# Now for every x value we have we want the y values that the equation
# predicts in order to plot the best fit line. We can extract these as a
# vector by using the function as.vector() and the function fitted().
ycalc <- as.vector(fitted(fit))
# Now let's plot our data with the best fit line using the function lines()
plot(x, y)
lines(x, ycalc)
# To produce a plot with colored lines and solid black dots use this
plot(x, y,
pch = 20)
lines(x, ycalc, col = "blue")
Adding Axis Labels and Captions with Superscripts and Subscripts)
Now let's reassign x to be concentration of persulfate and y to be rate when varying persulfate concentration
# Add caption title within quotes above
# reassigning x and y
rate <- y
persulfate.conc <- x
fitted.rate <- ycalc
# Plot of rate vs persulfate concentration with appropriate labels that include units
# Within expression function, ~ is for a space while * is for no space, [] is for
# subscript, ^ is for superscript
plot(persulfate.conc, rate,
xlab = expression("[" ~ S[2] * O[8]^"2-" ~ "]" ~ (M)),
ylab = expression("Rate" ~ ("M" * s^-1)),
pch = 20)
lines(persulfate.conc, fitted.rate, col = "green")
Example: Creating Tables
# Making a dataframe with newly named x and y values
rate.and.conc <- data_frame(rate, persulfate.conc)
# Renaming column names for the table
rate.and.conc <- rename(rate.and.conc, "Rate (M/s)" = rate, "Persulfate Concentration (M)" = persulfate.conc)
bold_all_col_names <- function(x) {paste('\\textbf{', x, '}', sep ='')} # function to bold column names
title <- 'Rate and Persulfate Concentration' # Giving the table a title
print(xtable(rate.and.conc, #This is the data frame you're going to use for the table
caption = title, # set the caption to be the specified title above
align = "|r|r|r|", # right align all columns and create vertical lines, need one more |r| than total columns. Use l or c for left or center aligned
digits = c(0, 1, 2), # number of decimal places for each column
display = c("d", "f", "f") # This is the type of number you want. Like in excel where you can display it scientifically (E), as an integer (d), or as a number (f), or changing a number into an obect (s). The first letter corresponds to an unseen row number. It must stay there but can be ignored.
),
caption.placement = 'top',
hline.after = seq(-1, nrow(rate.and.conc)), # Horizontal lines on top through bottom of table, must match datframe name, here rate.and.conc
include.rownames = FALSE,
comment = FALSE,
caption.width = '2.7in',
sanitize.colnames.function = bold_all_col_names
)
ismayc/chemistr documentation built on Feb. 4, 2023, 12:44 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Files with the extension .rmd are known as R markdown files. These files combine the use of markdown, which can convert text into many different formats (html, pdf, Microsoft word, etc.), with the use of R code. This allows you to create documents with pretty text and data analysis all in one. This file will knit without errors and is a resource for you to see how what is written in a .rmd translates when it is knit to a pdf.
In this document the white space contains markdown text while the gray boxes contain R code. In markdown text, spaces between words actually produce spaces. Here are some other examples of how to format your document.
Example: Starting a New Paragraph
I want this to be in paragraph 1. I want this to be in paragraph 2.
vs
I want this to be in paragraph 1.
I want this to be in paragraph 2.
By putting two line spaces in between text you can break the line.
Example: Bold and Italic Text
This is normal text
This is bold text
This is italicized text
Example: Making Headers
Header size 1
Header size 2
Header size 3
Header size 4
How to Add Links
In [] add the name for the link and in () add the URL for the link
Example: How to Make Pretty Equations!
We can use Latex code in a markdown file to format equations by putting it in between two $ signs
For an in line equation we can use $y = mx + b$
For an stand alone equation we want to be centered on the page we can use $$ y = mx + b $$
Here are some common examples of equations you will use in chemistry.
Beer's law is $A = a b c$ where A is the absorbance, $a$ is the molar absorbtivity in units of $M^{-1} cm^{-1}$ $b$ is the path length in $cm$, and $c$ is the concentration in $M$.
Conversions
$P_{atm} = 29.83\: in\: Hg\: * \frac{2.54\: cm}{1\: in} * \frac{1000\: mm}{1\: cm} * \frac{1\: atm}{760\: mm\: Hg}$
In equations to add spaces, $29.83 in Hg$ must be written as $29.83\: in \: Hg$.
Supercript and Subscript
$P_{atm}$ vs $P^{atm}$, the sub-scripted or super-scripted text must be written within the {}
$1.3 \times 10^{-3}$
$S_{2}O_{8}^{2-}$
Fractions
$\frac{a}{b}$ $\frac{1}{1000}$
You can also do sub scripts and super scripts within fractions...
$K_{a} = \frac{[A^{-}][H_{3}O^{+}]}{[HA]}$
Commonly Used Symbols
Degree Symbol: $^\circ$, e.g. 25 $^\circ$C
Delta Symbol: $\Delta$, e.g. $\Delta{A}$
Less Than/Greater Than: < / > , e.g. 10 < 30
Plus or Minus Sign: $\pm$, e.g. 5.0 $\pm$ 0.2
Percent Sign: %, e.g. 25 %
More Example Equations
$P = \frac{nRT}{V}$
$x = \sqrt{x^{2}}$
$rate = k[I^{-}]^{m}\,[S_{2}O_{8}^{2-}]^{n}$
Arrhenius Equation
$k = Ae^{-E_{a}/RT}$
\clearpage This pushes everything after it to the next page
If you want to get fancy...you can also write reaction equations
Mechanism A:
$S_{2}O_{8}^{2-} \rightarrow SO_{4} + SO_{4}^{2-} \: (slow)$
$SO_{4} + I^{-} \rightarrow SO_{4}^{2-} + I^{+}$
$I^{+} + I^{-} \rightarrow I_{2}$
$I_{2} + I^{-} \rightarrow I_{3}^{-}$
Reactions in Equilibrium
$X_{(l)} \rightleftharpoons X_{(g)}$
$2H_{2}O_{l} \rightleftharpoons H_{3}O^{+}{aq} + OH^{-}{aq}$
Example: Adding Images
Follow this format without the and make sure the image is in the same folder as your .rmd file to which you are trying to add the image.
Now for some R code Examples
R code is written in gray chunks, which start with r and end with (see below)
Comments can be added to the code by adding a # in front of text
x <- 10 + 5 # x is the number 15 print(x) #this function prints what x is x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It converts X to NA and is warning that this is what is happening pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2") new.pkg <- pkg[!(pkg %in% installed.packages())] if (length(new.pkg)) { install.packages(new.pkg, repos = "http://cran.rstudio.com") } library(dplyr) # Code that produces messages library(xtable)
We can choose not to show messages from the code in the pdf by adding messages = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15 print(x) #this function prints what x is x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It converts X to NA and is warning that this is what is happening pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2") new.pkg <- pkg[!(pkg %in% installed.packages())] if (length(new.pkg)) { install.packages(new.pkg, repos = "http://cran.rstudio.com") } library(dplyr) # Code that produces messages
We can control whether or not the code is shown in the pdf by adding echo = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15 print(x) #this function prints what x is x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. # It converts X to NA and is warning that this is what is happening pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2") new.pkg <- pkg[!(pkg %in% installed.packages())] if (length(new.pkg)) { install.packages(new.pkg, repos = "http://cran.rstudio.com") } library(dplyr) # Code that produces messages
We can choose not to show warnings from the code in the pdf by adding warning = FALSE to the beginning of the chunk ```r (see below)
x <- 10 + 5 # x is the number 15 print(x) #this function prints what x is x <- as.numeric(c("1", "2", "X")) # Code that gives a warning. It # converts X to NA and is warning that this is what is happening pkg <- c("dplyr", "knitr", "xtable", "rmarkdown", "readr", "ggplot2") new.pkg <- pkg[!(pkg %in% installed.packages())] if (length(new.pkg)) { install.packages(new.pkg, repos = "http://cran.rstudio.com") } library(dplyr) # Code that produces messages
\clearpage
The % symbol in LaTex is used for comments. When writing r code (only gray chunks) either avoid using the percent symbol (in captions for tables and such) or use \%. If when trying to knit to pdf you get an error message in red that reads, ! File ended while scanning use of \textbf, then you have used the percent symbol somewhere in the file where it is being read as a comment in LaTex. To fix the error, try either removing % symbols from r code or using \%.
Example: Creating Plots in R
# Add caption title within quotes above #Defining values for x and y to plot x <- c(1, 2.2, 4, 6.3, 8.1) y <- c(5, 7.2, 8.4, 9.5, 12.3) #Basic plot of y vs x (2 options) plot(x, y) #or plot(y ~ x) # The data look pretty linear, so let's fit a straight line (y = mx + b) to it # and plot with the best fit line # First, let's put x and y values into a dataframe, much like columns in excel x.and.y <- data_frame(x, y) # Take a look at the data frame by typing the name for the data frame x.and.y # Let's fit the data to our equation y = mx + b fit <- nls(y ~ m*x + b, data = x.and.y, start = list(m = 1, b = 4)) # put in # very rough guesses for slope (m) and y intercept (b) # Now for every x value we have we want the y values that the equation # predicts in order to plot the best fit line. We can extract these as a # vector by using the function as.vector() and the function fitted(). ycalc <- as.vector(fitted(fit)) # Now let's plot our data with the best fit line using the function lines() plot(x, y) lines(x, ycalc) # To produce a plot with colored lines and solid black dots use this plot(x, y, pch = 20) lines(x, ycalc, col = "blue")
Adding Axis Labels and Captions with Superscripts and Subscripts)
Now let's reassign x to be concentration of persulfate and y to be rate when varying persulfate concentration
# Add caption title within quotes above # reassigning x and y rate <- y persulfate.conc <- x fitted.rate <- ycalc # Plot of rate vs persulfate concentration with appropriate labels that include units # Within expression function, ~ is for a space while * is for no space, [] is for # subscript, ^ is for superscript plot(persulfate.conc, rate, xlab = expression("[" ~ S[2] * O[8]^"2-" ~ "]" ~ (M)), ylab = expression("Rate" ~ ("M" * s^-1)), pch = 20) lines(persulfate.conc, fitted.rate, col = "green")
Example: Creating Tables
# Making a dataframe with newly named x and y values rate.and.conc <- data_frame(rate, persulfate.conc) # Renaming column names for the table rate.and.conc <- rename(rate.and.conc, "Rate (M/s)" = rate, "Persulfate Concentration (M)" = persulfate.conc) bold_all_col_names <- function(x) {paste('\\textbf{', x, '}', sep ='')} # function to bold column names title <- 'Rate and Persulfate Concentration' # Giving the table a title print(xtable(rate.and.conc, #This is the data frame you're going to use for the table caption = title, # set the caption to be the specified title above align = "|r|r|r|", # right align all columns and create vertical lines, need one more |r| than total columns. Use l or c for left or center aligned digits = c(0, 1, 2), # number of decimal places for each column display = c("d", "f", "f") # This is the type of number you want. Like in excel where you can display it scientifically (E), as an integer (d), or as a number (f), or changing a number into an obect (s). The first letter corresponds to an unseen row number. It must stay there but can be ignored. ), caption.placement = 'top', hline.after = seq(-1, nrow(rate.and.conc)), # Horizontal lines on top through bottom of table, must match datframe name, here rate.and.conc include.rownames = FALSE, comment = FALSE, caption.width = '2.7in', sanitize.colnames.function = bold_all_col_names )
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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