A spectrophotometer is an essential analytical instrument widely used in various scientific disciplines, including chemistry, biology, physics, environmental science, clinical diagnostics, and materials science, for the quantitative analysis of substances based on their interaction with light. At its core, a spectrophotometer measures the amount of light that a chemical substance absorbs by determining the intensity of light as a beam of light passes through the sample solution. The fundamental principle behind the spectrophotometer is the Beer-Lambert law, which relates the absorption of light to the properties of the material through which the light is traveling. According to this law, the absorbance is directly proportional to the concentration of the absorbing species in the material and the path length that the light travels through the sample. By exploiting this principle, a spectrophotometer provides a powerful, non-destructive means of identifying and quantifying substances in both qualitative and quantitative studies.
The construction of a spectrophotometer involves several key components, each playing a vital role in the overall functioning of the instrument. The first critical component is the light source. The choice of the light source depends on the range of wavelengths needed for analysis. For ultraviolet (UV) light, typically a deuterium lamp is used, while tungsten filament lamps are commonly used for the visible light range. In some advanced spectrophotometers, xenon lamps or other broad-spectrum sources may be used to cover a wider range of wavelengths. The light emitted from the source is then directed toward a monochromator, which isolates the desired wavelength of light from the full spectrum emitted by the lamp. Monochromators generally consist of a prism or a diffraction grating, which disperses the light into its component wavelengths. By rotating the monochromator, the instrument can select and pass a narrow band of wavelengths to the sample, ensuring that only light of the desired wavelength reaches the sample compartment.
The sample is typically held in a cuvette, a small transparent container made of quartz, glass, or plastic, depending on the wavelength range of interest. Quartz cuvettes are used for UV measurements since they do not absorb UV light, while plastic or glass cuvettes are sufficient for visible light applications. The path length of the cuvette, usually 1 cm, is a critical parameter because it influences the absorbance readings according to the Beer-Lambert law. Once the monochromatic light passes through the sample, it emerges with reduced intensity due to absorption by the sample. The transmitted light is then collected by a photodetector, which converts the light signal into an electrical signal. This electrical signal is proportional to the intensity of the transmitted light and is processed by the instrument’s electronics to calculate absorbance or transmittance values. These values are then give
A spectrophotometer is an essential analytical instrument widely used in various scientific disciplines, including chemistry, biology, physics, environmental science, clinical diagnostics, and materials science, for the quantitative analysis of substances based on their interaction with light. At its core, a spectrophotometer measures the amount of light that a chemical substance absorbs by determining the intensity of light as a beam of light passes through the sample solution. The fundamental principle behind the spectrophotometer is the Beer-Lambert law, which relates the absorption of light to the properties of the material through which the light is traveling. According to this law, the absorbance is directly proportional to the concentration of the absorbing species in the material and the path length that the light travels through the sample. By exploiting this principle, a spectrophotometer provides a powerful, non-destructive means of identifying and quantifying substances in both qualitative and quantitative studies.
The construction of a spectrophotometer involves several key components, each playing a vital role in the overall functioning of the instrument. The first critical component is the light source. The choice of the light source depends on the range of wavelengths needed for analysis. For ultraviolet (UV) light, typically a deuterium lamp is used, while tungsten filament lamps are commonly used for the visible light range. In some advanced spectrophotometers, xenon lamps or other broad-spectrum sources may be used to cover a wider range of wavelengths. The light emitted from the source is then directed toward a monochromator, which isolates the desired wavelength of light from the full spectrum emitted by the lamp. Monochromators generally consist of a prism or a diffraction grating, which disperses the light into its component wavelengths. By rotating the monochromator, the instrument can select and pass a narrow band of wavelengths to the sample, ensuring that only light of the desired wavelength reaches the sample compartment.
The sample is typically held in a cuvette, a small transparent container made of quartz, glass, or plastic, depending on the wavelength range of interest. Quartz cuvettes are used for UV measurements since they do not absorb UV light, while plastic or glass cuvettes are sufficient for visible light applications. The path length of the cuvette, usually 1 cm, is a critical parameter because it influences the absorbance readings according to the Beer-Lambert law. Once the monochromatic light passes through the sample, it emerges with reduced intensity due to absorption by the sample. The transmitted light is then collected by a photodetector, which converts the light signal into an electrical signal. This electrical signal is proportional to the intensity of the transmitted light and is processed by the instrument’s electronics to calculate absorbance or transmittance values. These values are then give
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3. Loop
There are three kinds of loops in R:
Repeat
While, and for
they can still come in handy for repeatedly executing code
Repeat:
i<-0
repeat
{
print(i)
i<-i+1
if(i>=3)
break
}
6. Functions
A function is a block of code which only runs when
it is called.
You can pass data, known as parameters, into a
function.
A function can return data as a result.
7. Creating and Calling Function in R
In order to understand functions better, let’s take a look
at what they consist of.
Typing the name of a function shows you the code that
runs when you call it.
The terms "parameter" and "argument" can be used for the
same thing: information that are passed into a function.
From a function's perspective:
A parameter is the variable listed inside the parentheses
in the function definition.
An argument is the value that is sent to the function when
it is called.
9. Passing Functions to and from Other
Functions
Functions can be used just like other variable
types, so we can pass them as arguments to other
functions, and return them from functions.
One common example of a function that takes
another function as an argument is do.call.
do.call(function(x, y) x + y, list(1:5, 5:1))
## [1] 6 6 6 6 6
10. do.call()
#create three data frames
df1 <- data.frame(team=c('A', 'B', 'C'), points=c(22, 27, 38))
df2 <- data.frame(team=c('D', 'E', 'F'), points=c(22, 14, 20))
df3 <- data.frame(team=c('G', 'H', 'I'), points=c(11, 15, 18))
#place three data frames into list
df_list <- list(df1, df2, df3)
#row bind together all three data frames
do.call(rbind, df_list)
11. Variable Scope
A variable’s scope is the set of places from which you can see the variable.
For example, when you define a variable inside a function, the rest of the
statements in that function will have access to that variable.
In R subfunctions will also have access to that variable.
In this next example, the function f takes a variable x and passes it to the
function g. f also defines a variable y, which is within the scope of g, since g
is a sub‐ function of f.
12. So, even though y isn’t defined inside g, the example works:
f <- function(x)
{
y <- 1
g <- function(x)
{
(x + y) / 2 #y is used, but is not a formal argument of g }
g(x)
}
f(sqrt(5)) #It works! y is magically found in the environment of f
## [1] 1.618
13. String Manipulation
String manipulation basically refers to the process of
handling and analyzing strings.
It involves various operations concerned with
modification and parsing of strings to use and change its
data.
Paste:
str <- paste(c(1:3), "4", sep = ":")
print (str)
## "1:4" "2:4" "3:4"
Concatenation:
# Concatenation using cat() function
str <- cat("learn", "code", "tech", sep = ":")
print (str)
## learn:code:tech
15. Loading and Packages
R is not limited to the code provided by the R Core Team.
It is very much a community effort, and
there are thousands of add-on packages available to
extend it.
The majority of R packages are currently installed in an
online repository called CRAN (the Comprehensive R
Archive Network1)
which is maintained by the R Core Team. Installing and
using these add-on packages is an important part of the R
experience
16. Loading Packages
To load a package that is already installed on your
machine, you call the library function
We can load it with the library function:
library(lattice)
the functions provided by lattice. For example,
displays a fancy dot plot of the famous Immer’s barley
dataset:
dotplot(
variety ~ yield | site,
data = barley,
groups = year
)
17. Scatter Plot
A "scatter plot" is a type of plot used to display the relationship between two
numerical variables, and plots one dot for each observation.
It needs two vectors of same length, one for the x-axis (horizontal) and one
for the y-axis (vertical):
Example
x <- c(5,7,8,7,2,2,9,4,11,12,9,6)
y <- c(99,86,87,88,111,103,87,94,78,77,85,86)
plot(x, y)