In IBAHCM/RPiR: Reproducible Programming in R
Some useful things...
Important functionality {.smaller}
- Loading files using
source(...)
- Vectors,
c(), seq(), head() and tail()
- for loops:
```{R, eval=FALSE}
for (...) { ... }
- functions:
```{R, eval=FALSE}
my_fun <- function() { ... }
- if statements
```{R, eval=FALSE}
if (...) { ... } else { ... }
- Using curly brackets `{ ... }`
- (joining) data frames
```{R, eval=FALSE}
data.frame(...)
rbind(df1, df2)
Loading files
```{R, eval=FALSE}
source("0105-step-birth-death.R")
step_deterministic_birth_death
```{R, echo=FALSE, comment=""}
source(system.file("dummy_project/0105-step-birth-death.R", package = "RPiR"))
step_deterministic_birth_death
Vectors
```{R, comment=""}
c("Hello", "Goodbye")
```{R, comment=""}
words <- c("Welcome", "Farewell")
words[2]
seq()
```{R, comment=""}
seq(2, 4)
```{R, comment=""}
wholes <- seq(from = 3, to = 6)
wholes
```{R, comment=""}
halves <- seq(from = 3, to = 7, by = 0.5)
halves
## `head()` and `tail()`
```{R, comment=""}
head(halves)
```{R, comment=""}
tail(halves, 1)
## `for (...)` loops
```{R, eval=FALSE}
for (item in vector) {
do something, probably to item
}
Remember, wholes was seq(from = 3, to = 6):
```{R, comment=""}
for (whole in wholes) {
print(whole)
}
## `for (...)` loops
```{R, comment=""}
halves <- seq(from = 0, to = 1, by = 0.5)
total <- 0
for (half in halves) {
print(half)
total <- total + half
}
total
Functions
```{R, comment=""}
add_up <- function(first, second) {
first + second
}
add_up(3, 5)
## Functions
```{R, comment=""}
add_up <- function(first, second) {
result <- first + second
}
add_up(3, 5)
Functions
```{R, comment=""}
add_up <- function(first, second) {
result <- first + second
result
}
add_up(3, 5)
## Functions
```{R, comment=""}
### <b>
add_up <- function(first, second) {
### </b>
result <- first + second
### <b>
second - first
}
add_up(3, 5) ### </b>
Functions
```{R, comment=""}
add_up <- function(first, second) {
# Calculate the result
result <- first + second
# And return it
result
}
add_up(3, 5)
## Functions
We want to calculate: $$(first + second) \times (first + second)$$
```{R, comment=""}
add_and_square <- function(first, second) {
# Calculate the result
added <- first + second
squared <- added * added
# And return it
squared
}
add_and_square(3, 5)
Functions
Doing it all in one go increases the risk of mistakes:
```{R, comment=""}
add_and_square <- function(first, second) {
(first + second) * first + second
}
add_and_square(3, 5)
## `if (...) {...}` statements
If statements allow us to do different things depending on what has gone before in the code.
## `if (...) {...}` statements
```{R, comment=""}
if (add_and_square(3, 5) == 64) {
print("Maths still works")
}
if (...) {...} else {...}
```{R, comment=""}
if (add_and_square(3, 5) == 64) {
print("Maths still works")
} else {
warning("We have a problem")
print(add_and_square(3, 5))
}
## `if (...) {...} else {...}`
```{R, comment=""}
add_and_square <- function(first, second) {
# Calculate the result
added <- first + second
squared <- added * added
# And return it
squared
}
if (...) {...} else {...}
```{R, comment=""}
if (add_and_square(3, 5) == 64) {
usethis::ui_done("Maths still works")
} else {
usethis::ui_oops("We have a problem")
}
## Using curly brackets `{ ... }`
Curly brackets allow us to do lots of things all in one go. You've seen them in for loops, if statements, function definitions. They turn multiple R statements into one block, like a code block in RMarkdown but in regular R. Make sure you don't forget them.
## Using curly brackets `{ ... }`
```{R, echo=FALSE}
added <- 0
```{R, comment=""}
add_and_square <- function(first, second)
added <- first + second
squared <- added * added
squared
add_and_square(3, 5)
## Using curly brackets `{ ... }`
```{R, comment=""}
added <- 0
add_and_square <- function(first, second)
added <- first + second
squared <- added * added
squared
add_and_square(3, 5)
Using curly brackets { ... }
```{R, comment=""}
added <- 0
add_and_square <- function(first, second) {
added <- first + second
}
squared <- added * added
squared
add_and_square(3, 5)
## Using curly brackets `{ ... }`
```{R, comment=""}
added <- 0
add_and_square <- function(first, second) {
added <- first + second
squared <- added * added
squared
}
add_and_square(3, 5)
Using curly brackets { ... }
Notice that they actually interfere with RMarkdown
#' ## Adding a header here works!
added <- 0
add_and_square <- function(first, second) {
#' ## Adding a header here doesn't work :(
added <- first + second
squared <- added * added
squared
}
(joining) data frames {.smaller}
```{R, comment=""}
first <- head(airquality)
first
```{R, comment=""}
class(first)
```{R, comment=""}
last <- tail(airquality, 1)
last
## (joining) data frames {.smaller}
```{R, comment=""}
full <- rbind(first, last)
full
```{R, comment=""}
nrow(full)
## Final comments
```{R, eval=FALSE}
rm(list=ls())
This clears the environment, but so does generating a report, and rm() can
accidentally delete useful things if it’s used in the wrong place, so never
use it. If you have to clear the environment, you can clear the environment
manually using Session->Clear Workspace, the brush in the Environment tab, or
even better use Session->Restart R to restart everything. Next:
```{R, eval=FALSE}
setwd("c/d") # and more importantly
setwd("c:\a\b\c\d")
This will set the working directory to a fixed place, which is very annoying
if you ever move your code or more importantly if someone else tries to use it.
Much better to use a Project, so please *never put `setwd()` into your code
anywhere*.
## Final comments
And finally:
```{R, eval=FALSE}
install.packages("tibble")
devtools::install_github("SBOHVM/RPiR")
This should be done before you run your code (and later we'll show you how
to make sure it is done as your code is downloaded), but your scripts should
not try to install packages themselves. It's enough that loading the library
will fail if the code is run. It's obvious what to do next if that happens.
IBAHCM/RPiR documentation built on Jan. 12, 2023, 7:41 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.
Some useful things...
Important functionality {.smaller}
- Loading files using
source(...) - Vectors,
c(),seq(),head()andtail() - for loops:
```{R, eval=FALSE} for (...) { ... }
- functions: ```{R, eval=FALSE} my_fun <- function() { ... }
- if statements
```{R, eval=FALSE} if (...) { ... } else { ... }
- Using curly brackets `{ ... }`
- (joining) data frames
```{R, eval=FALSE}
data.frame(...)
rbind(df1, df2)
Loading files
```{R, eval=FALSE} source("0105-step-birth-death.R") step_deterministic_birth_death
```{R, echo=FALSE, comment=""}
source(system.file("dummy_project/0105-step-birth-death.R", package = "RPiR"))
step_deterministic_birth_death
Vectors
```{R, comment=""} c("Hello", "Goodbye")
```{R, comment=""}
words <- c("Welcome", "Farewell")
words[2]
seq()
```{R, comment=""} seq(2, 4)
```{R, comment=""}
wholes <- seq(from = 3, to = 6)
wholes
```{R, comment=""} halves <- seq(from = 3, to = 7, by = 0.5) halves
## `head()` and `tail()`
```{R, comment=""}
head(halves)
```{R, comment=""} tail(halves, 1)
## `for (...)` loops
```{R, eval=FALSE}
for (item in vector) {
do something, probably to item
}
Remember, wholes was seq(from = 3, to = 6):
```{R, comment=""} for (whole in wholes) { print(whole) }
## `for (...)` loops ```{R, comment=""} halves <- seq(from = 0, to = 1, by = 0.5) total <- 0 for (half in halves) { print(half) total <- total + half } total
Functions
```{R, comment=""} add_up <- function(first, second) { first + second } add_up(3, 5)
## Functions ```{R, comment=""} add_up <- function(first, second) { result <- first + second } add_up(3, 5)
Functions
```{R, comment=""} add_up <- function(first, second) { result <- first + second result } add_up(3, 5)
## Functions
```{R, comment=""}
### <b>
add_up <- function(first, second) {
### </b>
result <- first + second
### <b>
second - first
}
add_up(3, 5) ### </b>
Functions
```{R, comment=""} add_up <- function(first, second) { # Calculate the result result <- first + second # And return it
result
} add_up(3, 5)
## Functions We want to calculate: $$(first + second) \times (first + second)$$ ```{R, comment=""} add_and_square <- function(first, second) { # Calculate the result added <- first + second squared <- added * added # And return it squared } add_and_square(3, 5)
Functions
Doing it all in one go increases the risk of mistakes:
```{R, comment=""} add_and_square <- function(first, second) { (first + second) * first + second } add_and_square(3, 5)
## `if (...) {...}` statements
If statements allow us to do different things depending on what has gone before in the code.
## `if (...) {...}` statements
```{R, comment=""}
if (add_and_square(3, 5) == 64) {
print("Maths still works")
}
if (...) {...} else {...}
```{R, comment=""} if (add_and_square(3, 5) == 64) { print("Maths still works") } else { warning("We have a problem") print(add_and_square(3, 5)) }
## `if (...) {...} else {...}` ```{R, comment=""} add_and_square <- function(first, second) { # Calculate the result added <- first + second squared <- added * added # And return it squared }
if (...) {...} else {...}
```{R, comment=""} if (add_and_square(3, 5) == 64) { usethis::ui_done("Maths still works") } else { usethis::ui_oops("We have a problem") }
## Using curly brackets `{ ... }` Curly brackets allow us to do lots of things all in one go. You've seen them in for loops, if statements, function definitions. They turn multiple R statements into one block, like a code block in RMarkdown but in regular R. Make sure you don't forget them. ## Using curly brackets `{ ... }` ```{R, echo=FALSE} added <- 0
```{R, comment=""} add_and_square <- function(first, second) added <- first + second squared <- added * added squared
add_and_square(3, 5)
## Using curly brackets `{ ... }` ```{R, comment=""} added <- 0 add_and_square <- function(first, second) added <- first + second squared <- added * added squared add_and_square(3, 5)
Using curly brackets { ... }
```{R, comment=""} added <- 0 add_and_square <- function(first, second) { added <- first + second } squared <- added * added squared
add_and_square(3, 5)
## Using curly brackets `{ ... }` ```{R, comment=""} added <- 0 add_and_square <- function(first, second) { added <- first + second squared <- added * added squared } add_and_square(3, 5)
Using curly brackets { ... }
Notice that they actually interfere with RMarkdown
#' ## Adding a header here works! added <- 0 add_and_square <- function(first, second) { #' ## Adding a header here doesn't work :( added <- first + second squared <- added * added squared }
(joining) data frames {.smaller}
```{R, comment=""} first <- head(airquality) first
```{R, comment=""}
class(first)
```{R, comment=""} last <- tail(airquality, 1) last
## (joining) data frames {.smaller} ```{R, comment=""} full <- rbind(first, last) full
```{R, comment=""} nrow(full)
## Final comments
```{R, eval=FALSE}
rm(list=ls())
This clears the environment, but so does generating a report, and rm() can
accidentally delete useful things if it’s used in the wrong place, so never
use it. If you have to clear the environment, you can clear the environment
manually using Session->Clear Workspace, the brush in the Environment tab, or
even better use Session->Restart R to restart everything. Next:
```{R, eval=FALSE}
setwd("c/d") # and more importantly
setwd("c:\a\b\c\d")
This will set the working directory to a fixed place, which is very annoying
if you ever move your code or more importantly if someone else tries to use it.
Much better to use a Project, so please *never put `setwd()` into your code
anywhere*.
## Final comments
And finally:
```{R, eval=FALSE}
install.packages("tibble")
devtools::install_github("SBOHVM/RPiR")
This should be done before you run your code (and later we'll show you how to make sure it is done as your code is downloaded), but your scripts should not try to install packages themselves. It's enough that loading the library will fail if the code is run. It's obvious what to do next if that happens.
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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