Kevin Cazelles David Beauchesne

In comes

Note that while some tips might be obvious for careful documentation readers (God bless them for their wisdom), we do our best to present what we find very useful and underestimated. By the way, there are undoubtedly similar initiatives on the web (

`apropos()`

functionA powerful way to look for a function you can barely remember the name of directly in R, *i.e* without googling!

```
apropos('Sys')
#R> [1] ".First.sys" "R_system_version" "sys.call"
#R> [4] "sys.calls" "Sys.chmod" "Sys.Date"
#R> [7] "sys.frame" "sys.frames" "sys.function"
#R> [10] "Sys.getenv" "Sys.getlocale" "Sys.getpid"
#R> [13] "Sys.glob" "Sys.info" "sys.load.image"
#R> [16] "Sys.localeconv" "sys.nframe" "sys.on.exit"
#R> [19] "sys.parent" "sys.parents" "Sys.readlink"
#R> [22] "sys.save.image" "Sys.setenv" "Sys.setFileTime"
#R> [25] "Sys.setlocale" "Sys.sleep" "sys.source"
#R> [28] "sys.status" "Sys.time" "Sys.timezone"
#R> [31] "Sys.umask" "Sys.unsetenv" "Sys.which"
#R> [34] "system" "system.file" "system.time"
#R> [37] "system2"
```

You can also take advantage of regular expressions to narrow down you research:

```
apropos('^Sys')
#R> [1] "sys.call" "sys.calls" "Sys.chmod"
#R> [4] "Sys.Date" "sys.frame" "sys.frames"
#R> [7] "sys.function" "Sys.getenv" "Sys.getlocale"
#R> [10] "Sys.getpid" "Sys.glob" "Sys.info"
#R> [13] "sys.load.image" "Sys.localeconv" "sys.nframe"
#R> [16] "sys.on.exit" "sys.parent" "sys.parents"
#R> [19] "Sys.readlink" "sys.save.image" "Sys.setenv"
#R> [22] "Sys.setFileTime" "Sys.setlocale" "Sys.sleep"
#R> [25] "sys.source" "sys.status" "Sys.time"
#R> [28] "Sys.timezone" "Sys.umask" "Sys.unsetenv"
#R> [31] "Sys.which" "system" "system.file"
#R> [34] "system.time" "system2"
```

Or even better:

```
apropos('^Sys.*time$', ignore.case = FALSE)
#R> [1] "Sys.time"
```

`table()`

functionOftentimes we wish to extract the frequency of certain elements in a dataset. There is a very useful function that allows us to achieve this quite efficiently: `table()`

. Let’s see how this works:

```
df <- data.frame(data = sample(1:5, 20, replace = T))
table(df$data)
#R>
#R> 1 2 3 4 5
#R> 6 6 3 2 3
```

You can also get the frequency for a data.frame with multiple columns. For example, if you observed species at a site throughout multiple years and wanted to know the frequency of observations per species per year:

```
df <- data.frame(observations = paste0('species', sample(1:5, 50, replace = T)),
year = sort(sample(2015:2018, 50, replace = T)))
table(df)
#R> year
#R> observations 2015 2016 2017 2018
#R> species1 3 1 1 2
#R> species2 2 2 1 3
#R> species3 3 1 3 2
#R> species4 1 4 6 2
#R> species5 3 3 3 4
```

You can actually do so for more than two columns.

```
df$atr1 <- rep(c("val1", "val2"), each = 25)
tb <- table(df)
tb
#R> , , atr1 = val1
#R>
#R> year
#R> observations 2015 2016 2017 2018
#R> species1 3 1 0 0
#R> species2 2 2 0 0
#R> species3 3 1 1 0
#R> species4 1 4 1 0
#R> species5 3 3 0 0
#R>
#R> , , atr1 = val2
#R>
#R> year
#R> observations 2015 2016 2017 2018
#R> species1 0 0 1 2
#R> species2 0 0 1 3
#R> species3 0 0 2 2
#R> species4 0 0 5 2
#R> species5 0 0 3 4
```

As you can see, in such case, you will have to deal with arrays:

```
tb[, , 1]
#R> year
#R> observations 2015 2016 2017 2018
#R> species1 3 1 0 0
#R> species2 2 2 0 0
#R> species3 3 1 1 0
#R> species4 1 4 1 0
#R> species5 3 3 0 0
```

With further development and by combining `table()`

with `paste0()`

(see fish and tips 001 for an explanation of this useful function!), you can create your desired data.frame:

```
as.data.frame(table(paste0(df$year,'_',df$observations)))
#R> Var1 Freq
#R> 1 2015_species1 3
#R> 2 2015_species2 2
#R> 3 2015_species3 3
#R> 4 2015_species4 1
#R> 5 2015_species5 3
#R> 6 2016_species1 1
#R> 7 2016_species2 2
#R> 8 2016_species3 1
#R> 9 2016_species4 4
#R> 10 2016_species5 3
#R> 11 2017_species1 1
#R> 12 2017_species2 1
#R> 13 2017_species3 3
#R> 14 2017_species4 6
#R> 15 2017_species5 3
#R> 16 2018_species1 2
#R> 17 2018_species2 3
#R> 18 2018_species3 2
#R> 19 2018_species4 2
#R> 20 2018_species5 4
```

This is a well-known trick for developers that may be useful for many beginners. In R when performing a logical test, every numeric is considered as `TRUE`

but `0`

(which is `FALSE`

):

```
0 == FALSE
!0
!1
!7.45
#R> [1] TRUE
#R> [1] TRUE
#R> [1] FALSE
#R> [1] FALSE
```

This can actually be very helpful, for instance when we are testing whether or not a vector is empty!

```
vec0 <- 1:7
vec1 <- vec0[vec0>5]
vec2 <- vec0[vec0>7]
!(length(vec1))
!(length(vec2))
#R> [1] FALSE
#R> [1] TRUE
```

`expand.grid()`

vs.`combn()`

If you often create empty data.frame, you are very likely already familiar with the `expand.grid()`

function:

```
expand.grid(LETTERS[1:4], LETTERS[5:6])
#R> Var1 Var2
#R> 1 A E
#R> 2 B E
#R> 3 C E
#R> 4 D E
#R> 5 A F
#R> 6 B F
#R> 7 C F
#R> 8 D F
```

But if you are looking for unique combinations (think about all combinations of games in a tournament of four team), you may feel that `expand.grid()`

is not what you need:

```
expand.grid(LETTERS[1:4], LETTERS[1:4])
#R> Var1 Var2
#R> 1 A A
#R> 2 B A
#R> 3 C A
#R> 4 D A
#R> 5 A B
#R> 6 B B
#R> 7 C B
#R> 8 D B
#R> 9 A C
#R> 10 B C
#R> 11 C C
#R> 12 D C
#R> 13 A D
#R> 14 B D
#R> 15 C D
#R> 16 D D
```

In comes `combn`

:

```
combn(LETTERS[1:5], 2)
#R> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#R> [1,] "A" "A" "A" "A" "B" "B" "B" "C" "C" "D"
#R> [2,] "B" "C" "D" "E" "C" "D" "E" "D" "E" "E"
```

As you can see you need to specify the number of elements in the combination as `combn`

can compute all combination

```
combn(LETTERS[1:5], 4)
#R> [,1] [,2] [,3] [,4] [,5]
#R> [1,] "A" "A" "A" "A" "B"
#R> [2,] "B" "B" "B" "C" "C"
#R> [3,] "C" "C" "D" "D" "D"
#R> [4,] "D" "E" "E" "E" "E"
```

Also if you want a dataframe, a small extra step is required:

```
as.data.frame(t(combn(LETTERS[1:5], 2)))
#R> V1 V2
#R> 1 A B
#R> 2 A C
#R> 3 A D
#R> 4 A E
#R> 5 B C
#R> 6 B D
#R> 7 B E
#R> 8 C D
#R> 9 C E
#R> 10 D E
```

If you are always thinking outside the box you may want to learn how to plot something outside the margins! This is possible using the `xpd`

parameter of the `par()`

function.

```
par(mfrow = c(1, 2))
plot(c(0, 2), c(0, 2))
lines(c(-1,3), c(1,1), lwd = 4)
##
par(xpd = TRUE)
plot(c(0, 2), c(0, 2))
lines(c(-1,3), c(1,1), lwd = 4)
```