# How to reconstruct several patterns

#### Maximilian H.K. Hesselbarth

#### 2024-03-14

Source:`vignettes/articles/reconstruct_several_patterns.Rmd`

`reconstruct_several_patterns.Rmd`

In case you want to reconstruct several patterns at once (e.g. for different points in time if repeated censuses are available), you can use the following code.

Please note that the maximum number of iterations has been set to

`max_runs = 1000`

and`n_random = 3`

to keep computational time low for this example. For real-world applications, it is advisable to raise these values. Additionally, we set`verbose = FALSE`

in the vignette to minimize printed output. We recommend using the default setting`verbose = TRUE`

when executing the code to view progress reports.

In case you want to only create the spatial characteristics, this is
straightforward using `lapply()`

.

```
# create list with patterns
list_pattern <- list(species_a, species_b)
# reconstruct all patterns in list
result <- lapply(list_pattern, function(x) reconstruct_pattern(pattern = x, n_random = 3,
max_runs = 1000, verbose = FALSE))
```

The result will be a nested list including all *m*
randomization (including the observed pattern) of the *n*
provided input patterns.

```
# get mean energy
lapply(result, function(x) calculate_energy(pattern = x,
verbose = FALSE))
#> [[1]]
#> randomized_1 randomized_2 randomized_3
#> 0.02121578 0.01976184 0.02181316
#>
#> [[2]]
#> randomized_1 randomized_2 randomized_3
#> 0.03079873 0.04046341 0.03398510
```

Another possible would be to first reconstruct *n* times the
spatial characteristics and afterwards reconstruct the marks *m*
times for each of the *n* spatial reconstructions.

Firstly, reconstruct only the spatial characteristics *n*
times. The observed pattern is not needed in this case, so you can put
`return_input = FALSE`

.

```
# reconstruct spatial strucutre
reconstructed_pattern <- reconstruct_pattern(species_a, n_random = 3,
max_runs = 1000, return_input = FALSE,
verbose = FALSE)
```

Secondly, to reconstruct the (numeric) marks of the observed pattern
for each of the spatially reconstructed patterns, just use
`lapply()`

in combination with
`reconstruct_pattern_marks()`

.

```
# get only selected marks of input (numeric marks)
species_a_marks <- subset(species_a, select = dbh)
# reconstruct marks 3 times for each input pattern
result_marks <- lapply(reconstructed_pattern$randomized,
function(x) reconstruct_pattern_marks(pattern = x,
marked_pattern = species_a_marks,
max_runs = 1000,
n_random = 3, verbose = FALSE))
```

Again, the result is a nested list with the same dimensions as provided input patterns and reconstructions.

```
# get energy
lapply(result_marks, function(x) calculate_energy(pattern = x,
verbose = FALSE))
#> $randomized_1
#> randomized_1 randomized_2 randomized_3
#> 0.009258516 0.009975463 0.009858007
#>
#> $randomized_2
#> randomized_1 randomized_2 randomized_3
#> 0.009995799 0.009691552 0.008402482
#>
#> $randomized_3
#> randomized_1 randomized_2 randomized_3
#> 0.009932602 0.009880717 0.009899017
```