R/calculate_regeneration.R
calculate_regeneration.RdThis function makes aggregations of tree generation data on the levels of
plot and year (and subplot for core area)
plot, height class and year (and subplot for core area)
plot, tree species and year (and subplot for core area)
plot, height class, tree species and year (and subplot for core area)
For core area plots it makes additional aggregations on the levels of
core area, tree species and year
core area, height class, tree species and year
calculate_regeneration(data_regeneration)List of dataframes that are mentioned in the above description
library(forrescalc)
# (add path to your own fieldmap database here)
path_to_fieldmapdb <-
system.file("example/database/mdb_bosres.sqlite", package = "forrescalc")
data_regeneration <- load_data_regeneration(path_to_fieldmapdb)
calculate_regeneration(data_regeneration)
#> $reg_by_plot
#> # A tibble: 30 × 25
#> plottype plot_id subplot_id period year number_of_tree_species
#> <chr> <int> <int> <int> <int> <int>
#> 1 CA 11000 155511 1 2000 0
#> 2 CA 11000 155511 2 2011 1
#> 3 CA 11000 155511 3 2021 1
#> 4 CA 11000 155512 1 2000 0
#> 5 CA 11000 155513 1 2000 0
#> 6 CA 11000 155521 2 2011 2
#> 7 CA 11000 155521 3 2021 1
#> 8 CA 11000 155531 2 2011 2
#> 9 CA 11000 155531 3 2021 3
#> 10 CA 21000 1 1 2009 4
#> # ℹ 20 more rows
#> # ℹ 19 more variables: nr_of_tree_species_established <int>,
#> # approx_nr_established_ha <dbl>, approx_nr_seedlings_ha <dbl>,
#> # approx_rubbing_damage_perc_established <dbl>,
#> # approx_rubbing_damage_perc_seedlings <dbl>,
#> # rubbing_damage_nr_established_ha <dbl>,
#> # rubbing_damage_nr_seedlings_ha <dbl>, mean_number_established_ha <dbl>, …
#>
#> $reg_by_plot_height
#> # A tibble: 76 × 13
#> plottype plot_id subplot_id period year height_class number_of_tree_species
#> <chr> <int> <int> <int> <int> <int> <int>
#> 1 CA 11000 155511 1 2000 NA 0
#> 2 CA 11000 155511 2 2011 1000 1
#> 3 CA 11000 155511 2 2011 2000 1
#> 4 CA 11000 155511 2 2011 3000 1
#> 5 CA 11000 155511 3 2021 1000 1
#> 6 CA 11000 155511 3 2021 2000 1
#> 7 CA 11000 155511 3 2021 3000 1
#> 8 CA 11000 155511 3 2021 4000 1
#> 9 CA 11000 155512 1 2000 NA 0
#> 10 CA 11000 155513 1 2000 NA 0
#> # ℹ 66 more rows
#> # ℹ 6 more variables: approx_nr_regeneration_ha <dbl>,
#> # approx_rubbing_damage_perc <dbl>, rubbing_damage_number_ha <dbl>,
#> # mean_number_of_regeneration_ha <dbl>, lci_number_of_regeneration_ha <dbl>,
#> # uci_number_of_regeneration_ha <dbl>
#>
#> $reg_by_plot_species
#> # A tibble: 99 × 24
#> plottype plot_id subplot_id period year species approx_nr_established_ha
#> <chr> <int> <int> <int> <int> <int> <dbl>
#> 1 CA 11000 155511 1 2000 NA 0
#> 2 CA 11000 155511 2 2011 7 200
#> 3 CA 11000 155511 3 2021 7 1000
#> 4 CA 11000 155512 1 2000 NA 0
#> 5 CA 11000 155513 1 2000 NA 0
#> 6 CA 11000 155521 2 2011 7 0
#> 7 CA 11000 155521 2 2011 87 0
#> 8 CA 11000 155521 3 2021 7 1700
#> 9 CA 11000 155531 2 2011 7 0
#> 10 CA 11000 155531 2 2011 87 0
#> # ℹ 89 more rows
#> # ℹ 17 more variables: approx_nr_seedlings_ha <dbl>,
#> # approx_rubbing_damage_perc_established <dbl>,
#> # approx_rubbing_damage_perc_seedlings <dbl>,
#> # rubbing_damage_nr_established_ha <dbl>,
#> # rubbing_damage_nr_seedlings_ha <dbl>, mean_number_established_ha <dbl>,
#> # lci_number_established_ha <dbl>, uci_number_established_ha <dbl>, …
#>
#> $reg_by_plot_height_species
#> # A tibble: 167 × 13
#> plottype plot_id subplot_id period year height_class species
#> <chr> <int> <int> <int> <int> <int> <int>
#> 1 CA 11000 155511 1 2000 NA NA
#> 2 CA 11000 155511 2 2011 1000 7
#> 3 CA 11000 155511 2 2011 2000 7
#> 4 CA 11000 155511 2 2011 3000 7
#> 5 CA 11000 155511 3 2021 1000 7
#> 6 CA 11000 155511 3 2021 2000 7
#> 7 CA 11000 155511 3 2021 3000 7
#> 8 CA 11000 155511 3 2021 4000 7
#> 9 CA 11000 155512 1 2000 NA NA
#> 10 CA 11000 155513 1 2000 NA NA
#> # ℹ 157 more rows
#> # ℹ 6 more variables: approx_nr_regeneration_ha <dbl>,
#> # approx_rubbing_damage_perc <dbl>, rubbing_damage_number_ha <dbl>,
#> # mean_number_of_regeneration_ha <dbl>, lci_number_of_regeneration_ha <dbl>,
#> # uci_number_of_regeneration_ha <dbl>
#>
#> $reg_by_core_area_species
#> # A tibble: 32 × 25
#> plottype plot_id period year species nr_of_subplots_with_regeneration
#> <chr> <int> <int> <int> <int> <int>
#> 1 CA 11000 1 2000 NA 3
#> 2 CA 11000 2 2011 7 3
#> 3 CA 11000 2 2011 87 2
#> 4 CA 11000 3 2021 7 3
#> 5 CA 11000 3 2021 16 1
#> 6 CA 11000 3 2021 87 1
#> 7 CA 21000 1 2009 7 3
#> 8 CA 21000 1 2009 16 3
#> 9 CA 21000 1 2009 27 3
#> 10 CA 21000 1 2009 87 3
#> # ℹ 22 more rows
#> # ℹ 19 more variables: perc_subplots_with_regeneration <dbl>,
#> # approx_nr_established_ha <dbl>, approx_nr_seedlings_ha <dbl>,
#> # approx_rubbing_damage_perc_established <dbl>,
#> # approx_rubbing_damage_perc_seedlings <dbl>,
#> # rubbing_damage_nr_established_ha <dbl>,
#> # rubbing_damage_nr_seedlings_ha <dbl>, mean_number_established_ha <dbl>, …
#>
#> $reg_by_core_area_height_species
#> # A tibble: 65 × 14
#> plottype plot_id period year height_class species nr_of_subplots_with_rege…¹
#> <chr> <int> <int> <int> <int> <int> <int>
#> 1 CA 11000 1 2000 NA NA 3
#> 2 CA 11000 2 2011 1000 7 3
#> 3 CA 11000 2 2011 1000 87 2
#> 4 CA 11000 2 2011 2000 7 2
#> 5 CA 11000 2 2011 3000 7 1
#> 6 CA 11000 3 2021 1000 7 3
#> 7 CA 11000 3 2021 1000 16 1
#> 8 CA 11000 3 2021 1000 87 1
#> 9 CA 11000 3 2021 2000 7 3
#> 10 CA 11000 3 2021 3000 7 3
#> # ℹ 55 more rows
#> # ℹ abbreviated name: ¹nr_of_subplots_with_regeneration
#> # ℹ 7 more variables: perc_subplots_with_regeneration <dbl>,
#> # approx_nr_regeneration_ha <dbl>, approx_rubbing_damage_perc <dbl>,
#> # rubbing_damage_number_ha <dbl>, mean_number_of_regeneration_ha <dbl>,
#> # lci_number_of_regeneration_ha <dbl>, uci_number_of_regeneration_ha <dbl>
#>