README.md
In PaulESantos/diversity.tool: Tools for biodiversity data manipulation
diversity.tool
The goal of diversity.tool is to …
Installation
You can install the development version from
GitHub with:
# install.packages("devtools")
devtools::install_github("PaulESantos/diversity.tool")
Example
This is a basic example which shows you how to solve a common problem:
- Transform community matrix to tibble:
library(diversity.tool)
library(vegan)
data("dune")
dune_tbl <- dune %>% comm_to_tbl()
dune_tbl
#> # A tibble: 197 x 3
#> site species abundance
#> <chr> <chr> <dbl>
#> 1 1 Achimill 1
#> 2 1 Elymrepe 4
#> 3 1 Lolipere 7
#> 4 1 Poaprat 4
#> 5 1 Poatriv 2
#> 6 2 Achimill 3
#> 7 2 Alopgeni 2
#> 8 2 Bellpere 3
#> 9 2 Bromhord 4
#> 10 2 Elymrepe 4
#> # ... with 187 more rows
- Or build a community matrix from a tibble:
dune_comm <- dune_tbl %>%
tbl_to_comm(site, species, abundance)
dune_comm[1:6, 1:6]
#> Achimill Elymrepe Lolipere Poaprat Poatriv Alopgeni
#> 1 1 4 7 4 2 0
#> 2 3 4 5 4 7 2
#> 3 0 4 6 5 6 7
#> 4 0 4 5 4 5 2
#> 5 2 4 2 2 6 0
#> 6 2 0 6 3 4 0
- IVI index
data("bci")
bci %>%
ivi_index(sub_plot, species, area_basal)
#> # A tibble: 93 x 8
#> # Rowwise:
#> species abundance n_splot area_basal dens_rela freq_rela dom_rela ivi
#> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Alseis.black~ 25 25 29302. 4.97 5.61 5.37 5.32
#> 2 Oenocarpus.m~ 22 22 25945. 4.37 4.93 4.76 4.69
#> 3 Poulsenia.ar~ 24 24 18738. 4.77 5.38 3.43 4.53
#> 4 Hirtella.tri~ 21 21 22910. 4.17 4.71 4.20 4.36
#> 5 Cecropia.ins~ 22 12 28362. 4.37 2.69 5.20 4.09
#> 6 Virola.sebif~ 17 17 18487. 3.38 3.81 3.39 3.53
#> 7 Trichilia.tu~ 18 18 13994. 3.58 4.04 2.56 3.39
#> 8 Prioria.copa~ 20 13 15690. 3.98 2.91 2.88 3.26
#> 9 Socratea.exo~ 15 15 17793. 2.98 3.36 3.26 3.20
#> 10 Simarouba.am~ 14 14 18723. 2.78 3.14 3.43 3.12
#> # ... with 83 more rows
-
Rank-abundance calculation:
- All sample units as one community
dune %>%
rankabund()
#> # A tibble: 30 x 7
#> species abun rank proportion acumfreq logabun rel.abund
#> <chr> <dbl> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 Poatriv 63 1 9.20 9.20 1.80 0.0920
#> 2 Lolipere 58 2 8.47 17.7 1.76 0.0847
#> 3 Scorautu 54 3 7.88 25.5 1.73 0.0788
#> 4 Bracruta 49 4 7.15 32.7 1.69 0.0715
#> 5 Agrostol 48 5 7.01 39.7 1.68 0.0701
#> 6 Poaprat 48 6 7.01 46.7 1.68 0.0701
#> 7 Trifrepe 47 7 6.86 53.6 1.67 0.0686
#> 8 Alopgeni 36 8 5.26 58.8 1.56 0.0526
#> 9 Elymrepe 26 9 3.80 62.6 1.41 0.0380
#> 10 Planlanc 26 10 3.80 66.4 1.41 0.0380
#> # ... with 20 more rows
- Each sample units as a different community
dune %>%
rankabund(group = "site")
#> # A tibble: 197 x 8
#> # Groups: sites [20]
#> sites species abundance rank proportion acumfreq logabun rel.abund
#> <chr> <chr> <dbl> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 Lolipere 7 1 38.9 38.9 0.845 0.389
#> 2 1 Elymrepe 4 2 22.2 61.1 0.602 0.222
#> 3 1 Poaprat 4 3 22.2 83.3 0.602 0.222
#> 4 1 Poatriv 2 4 11.1 94.4 0.301 0.111
#> 5 1 Achimill 1 5 5.56 100 0 0.0556
#> 6 10 Lolipere 6 1 14.0 14.0 0.778 0.140
#> 7 10 Trifrepe 6 2 14.0 27.9 0.778 0.140
#> 8 10 Achimill 4 3 9.30 37.2 0.602 0.0930
#> 9 10 Anthodor 4 4 9.30 46.5 0.602 0.0930
#> 10 10 Bromhord 4 5 9.30 55.8 0.602 0.0930
#> # ... with 187 more rows
+Rank-abundance plot
dune %>%
rankabund_plot()
- Transform a
dist matrix to tibble:
dune_dist <- vegdist(dune[1:10, 1:10])
dune_dist
#> 1 2 3 4 5 6 7
#> 2 0.8461538
#> 3 1.0000000 0.6800000
#> 4 1.0000000 0.5172414 0.4666667
#> 5 0.8181818 0.4545455 0.8260870 0.7037037
#> 6 0.6666667 0.7647059 1.0000000 1.0000000 0.3333333
#> 7 0.7142857 0.5555556 1.0000000 0.8260870 0.2500000 0.2727273
#> 8 1.0000000 0.8095238 0.1818182 0.5384615 1.0000000 1.0000000 1.0000000
#> 9 1.0000000 0.7777778 0.3684211 0.5652174 1.0000000 1.0000000 1.0000000
#> 10 0.8666667 0.3076923 0.8518519 0.6774194 0.1666667 0.4736842 0.4000000
#> 8 9
#> 2
#> 3
#> 4
#> 5
#> 6
#> 7
#> 8
#> 9 0.2000000
#> 10 1.0000000 1.0000000
dune_dist_tbl <- dune_dist %>%
as_distbl()
dune_dist_tbl
#> # A tibble: 10 x 11
#> comm `1` `2` `3` `4` `5` `6` `7` `8` `9` `10`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 NA 0.846 1 1 0.818 0.667 0.714 1 1 0.867
#> 2 2 0.846 NA 0.68 0.517 0.455 0.765 0.556 0.810 0.778 0.308
#> 3 3 1 0.68 NA 0.467 0.826 1 1 0.182 0.368 0.852
#> 4 4 1 0.517 0.467 NA 0.704 1 0.826 0.538 0.565 0.677
#> 5 5 0.818 0.455 0.826 0.704 NA 0.333 0.25 1 1 0.167
#> 6 6 0.667 0.765 1 1 0.333 NA 0.273 1 1 0.474
#> 7 7 0.714 0.556 1 0.826 0.25 0.273 NA 1 1 0.4
#> 8 8 1 0.810 0.182 0.538 1 1 1 NA 0.2 1
#> 9 9 1 0.778 0.368 0.565 1 1 1 0.2 NA 1
#> 10 10 0.867 0.308 0.852 0.677 0.167 0.474 0.4 1 1 NA
- Transform to long format:
dune_dist_tbl %>%
long_distbl()
#> # A tibble: 45 x 3
#> comm_x comm_y index
#> <chr> <chr> <dbl>
#> 1 2 1 0.846
#> 2 3 1 1
#> 3 3 2 0.68
#> 4 4 1 1
#> 5 4 2 0.517
#> 6 4 3 0.467
#> 7 5 1 0.818
#> 8 5 2 0.455
#> 9 5 3 0.826
#> 10 5 4 0.704
#> # ... with 35 more rows
Citation
To cite the ppendemic package, please use:
citation("diversity.tool")
#>
#> To cite package 'diversity.tool' in publications use:
#>
#> Paul Efren Santos Andrade (2021). diversity.tool: Tools for
#> biodiversity data manipulation. R package version 0.0.0.1.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {diversity.tool: Tools for biodiversity data manipulation},
#> author = {Paul Efren {Santos Andrade}},
#> year = {2021},
#> note = {R package version 0.0.0.1},
#> }
PaulESantos/diversity.tool documentation built on July 29, 2022, 8:20 a.m.
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
diversity.tool
The goal of diversity.tool is to …
Installation
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("PaulESantos/diversity.tool")
Example
This is a basic example which shows you how to solve a common problem:
- Transform community matrix to tibble:
library(diversity.tool)
library(vegan)
data("dune")
dune_tbl <- dune %>% comm_to_tbl()
dune_tbl
#> # A tibble: 197 x 3
#> site species abundance
#> <chr> <chr> <dbl>
#> 1 1 Achimill 1
#> 2 1 Elymrepe 4
#> 3 1 Lolipere 7
#> 4 1 Poaprat 4
#> 5 1 Poatriv 2
#> 6 2 Achimill 3
#> 7 2 Alopgeni 2
#> 8 2 Bellpere 3
#> 9 2 Bromhord 4
#> 10 2 Elymrepe 4
#> # ... with 187 more rows
- Or build a community matrix from a tibble:
dune_comm <- dune_tbl %>%
tbl_to_comm(site, species, abundance)
dune_comm[1:6, 1:6]
#> Achimill Elymrepe Lolipere Poaprat Poatriv Alopgeni
#> 1 1 4 7 4 2 0
#> 2 3 4 5 4 7 2
#> 3 0 4 6 5 6 7
#> 4 0 4 5 4 5 2
#> 5 2 4 2 2 6 0
#> 6 2 0 6 3 4 0
- IVI index
data("bci")
bci %>%
ivi_index(sub_plot, species, area_basal)
#> # A tibble: 93 x 8
#> # Rowwise:
#> species abundance n_splot area_basal dens_rela freq_rela dom_rela ivi
#> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Alseis.black~ 25 25 29302. 4.97 5.61 5.37 5.32
#> 2 Oenocarpus.m~ 22 22 25945. 4.37 4.93 4.76 4.69
#> 3 Poulsenia.ar~ 24 24 18738. 4.77 5.38 3.43 4.53
#> 4 Hirtella.tri~ 21 21 22910. 4.17 4.71 4.20 4.36
#> 5 Cecropia.ins~ 22 12 28362. 4.37 2.69 5.20 4.09
#> 6 Virola.sebif~ 17 17 18487. 3.38 3.81 3.39 3.53
#> 7 Trichilia.tu~ 18 18 13994. 3.58 4.04 2.56 3.39
#> 8 Prioria.copa~ 20 13 15690. 3.98 2.91 2.88 3.26
#> 9 Socratea.exo~ 15 15 17793. 2.98 3.36 3.26 3.20
#> 10 Simarouba.am~ 14 14 18723. 2.78 3.14 3.43 3.12
#> # ... with 83 more rows
-
Rank-abundance calculation:
- All sample units as one community
dune %>%
rankabund()
#> # A tibble: 30 x 7
#> species abun rank proportion acumfreq logabun rel.abund
#> <chr> <dbl> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 Poatriv 63 1 9.20 9.20 1.80 0.0920
#> 2 Lolipere 58 2 8.47 17.7 1.76 0.0847
#> 3 Scorautu 54 3 7.88 25.5 1.73 0.0788
#> 4 Bracruta 49 4 7.15 32.7 1.69 0.0715
#> 5 Agrostol 48 5 7.01 39.7 1.68 0.0701
#> 6 Poaprat 48 6 7.01 46.7 1.68 0.0701
#> 7 Trifrepe 47 7 6.86 53.6 1.67 0.0686
#> 8 Alopgeni 36 8 5.26 58.8 1.56 0.0526
#> 9 Elymrepe 26 9 3.80 62.6 1.41 0.0380
#> 10 Planlanc 26 10 3.80 66.4 1.41 0.0380
#> # ... with 20 more rows
- Each sample units as a different community
dune %>%
rankabund(group = "site")
#> # A tibble: 197 x 8
#> # Groups: sites [20]
#> sites species abundance rank proportion acumfreq logabun rel.abund
#> <chr> <chr> <dbl> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 Lolipere 7 1 38.9 38.9 0.845 0.389
#> 2 1 Elymrepe 4 2 22.2 61.1 0.602 0.222
#> 3 1 Poaprat 4 3 22.2 83.3 0.602 0.222
#> 4 1 Poatriv 2 4 11.1 94.4 0.301 0.111
#> 5 1 Achimill 1 5 5.56 100 0 0.0556
#> 6 10 Lolipere 6 1 14.0 14.0 0.778 0.140
#> 7 10 Trifrepe 6 2 14.0 27.9 0.778 0.140
#> 8 10 Achimill 4 3 9.30 37.2 0.602 0.0930
#> 9 10 Anthodor 4 4 9.30 46.5 0.602 0.0930
#> 10 10 Bromhord 4 5 9.30 55.8 0.602 0.0930
#> # ... with 187 more rows
+Rank-abundance plot
dune %>%
rankabund_plot()
- Transform a
distmatrix to tibble:
dune_dist <- vegdist(dune[1:10, 1:10])
dune_dist
#> 1 2 3 4 5 6 7
#> 2 0.8461538
#> 3 1.0000000 0.6800000
#> 4 1.0000000 0.5172414 0.4666667
#> 5 0.8181818 0.4545455 0.8260870 0.7037037
#> 6 0.6666667 0.7647059 1.0000000 1.0000000 0.3333333
#> 7 0.7142857 0.5555556 1.0000000 0.8260870 0.2500000 0.2727273
#> 8 1.0000000 0.8095238 0.1818182 0.5384615 1.0000000 1.0000000 1.0000000
#> 9 1.0000000 0.7777778 0.3684211 0.5652174 1.0000000 1.0000000 1.0000000
#> 10 0.8666667 0.3076923 0.8518519 0.6774194 0.1666667 0.4736842 0.4000000
#> 8 9
#> 2
#> 3
#> 4
#> 5
#> 6
#> 7
#> 8
#> 9 0.2000000
#> 10 1.0000000 1.0000000
dune_dist_tbl <- dune_dist %>%
as_distbl()
dune_dist_tbl
#> # A tibble: 10 x 11
#> comm `1` `2` `3` `4` `5` `6` `7` `8` `9` `10`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 NA 0.846 1 1 0.818 0.667 0.714 1 1 0.867
#> 2 2 0.846 NA 0.68 0.517 0.455 0.765 0.556 0.810 0.778 0.308
#> 3 3 1 0.68 NA 0.467 0.826 1 1 0.182 0.368 0.852
#> 4 4 1 0.517 0.467 NA 0.704 1 0.826 0.538 0.565 0.677
#> 5 5 0.818 0.455 0.826 0.704 NA 0.333 0.25 1 1 0.167
#> 6 6 0.667 0.765 1 1 0.333 NA 0.273 1 1 0.474
#> 7 7 0.714 0.556 1 0.826 0.25 0.273 NA 1 1 0.4
#> 8 8 1 0.810 0.182 0.538 1 1 1 NA 0.2 1
#> 9 9 1 0.778 0.368 0.565 1 1 1 0.2 NA 1
#> 10 10 0.867 0.308 0.852 0.677 0.167 0.474 0.4 1 1 NA
- Transform to long format:
dune_dist_tbl %>%
long_distbl()
#> # A tibble: 45 x 3
#> comm_x comm_y index
#> <chr> <chr> <dbl>
#> 1 2 1 0.846
#> 2 3 1 1
#> 3 3 2 0.68
#> 4 4 1 1
#> 5 4 2 0.517
#> 6 4 3 0.467
#> 7 5 1 0.818
#> 8 5 2 0.455
#> 9 5 3 0.826
#> 10 5 4 0.704
#> # ... with 35 more rows
Citation
To cite the ppendemic package, please use:
citation("diversity.tool")
#>
#> To cite package 'diversity.tool' in publications use:
#>
#> Paul Efren Santos Andrade (2021). diversity.tool: Tools for
#> biodiversity data manipulation. R package version 0.0.0.1.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {diversity.tool: Tools for biodiversity data manipulation},
#> author = {Paul Efren {Santos Andrade}},
#> year = {2021},
#> note = {R package version 0.0.0.1},
#> }
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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