| Title: | Computes Diversity Indices for Archaeological Data |
|---|---|
| Description: | Companion package of Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>. It computes Diversity Indices, decomposes several of them and computes bootstrap confidence intervals. |
| Authors: | Andreu Sansó [aut, cre], Arnaud Barat [aut], Jordi Rosell [aut] |
| Maintainer: | Andreu Sansó <[email protected]> |
| License: | GPL-2 |
| Version: | 0.4.0 |
| Built: | 2026-10-11 09:47:35 UTC |
| Source: | https://github.com/cran/diversityArch |
Computes and prints all the diversity indices
all_indices(x, groups = NULL, B = 1000, cl = 0.95)all_indices(x, groups = NULL, B = 1000, cl = 0.95)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species (in this case the Margalef and Menhinick indices and bootstrap intervals are not computed). NA values are allowed. |
groups |
Vector of dimension S of factors indicating the groups. If omitted, the decomposition of the indicators is not done. |
B |
Number of bootstrap samples. The default value is 1000. |
cl |
Confidence level. A value between 0 and 1. The default value is 0.95. |
No return value. It prints the value of all indicators
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
shannon, dec_shannon, dominance, equitability, evenness, margalef, menhinick, simpson_D, simpson_E
data(Qesem_s) all_indices(Qesem_s$HU) all_indices(Qesem_s$HU, Qesem_s$Group)data(Qesem_s) all_indices(Qesem_s$HU) all_indices(Qesem_s$HU, Qesem_s$Group)
Computes bootstrap standard error and confidence interval of the diversity indices
bs(x, ind = "shannon", B = 1000, cl = 0.95)bs(x, ind = "shannon", B = 1000, cl = 0.95)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. |
ind |
Index to be computed. The default value is "shannon". Other possible values are: "simpson_E", "simpson_D", "menhinick", "margalef", "evenness", "equitability" and "dominance". |
B |
Number of bootstrap samples. The default is 1000. |
cl |
Confidence level. A value between 0 and 1. The default is 0.95. |
s: Boostrap standard error.
ci: Confidence interval.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
shannon, dec_shannon, dominance, equitability, evenness, margalef, menhinick, simpson_D, simpson_E
data(Qesem_s) bs(Qesem_s$HU)data(Qesem_s) bs(Qesem_s$HU)
Computes bootstrap confidence intervals of the Shannon's diversity index
bs_dec(x, groups, B = 1000, cl = 0.95)bs_dec(x, groups, B = 1000, cl = 0.95)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. |
groups |
Vector of dimension S of factors indicating the groups of each species. |
B |
Number of bootstrap samples. The default is 1000. |
cl |
Confidence level. A value between 0 and 1. The default is 0.95. |
ci_bt: Confidence interval for "between groups".
ci_wt: Confidence interval for "within groups".
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) bs_dec(Qesem_s$HU, Qesem_s$Group)data(Qesem_s) bs_dec(Qesem_s$HU, Qesem_s$Group)
Computes bootstrap confidence intervals of the decomposed Shannon's diversity index using evidence from fragments
bs_frag(x, gx, f, gf, B = 1000, cl = 0.95)bs_frag(x, gx, f, gf, B = 1000, cl = 0.95)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. |
gx |
Vector of dimension S of factors indicating the group of each species. G groups. |
f |
Vector of dimension G with the number (>0) of fragments in each group |
gf |
Vector of dimension G of factors indicating the groups to which the fragments "f" belong. |
B |
Number of bootstrap samples. The default is 1000. |
cl |
Confidence level. A value between 0 and 1. The default is 0.95. |
ci_sh: Confidence interval for Shannon's diversity index with fragments.
ci_bt: Confidence interval for "between groups".
ci_wt: Confidence interval for "within groups".
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
shannon, dec_shannon, shannon_frag
data(Qesem_s) data(Qesem_f) bs_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)data(Qesem_s) data(Qesem_f) bs_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)
Computes equitability and its decomposition
dec_equit(x, groups)dec_equit(x, groups)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
groups |
Vector of dimension S of factors indicating the group of each species. |
equitability: Equitability index.
within: Within groups equitability.
between: Between groups equitability.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) dec_equit(Qesem_s$HU, Qesem_s$Group)data(Qesem_s) dec_equit(Qesem_s$HU, Qesem_s$Group)
Computes Shannon diversity and its decomposition
dec_shannon(x, groups)dec_shannon(x, groups)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
groups |
Vector of dimension S of factors indicating the group of each species. |
shannon: Shannon's total Entropy.
within: Within groups entropy.
between: Between groups entropy.
groups: A data frame with information about each group: relative frequency, internal entropy and number of species.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) dec_shannon(Qesem_s$HU, Qesem_s$Group)data(Qesem_s) dec_shannon(Qesem_s$HU, Qesem_s$Group)
Modification of the Simpson's dominance index to be restricted between 0 and 1.
dominance(x)dominance(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Dominance index (Modified Simpson's dominance index).
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) dominance(Qesem_s$HU)data(Qesem_s) dominance(Qesem_s$HU)
Computes J Pielou index know as equitability
equitability(x)equitability(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Equitability. J Pielou index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) equitability(Qesem_s$HU)data(Qesem_s) equitability(Qesem_s$HU)
Modification of Simpson's evenness index to be restricted between 0 an 1.
evenness(x)evenness(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Evenness index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) evenness(Qesem_s$HU)data(Qesem_s) evenness(Qesem_s$HU)
Computes Margalef's index
margalef(x)margalef(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. |
Margalef index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) margalef(Qesem_s$HU)data(Qesem_s) margalef(Qesem_s$HU)
Computes Menhinick's index
menhinick(x)menhinick(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. |
Menhinick index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) menhinick(Qesem_s$HU)data(Qesem_s) menhinick(Qesem_s$HU)
Data frame with number of fragments of bones of unidentified species but identified group for several levels in Qesem (Israel). Data source: Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., (2024)
data(Qesem_f)data(Qesem_f)
Data frame with 4 observations (groups) and 7 levels.
Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A.
Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024 <doi:10.1016/j.jhevol.2024.103509>
Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., Gopher, A. & Rosell-Ardèvol, J., 2026 <doi:10.1007/s10816-026-09802-3>. Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024 <doi:10.1016/j.jhevol.2024.103509>
data(Qesem_f) names(data) # The following example replicates some of the results in # Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., # Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., # Gopher, A. & Rosell-Ardèvol, J. 2026. <doi:10.1007/s10816-026-09802-3>. shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)data(Qesem_f) names(data) # The following example replicates some of the results in # Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., # Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., # Gopher, A. & Rosell-Ardèvol, J. 2026. <doi:10.1007/s10816-026-09802-3>. shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)
Data frame with number of bones of different species and diferent levels in Qesem (Israel), and a factor related to the size of the animal. Data source: Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., (2024)
data(Qesem_s)data(Qesem_s)
Data frame with 15 observations and 7 levels.
Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A.
Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024 <doi:10.1016/j.jhevol.2024.103509>
Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., Gopher, A. & Rosell-Ardèvol, J., 2026 <doi:10.1007/s10816-026-09802-3>. Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024 <doi:10.1016/j.jhevol.2024.103509>
data(Qesem_s) names(Qesem_s) # The following example replicates some of the results in # Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., # Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., # Gopher, A. & Rosell-Ardèvol, J. 2026. <doi:10.1007/s10816-026-09802-3>. all_indices(Qesem_s$HU)data(Qesem_s) names(Qesem_s) # The following example replicates some of the results in # Barat, A. Sansó, A. Arilla-Osuna, M. Blasco, R., Pérez-Fernández, I., # Cifuentes-Alcobenda, G. Llorente, R., Vivar-Ríos, D., Assaf, E. Barkai, R., # Gopher, A. & Rosell-Ardèvol, J. 2026. <doi:10.1007/s10816-026-09802-3>. all_indices(Qesem_s$HU)
Computes Shannon's diversity index
shannon(x)shannon(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Shannon's diversity index (Entropy).
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) shannon(Qesem_s$HU)data(Qesem_s) shannon(Qesem_s$HU)
Computes Shannon diversity and its decomposition
shannon_frag(x, gx, f, gf)shannon_frag(x, gx, f, gf)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species. NA values are allowed. 0 values are converted to NA. |
gx |
Vector of dimension S of factors indicating the group of each species. G groups. |
f |
Vector of dimension G with the number (>0) of fragments in each group |
gf |
Vector of dimension G of factors indicating the groups to which the fragments "f" belong. |
shannon: Shannon's total Entropy.
within: Within groups entropy.
between: Between groups entropy.
groups: A data frame with information about each group: relative frequency, internal entropy and number of species.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) data(Qesem_f) shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)data(Qesem_s) data(Qesem_f) shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)
Computes Simpson's dominance index.
simpson_D(x)simpson_D(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Simpson's dominance index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) simpson_D(Qesem_s$HU)data(Qesem_s) simpson_D(Qesem_s$HU)
Computes Simpson's evenness index.
simpson_E(x)simpson_E(x)
x |
Vector of dimension S (number of species) with the number of individuals observed in each species, or the distribution frequencies of species. NA values are allowed. |
Simpson's evenness index.
Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>.
data(Qesem_s) simpson_E(Qesem_s$HU)data(Qesem_s) simpson_E(Qesem_s$HU)