Package 'diversityArch'

Diversity indices

Description

Computes and prints all the diversity indices

Usage

all_indices(x, groups = NULL, B = 1000, cl = 0.95)

Arguments

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.
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 is 1000.
cl	Confidence level. A value between 0 and 1. The default is 0.95.

Value

No return value. It prints the value of all indicators

References

"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): Quantifying Diversity through Entropy Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon, dec_shannon, dominance, equitability, evenness, margalef, menhinick, simpson_D, simpson_E

Examples

data(Qesem_s)
all_indices(Qesem_s$HU)
all_indices(Qesem_s$HU, Qesem_s$Group)

---

Bootstrap estimates of the diversity indices

Description

Computes bootstrap standard error and confidence interval of the diversity indices

Usage

bs(x, ind = "shannon", B = 1000, cl = 0.95)

Arguments

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.
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.

Value

• s: Boostrap standard error.

• ci: Confidence interval.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon, dec_shannon, dominance, equitability, evenness, margalef, menhinick, simpson_D, simpson_E

Examples

data(Qesem_s)
bs(Qesem_s$HU)

---

Bootstrap estimates of the decomposed Shannon's diversity index

Description

Computes bootstrap confidence intervals of the Shannon's diversity index

Usage

bs_dec(x, groups, B = 1000, cl = 0.95)

Arguments

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.
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.

Value

• ci_bt: Confidence interval for "between groups".

• ci_wt: Confidence interval for "within groups".

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon, dec_shannon

Examples

data(Qesem_s)
bs_dec(Qesem_s$HU, Qesem_s$Group)

---

Bootstrap estimates of the decomposed Shannon's diversity index with fragments

Description

Computes bootstrap confidence intervals of the decomposed Shannon's diversity index using evidence from fragments

Usage

bs_frag(x, gx, f, gf, B = 1000, cl = 0.95)

Arguments

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.
B	Number of bootstrap samples. The default is 1000.
cl	Confidence level. A value between 0 and 1. The default is 0.95.

Value

• 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".

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon, dec_shannon, shannon_frag

Examples

data(Qesem_s)
data(Qesem_f)
bs_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)

---

Decomposition of the equitability index

Description

Computes equitability and its decomposition

Usage

dec_equit(x, groups)

Arguments

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.
groups	Vector of dimension S of factors indicating the group of each species.

Value

• equitability: Equitability index.

• within: Within groups equitability.

• between: Between groups equitability.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

dec_shannon

Examples

data(Qesem_s)
dec_equit(Qesem_s$HU, Qesem_s$Group)

---

Shannon diversity decomposition

Description

Computes Shannon diversity and its decomposition

Usage

dec_shannon(x, groups)

Arguments

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.
groups	Vector of dimension S of factors indicating the group of each species.

Value

• 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.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon

Examples

data(Qesem_s)
dec_shannon(Qesem_s$HU, Qesem_s$Group)

---

Dominance index

Description

Modification of the Simpson's dominance index to be restricted between 0 and 1.

Usage

dominance(x)

Arguments

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.

Value

Dominance index (Modified Simpson's dominance index).

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

simpson_D

Examples

data(Qesem_s)
dominance(Qesem_s$HU)

---

Equitability. J Pielou index

Description

Computes J Pielou index know as equitability

Usage

equitability(x)

Arguments

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.

Value

Equitability. J Pielou index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon

Examples

data(Qesem_s)
equitability(Qesem_s$HU)

---

Evenness index

Description

Modification of Simpson's evenness index to be restricted between 0 an 1.

Usage

evenness(x)

Arguments

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.

Value

Evenness index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

simpson_E

Examples

data(Qesem_s)
evenness(Qesem_s$HU)

---

Margalef index

Description

Computes Margalef's index

Usage

margalef(x)

Arguments

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.

Value

Margalef index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

Examples

data(Qesem_s)
margalef(Qesem_s$HU)

---

Menhinick index

Description

Computes Menhinick's index

Usage

menhinick(x)

Arguments

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.

Value

Menhinick index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

Examples

data(Qesem_s)
menhinick(Qesem_s$HU)

---

Data used in the examples

Description

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)

Usage

data(Qesem_f)

Value

Data frame with 4 observations (groups) and 7 levels.

Author(s)

Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A.

Source

Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024. Exploring the lack of articular ends at the Middle Pleistocene site of Qesem Cave, Israel. Journal of Human Evolution 189, 103509. doi:10.1016/j.jhevol.2024.103509

References

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., 2025. Quantifying Diversity through Entropy Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave. Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024. Exploring the lack of articular ends at the Middle Pleistocene site of Qesem Cave, Israel. Journal of Human Evolution 189, 103509. doi:10.1016/j.jhevol.2024.103509

Examples

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., 2025. "Quantifying Diversity through Entropy
# Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave".
shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)

---

Data used in the examples

Description

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)

Usage

data(Qesem_s)

Value

Data frame with 15 observations and 7 levels.

Author(s)

Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A.

Source

Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024. Exploring the lack of articular ends at the Middle Pleistocene site of Qesem Cave, Israel. Journal of Human Evolution 189, 103509. doi:10.1016/j.jhevol.2024.103509

References

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., 2025. Quantifying Diversity through Entropy Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave. Blasco, R., Rosell, J., Assaf, E., Barkai, R., Gopher, A., 2024. Exploring the lack of articular ends at the Middle Pleistocene site of Qesem Cave, Israel. Journal of Human Evolution 189, 103509. doi:10.1016/j.jhevol.2024.103509

Examples

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., 2025. "Quantifying Diversity through Entropy
# Decomposition. Insights into Hominin Occupation and Carcass Processing at Qesem cave".
all_indices(Qesem_s$HU)

---

Shannon diversity index

Description

Computes Shannon's diversity index

Usage

shannon(x)

Arguments

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.

Value

Shannon's diversity index (Entropy).

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

dec_shannon, equitability

Examples

data(Qesem_s)
shannon(Qesem_s$HU)

---

Shannon diversity decomposition

Description

Computes Shannon diversity and its decomposition

Usage

shannon_frag(x, gx, f, gf)

Arguments

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.

Value

• 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.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

shannon

Examples

data(Qesem_s)
data(Qesem_f)
shannon_frag(Qesem_s$HU, Qesem_s$Group, Qesem_f$HU, Qesem_f$Group)

---

Simpson's dominance index

Description

Computes Simpson's dominance index.

Usage

simpson_D(x)

Arguments

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.

Value

Simpson's dominance index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

dominance, simpson_E

Examples

data(Qesem_s)
simpson_D(Qesem_s$HU)

---

Simpson's evenness index

Description

Computes Simpson's evenness index.

Usage

simpson_E(x)

Arguments

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.

Value

Simpson's evenness index.

References

"Quantifying Diversity through Entropy Decomposition: Insights into Hominin Occupation and Carcass Processing at Qesem cave"

See Also

evenness, simpson_D

Examples

data(Qesem_s)
simpson_E(Qesem_s$HU)

---