Quantitative ethnobotany analysis

Cory Whitney

2019-01-19

The ethnobotanyR package can be used to calculate common quantitative ethnobotany indices to assess the cultural significance of plant species based on informant consensus. The package closely follows two papers, one by Tardio and Pardo-de-Santayana (2008) and another by Whitney et al. (2018).

An example data set is provided to show what the layout for standard ethnobotany data should be like to interface with the ethnobotanyR package. Start by loading the ethnobotanydata.rda’ file using load("ethnobotanydata.rda"). This is an ethnobotany data set with a column of knowledge holder identifiers informant and one of species names sp_name. The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values). The file is included with this package but can also be downloaded from GitHub https://github.com/CWWhitney/ethnobotanyR/tree/master/data.

load("ethnobotanydata.rda")

The use report URs() function calculates the use report (UR) for each species in the data set.

ethnobotanyR::URs(ethnobotanydata)
#> [1] "Total number of Use Reports (URs) for each species in the data set"
#>   sp_name URs
#> 3    sp_c  52
#> 1    sp_a  43
#> 4    sp_d  43
#> 2    sp_b  36

The URum function calculates the sum of all ethnobotany use reports (UR) for each species in the data set.

ethnobotanyR::URsum(ethnobotanydata)
#> [1] "Sum of all Use Reports (UR) for all species in the data set"
#> [1] 174

The CIs function calculates the Cultural Importance Index (CI) for each species in the data set.

ethnobotanyR::CIs(ethnobotanydata)
#> [1] "Cultural Importance index (CI) for each species in the data set"
#>   sp_name        Ci
#> 3    sp_c 0.2363636
#> 1    sp_a 0.1954545
#> 4    sp_d 0.1954545
#> 2    sp_b 0.1636364

The FCs function calculates the frequency of citation (FC) for each species in the data set.

ethnobotanyR::FCs(ethnobotanydata)
#> [1] "Frequency of citation (FC) for each species in the data set"
#>   sp_name FCs
#> 3    sp_c  17
#> 1    sp_a  15
#> 2    sp_b  12
#> 4    sp_d  12

The NUs() function calculates the number of uses (NU) for each species in the data set.

ethnobotanyR::NUs(ethnobotanydata)
#> [1] "Number of Uses (NU) for each species in the data set"
#>   sp_name NUs
#> 3    sp_c   8
#> 4    sp_d   8
#> 1    sp_a   7
#> 2    sp_b   7

The RFCs() function calculates the relative frequency of citation (RFC) for each species in the data set.

ethnobotanyR::RFCs(ethnobotanydata)
#> [1] "Relative Frequency of Citation (RFC) for each species in the data set"
#>   sp_name RFCs
#> 3    sp_c 0.85
#> 1    sp_a 0.75
#> 2    sp_b 0.60
#> 4    sp_d 0.60

The RIs() function calculates the relative importance index (RI) for each species in the data set.

ethnobotanyR::RIs(ethnobotanydata)
#> [1] "Relative Importance Index (RI) for each species in the data set"
#>   sp_name       RIs
#> 3    sp_c 1.0000000
#> 1    sp_a 0.8786765
#> 4    sp_d 0.8529412
#> 2    sp_b 0.7904412

The UVS() function calculates the use value (UV) index for each species in the data set.

ethnobotanyR::UVs(ethnobotanydata)
#> [1] "Use Value index (UV) for each species in the data set"
#>   sp_name  UVs
#> 3    sp_c 2.60
#> 1    sp_a 2.15
#> 4    sp_d 2.15
#> 2    sp_b 1.80

The following chord plots are made using functions from the circlize package. An example of the application of chord plots in ethnobotany is described by Whitney et al. (2018).

The ethnoChord() function creates a chord diagram of ethnobotany uses and species.

ethnobotanyR::ethnoChord(ethnobotanydata)

#> [1] "Chord diagram for each use related to each species in the data set"

The ethnoChordUser() function creates a chord diagram of informants and species uses for ethnobotany studies.

ethnobotanyR::ethnoChordUser(ethnobotanydata)

#> [1] "Chord diagram for each use related to each informant in the data set"