A collection of classes that represent archaeological data. This package provides a set of S4 classes that represent different special types of matrix (absolute/relative frequency, presence/absence data, co-occurrence matrix, etc.) upon which package developers can build subclasses. It also provides a set of generic methods (mutators and coercion mechanisms) and functions (e.g. predicates). In addition, a few classes of general interest (e.g. that represent stratigraphic relationships) are implemented.
You can install the released version of arkhe from CRAN with:
install.packages("arkhe")
Or install the development version from GitHub with:
# install.packages("remotes") remotes::install_github("nfrerebeau/arkhe")
arkhe provides a set of S4 classes that represent different special types of matrix.
CountMatrix
represents absolute frequency data,AbundanceMatrix
represents relative frequency data,OccurrenceMatrix
represents a co-occurrence matrix,SimilarityMatrix
represents a (dis)similarity matrix,IncidenceMatrix
represents presence/absence data,StratigraphicMatrix
represents stratigraphic relationships.It assumes that you keep your data tidy: each variable (type/taxa) must be saved in its own column and each observation (assemblage/sample) must be saved in its own row.
These new classes are of simple use, on the same way as the base matrix
:
# Define a count data matrix # (data will be rounded to zero decimal places, then coerced with as.integer) quanti <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 10, ncol = 10) # Define a logical matrix # (data will be coerced with as.logical) quali <- IncidenceMatrix(data = sample(0:1, 100, TRUE), nrow = 10, ncol = 10)
arkhe uses coercing mechanisms (with validation methods) for data type conversions:
## Create a count matrix A0 <- matrix(data = sample(0:10, 100, TRUE), nrow = 10, ncol = 10) ## Coerce to absolute frequencies A1 <- as_count(A0) ## Coerce to relative frequencies B <- as_abundance(A1) ## Row sums are internally stored before coercing to a frequency matrix ## (use get_totals() to get these values) ## This allows to restore the source data A2 <- as_count(B) all(A1 == A2) #> [1] TRUE ## Coerce to presence/absence C <- as_incidence(A1) ## Coerce to a co-occurrence matrix D <- as_occurrence(A1)
Many familiar methods and group generic functions are available for all *Matrix
classes (such as length
, dim
, rowSums
, rowMeans
, Arith
, Compare
, Logic
…). In addition, all functions that call as.matrix
or as.data.frame
first on their main argument should work (e. g. apply
).
rowSums(A1) #> row1 row2 row3 row4 row5 row6 row7 row8 row9 row10 #> 48 51 54 46 47 44 61 49 60 50 apply(X = A1, MARGIN = 1, FUN = sum) #> row1 row2 row3 row4 row5 row6 row7 row8 row9 row10 #> 48 51 54 46 47 44 61 49 60 50
Please note that all *Matrix
classes extend the R base matrix
, but the S3 part of the object does not store the data. Values are stored in a specific slot (allowing type checking).
X <- CountMatrix(data = sample(0:10, 25, TRUE), nrow = 5, ncol = 5) ## Get the S3 part S3Part(X, strictS3 = TRUE) #> col1 col2 col3 col4 col5 #> row1 1 6 11 16 21 #> row2 2 7 12 17 22 #> row3 3 8 13 18 23 #> row4 4 9 14 19 24 #> row5 5 10 15 20 25 ## Coerce to an S3 matrix as.matrix(X) #> col1 col2 col3 col4 col5 #> row1 4 1 1 2 6 #> row2 10 0 5 0 8 #> row3 6 10 7 1 10 #> row4 9 0 7 2 7 #> row5 5 5 1 5 7
Please note that the arkhe project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.