R/bootstrap_glm.r
bootstrap_glm.RdUses bootstrap to estimate variance of matrix_glm estimates. Takes a matrix of observations, and fits the specified GLM on each species. It perfomrs N bootstrap pesudoreplicates and returns the matrix of coefficients, for the original dataset as well as bootstrap estimates. It uses glm_matrix() to fit each of the pseudoreplicates.
bootstrap_glm(x, ...) # S3 method for default bootstrap_glm(x, Map, formula, family = poisson(link = "log"), response.name = "Count", N = 100, verbose = FALSE, ...) # S3 method for Dataset bootstrap_glm(x, formula, family = poisson(link = "log"), response.name = "Count", N = 100, verbose = FALSE, ...)
| x | Either an abundance matrix with samples as columns or a Dataset object |
|---|---|
| ... | Extra parameters for matrix_glm, which will in turn pass them to glm. Typically it is seful to specify the 'control' option. |
| Map | A mapping file with sample metadata if x is a matrix. A data.frame containing the variables to be modelled as columns and samples as rows. The rows should be named with sample IDs and must correspond to the column names from x if an abundance matrix was passed. |
| formula | The formula for the GLM model.Only the right hand side of the equation must be passed, and anything on the left side wild be silently ignored. |
| family | The model family. See help of glm and family for details |
| response.name | The name to give to the response variable |
| N | The number of bootstrap pseudoreplicates |
| verbose | Logical. If true each call to matrix_glm will print progress information. |
A bootglm object which is a list containing the following elements:
A matrix.glm object containing the output of matrix.glm()
on the original data.
A list containing elements: 1) coefficients, a three-dimensioanl array containing the matrix of coefficients for each bootstrap pseudoreplicate; and 2) SE, a three-dimensional array containing the matrix of standard errors for each bootstrap pseudoreplicate.
A matrix of coefficients calculated as the mean accross each bootstrap pseudoreplicates.
Function call via match.call().
GLM model family. An object of class family.
Matrix of dimensions (number iof samples) x (number of pseudoreplicates), where the i-column gives the sample ID, of the samples used for the i-th pseudoreplicate.
Number of bootstrap pseudoreplicates performed.
This works by calling matrix_glm() on the original data, and each pf the N bootstrap pseudoreplicates generated.