| simmr_load {simmr} | R Documentation |
Function to load in simmr data and check for errors
Description
This function takes in the mixture data, food source means and standard
deviations, and (optionally) correction factor means and standard
deviations, and concentration proportions. It performs some (non-exhaustive)
checking of the data to make sure it will run through simmr. It outputs an
object of class simmr_input.
Usage
simmr_load(
mixtures,
source_names,
source_means,
source_sds,
correction_means = NULL,
correction_sds = NULL,
concentration_means = NULL,
group = NULL
)
Arguments
mixtures |
The mixture data given as a matrix where the number of rows is the number of observations and the number of columns is the number of tracers (usually isotopes) |
source_names |
The names of the sources given as a character string |
source_means |
The means of the source values, given as a matrix where the number of rows is the number of sources and the number of columns is the number of tracers |
source_sds |
The standard deviations of the source values, given as a matrix where the number of rows is the number of sources and the number of columns is the number of tracers |
correction_means |
The means of the correction values, given as a matrix where the number of rows is the number of sources and the number of columns is the number of tracers. If not provided these are set to 0. |
correction_sds |
The standard deviations of the correction values, given as a matrix where the number of rows is the number of sources and the number of columns is the number of tracers. If not provided these are set to 0. |
concentration_means |
The means of the concentration values, given as a matrix where the number of rows is the number of sources and the number of columns is the number of tracers. These should be between 0 and 1. If not provided these are all set to 1. |
group |
A grouping variable. These can be a character or factor variable |
Details
For standard stable isotope mixture modelling, the mixture matrix will
contain a row for each individual and a column for each isotopic value.
simmr will allow for any number of isotopes and any number of
observations, within computational limits. The source means/sds should be
provided for each food source on each isotope. The correction means (usually
trophic enrichment factors) can be set as zero if required, and should be of
the same shape as the source values. The concentration dependence means
should be estimated values of the proportion of each element in the food
source in question and should be given in proportion format between 0 and 1.
At present there is no means to include concentration standard deviations.
Value
An object of class simmr_input with the following elements:
mixtures |
The mixture data |
source_neams |
Source means |
sources_sds |
Source standard deviations |
correction_means |
Correction means |
correction_sds |
Correction standard deviations |
concentration_means |
Concentration dependence means |
n_obs |
The number of observations |
n_tracers |
The number of tracers/isotopes |
n_sources |
The number of sources |
n_groups |
The number of groups |
Author(s)
Andrew Parnell <andrew.parnell@mu.ie>
See Also
See simmr_mcmc for complete examples.
Examples
# A simple example with 10 observations, 2 tracers and 4 sources
data(geese_data_day1)
simmr_1 <- with(
geese_data_day1,
simmr_load(
mixtures = mixtures,
source_names = source_names,
source_means = source_means,
source_sds = source_sds,
correction_means = correction_means,
correction_sds = correction_sds,
concentration_means = concentration_means
)
)
print(simmr_1)