plot_factors | R Documentation |
plot_factors
plots factor loadings, average spatial factors, and spatio-temporal factors
plot_factors(
fit,
Report = fit$Report,
ParHat = fit$ParHat,
Data = fit$data_list,
Obj = fit$tmb_list$Obj,
SD = fit$parameter_estimates$SD,
year_labels = fit$year_labels,
category_names = fit$category_names,
RotationMethod = "PCA",
mapdetails_list = NULL,
Dim_year = NULL,
Dim_species = NULL,
projargs = "+proj=longlat",
plotdir = getwd(),
land_color = "grey",
zlim = NA,
testcutoff = 1e-04,
plot_value = "estimate",
...
)
Report |
output report, e.g., from |
ParHat |
Tagged list of fitted data, e.g., from |
Data |
tagged list of input data |
Obj |
Fitted TMB object from package 'VAST', i.e., output from ' |
SD |
standard deviation report, e.g., from |
year_labels |
character vector specifying names for labeling times |
category_names |
character-vector listing name for each category |
RotationMethod |
Method used for rotation when visualing factor decomposition results, Options: "PCA" (recommended) or "Varimax" |
mapdetails_list |
output from |
Dim_year |
Plotting dimension (row,column) for plot of years (default: square with sufficient size for number of years) |
Dim_species |
Plotting dimension (row,column) for plot of categories (default: square with sufficient size for number of categories) |
projargs |
Character passed to |
plotdir |
directory for saving plots |
land_color |
color for filling in land (use |
zlim |
two numeric values, specifying range for defining bounds of color scale.
If |
testcutoff |
tolerance for numerical rounding when confirming that rotation doesn't effect results |
plot_value |
either |
... |
additional arguments passed to |
For details regarding spatial factor analysis see https://doi.org/10.1111/2041-210X.12359
For details regarding multi-species ordination see https://doi.org/10.1016/j.fishres.2018.10.013
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