Perform PlasmoMAPI analysis — pm_analysis • PlasmoMAPI

TODO.

pm_analysis(
  proj,
  n_perms = 1000,
  n_breaks = 50,
  min_dist = 0,
  max_dist = Inf,
  min_group_size = 5,
  check_internal = FALSE,
  report_progress = TRUE,
  pb_markdown = FALSE
)

Arguments

proj	object of class `pm_project`.
n_perms	number of permutations in test.
n_breaks	values are broken into this many groups based on spatial distances. Permutation testing then occurs within groups. Hence, a larger value of `n_breaks` does a better job of conditioning on spatial distance, but comes at the cost of statistical power in permutation testing. A warning is printed if any group ends up containing fewer than 10 edges.
min_dist, max_dist	minimum and maximum edge lengths to be included in the analysis. Anything outside this range is ignored.
min_group_size	minimum number of edges within a spatial permutation group, otherwise edges within this group are replaced with `NA`.
check_internal	if `TRUE` then spatial distance is used as statistical distance in place of the loaded matrix. This option acts as an internal check, because statistical significance should not be seen when spatial distance is tested against itself. If you do see areas of significance then it is likely you are not using enough `n_breaks` to account for the trend with distance in the data.
report_progress	if `TRUE` then a progress bar is printed to the console during the permutation testing procedure.
pb_markdown	whether to run progress bars in markdown mode, in which case they are updated once at the end to avoid large amounts of output.