shark_plot: Individual contributions to dOFV

In xpose.xtras: Extra Functionality for the 'xpose' Package

Individual contributions to dOFV

Description

This is intended to match the overall behavior of dOFV.vs.id() in xpose4, within the framework of the xpose_set object.

dofv_vs_id is an alias of the function shark_plot, for recognition.

Usage

shark_plot(
  xpdb_s,
  ...,
  .inorder = FALSE,
  type = "plt",
  alpha = 0.05,
  df = "guess",
  text_cutoff = 0.8,
  title = "Individual contributions to dOFV | @run",
  subtitle = "Based on @nind individuals, OFVs: @ofv",
  caption = "@dir",
  tag = NULL,
  ylab = "dOFV",
  xlab = "Number of individuals removed",
  opt,
  facets = NULL,
  .problem,
  .subprob,
  .method,
  quiet
)

dofv_vs_id(
  xpdb_s,
  ...,
  .inorder = FALSE,
  type = "plt",
  alpha = 0.05,
  df = "guess",
  text_cutoff = 0.8,
  title = "Individual contributions to dOFV | @run",
  subtitle = "Based on @nind individuals, OFVs: @ofv",
  caption = "@dir",
  tag = NULL,
  ylab = "dOFV",
  xlab = "Number of individuals removed",
  opt,
  facets = NULL,
  .problem,
  .subprob,
  .method,
  quiet
)

Arguments

xpdb_s	<xpose_set> object
...	See <two_set_dots>
.inorder	See <two_set_dots>
type	See Details.
alpha	alpha for LRT
df	degrees of freedom for LRT. If "guess" (default), then use the difference in the number of unfixed parameters.
text_cutoff	If less than 1, the percentile of absolute individual dOFV values above which to show labels of IDs. If above 1, the absolute number of IDs to show. To show all, use an extreme positive number like 9999.
title	Plot title
subtitle	Plot subtitle
caption	Plot caption
tag	Plot tag
ylab	y-axis label
xlab	x-axis label
opt	User-specified data options. Only some of these will be used.
facets	<character> vector selecting facets, or NULL (default).
.problem	The problem to be used, by default returns the last one.
.subprob	The subproblem to be used, by default returns the last one.
.method	The estimation method to be used, by default returns the last one.
quiet	Silence extra debugging output

Details

For type-based customization of plots:

• p points (using aesthetics for sharkup and sharkdn)

• l lines for dOFV (both total dOFV and significance are plotted)

• t text (using aesthetics for shkuptxt and shkdntxt)

In xpose4, users can control sig.drop, but this function uses alpha and df to determine the critical delta by the likelihood ratio test. It is acknowledged there are situations where this may not be valid, but it is suggested that df or alpha be adjusted to meet the desired sig.drop.

my_alpha <- 0.05
my_df <- 1.34 # fractional, perhaps to account for different IIVs

my_sigdrop <- -stats::qchisq(1-my_alpha, my_df)
my_sigdrop
#> [1] -4.633671
# Then use alpha=my_alpha, df=my_df in `shark_plot` call.

Value

<xpose_plot> object

See Also

shark_colors()

Examples

pheno_set %>%
  # Make sure set has iofv var types defined
  focus_xpdb(everything()) %>%
  focus_function(backfill_iofv) %>%
  # Pick two models or consistent with two_set_dots()
  shark_plot(run6,run11)

pheno_set %>%
  # As before
  focus_xpdb(everything()) %>%
  focus_function(backfill_iofv) %>%
  # Add indicator (or use established covariate)
  mutate(APGRtest = as.numeric(as.character(APGR))<5) %>%
  # Pick two models or consistent with two_set_dots()
  shark_plot(run6,run11, facets = "APGRtest")

xpose.xtras documentation built on April 4, 2025, 2:13 a.m.