shark_plot: 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
)

Value

<xpose_plot> object

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.

Examples

Run this code

# \donttest{

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")

# }