comparison-tables • hyperion.tables

library(hyperion.tables)
library(hyperion)
#> 
#> 
#> ── pharos configuration ────────────────────────────────────────────────────────
#> ✔ pharos.toml found: /data/user-homes/tariq/projects/prism-pkgdocs-build/installed-pkgs/2026-03-02/hyperion.tables_0.3.0/vignettes/pharos.toml
#> ── hyperion options ────────────────────────────────────────────────────────────
#> ✔ hyperion.significant_number_display : 4
#> ── hyperion nonmem object options ──────────────────────────────────────────────
#> ✔ hyperion.nonmem_model.show_included_columns : FALSE
#> ✔ hyperion.nonmem_summary.rse_threshold : 50
#> ✔ hyperion.nonmem_summary.shrinkage_threshold : 30

library(gt)
library(flextable)

model_dir <- system.file("extdata", "models", "onecmt", package = "hyperion.tables")
model_run <- "run003"

Model Comparison

spec <- TableSpec() |>
  set_spec_transforms(omega = "cv") |>
  set_spec_sections(
    kind == "THETA" ~ "Structural model parameters",
    kind == "OMEGA" & diagonal ~ "Interindividual variance parameters",
    kind == "OMEGA" & !diagonal ~ "Interindividual covariance parameters",
    kind == "SIGMA" ~ "Residual variance",
    TRUE ~ "Other"
  ) |>
  set_spec_sigfig(3) |>
  drop_spec_columns("variability", "shrinkage", "rse") |>
  set_spec_pvalue(scientific = FALSE)

child_mod <- read_model(file.path(model_dir, paste0(model_run, ".mod")))
child_sum <- summary(child_mod)
child_info <- get_model_parameter_info(child_mod)

parent_mod <- read_model(file.path(model_dir, "run002.mod"))
mod_sum <- summary(parent_mod)
info <- get_model_parameter_info(parent_mod)

get_parameters(parent_mod) |>
  apply_table_spec(spec, info) |>
  add_summary_info(mod_sum) |>
  compare_with(
    get_parameters(child_mod) |>
      apply_table_spec(spec, child_info) |>
      add_summary_info(child_sum),
    labels = c("run002", "run003")
  ) |>
  make_comparison_table()
#> LRT suppressed for run002 vs run003: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.

Parameter	run002				run003
Model Parameters
Parameter	Symbol	Unit	Estimate	95% CI	Symbol	Unit	Estimate	95% CI	% Change
Structural model parameters
TVCL	$\theta_{1}$	L/hr	1.25	[0.994, 1.50]	$\theta_{1}$	L/hr	1.33	[1.11, 1.54]	6.31
TVV	$\theta_{2}$	L	40.8	[34.9, 46.8]	$\theta_{2}$	L	40.2	[34.6, 45.7]	-1.68
TVKA	$\theta_{3}$	1/hr	1.24	[1.02, 1.47]	$\theta_{3}$	1/hr	1.21	[0.997, 1.43]	-2.59
Interindividual variance parameters
OM1 TVCL	$\Omega_{(1,1)}$		0.130	[0.0125, 0.248]	$\Omega_{(1,1)}$		0.122	[0.0236, 0.221]	-6.19
OM2 TVV	$\Omega_{(2,2)}$		0.136	[0.0585, 0.214]	$\Omega_{(2,2)}$		0.124	[0.0519, 0.196]	-9.14
OM3 TVKA	$\Omega_{(3,3)}$		0.114	[-0.00602, 0.235]	$\Omega_{(3,3)}$		0.122	[0.0121, 0.233]	7.00
Interindividual covariance parameters
OM1,2 TVCL, TVV					$\Omega_{(2,1)}$		0.0745	[0.0131, 0.136]
Residual variance
SIG1	$\Sigma_{(1,1)}$		0.0372	[0.0145, 0.0600]	$\Sigma_{(1,1)}$		0.0375	[0.0257, 0.0494]	0.820
SIG2	$\Sigma_{(2,2)}$		0.00661	[-0.0481, 0.0613]	$\Sigma_{(2,2)}$		0.00527	[-0.0128, 0.0233]	-20.2
Condition Number: 29.6 (run002), 6.17 (run003)
No. of Observations: 210 (run002), 210 (run003)
OFV: -103.468 (run002), -109.826 (run003)
95% CI: $\mathrm{Estimate} \pm z_{0.025} \cdot \mathrm{SE}$
% Change: $\frac{\mathrm{Estimate}_{\mathrm{model}} - \mathrm{Estimate}_{\mathrm{ref}}}{\mathrm{Estimate}_{\mathrm{ref}}} \cdot 100$
Abbreviations:
CI = confidence intervals; RSE = relative standard error; SE = standard error;
OFV = Objective Function Value

Multiple Comparison Table

spec <- TableSpec() |>
  set_spec_transforms(omega = "cv") |>
  set_spec_sections(
    kind == "THETA" ~ "Structural model parameters",
    kind == "OMEGA" & diagonal ~ "Interindividual variance parameters",
    kind == "OMEGA" & !diagonal ~ "Interindividual covariance parameters",
    kind == "SIGMA" ~ "Residual error",
    TRUE ~ "Other"
  ) |>
  set_spec_sigfig(3) |>
  set_spec_columns("symbol", "estimate", "ci", "rse", "pct_change") |>
  set_spec_hide_empty(FALSE)

mod1 <- read_model(file.path(model_dir, "run002.mod"))
mod_sum1 <- summary(mod1)
info1 <- get_model_parameter_info(mod1)

mod2 <- read_model(file.path(model_dir, "run003.mod"))
mod_sum2 <- summary(mod2)
info2 <- get_model_parameter_info(mod2)

mod3 <- read_model(file.path(model_dir, "run003b1.mod"))
mod_sum3 <- summary(mod3)
info3 <- get_model_parameter_info(mod3)

comp <- get_parameters(mod1) |>
  apply_table_spec(spec, info1) |>
  add_summary_info(mod_sum1) |>
  compare_with(
    get_parameters(mod2) |>
      apply_table_spec(spec, info2) |>
      add_summary_info(mod_sum2),
    labels = c("run002", "run003")
  ) |>
  compare_with(
    get_parameters(mod3) |>
      apply_table_spec(spec, info3) |>
      add_summary_info(mod_sum3),
    labels = c("run003b1")
  )

comp |>
  make_comparison_table()
#> LRT suppressed for run002 vs run003: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.
#> LRT suppressed for run003 vs run003b1: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.

Parameter	run002				run003					run003b1
Model Parameters
Parameter	Symbol	Estimate	95% CI	RSE (%)	Symbol	Estimate	95% CI	RSE (%)	% Change vs run002	Symbol	Estimate	95% CI	RSE (%)	% Change vs run003
Structural model parameters
TVCL	$\theta_{1}$	1.25	[0.994, 1.50]	10.3	$\theta_{1}$	1.33	[1.11, 1.54]	8.41	6.31	$\theta_{1}$	1.25			-5.67
TVV	$\theta_{2}$	40.8	[34.9, 46.8]	7.41	$\theta_{2}$	40.2	[34.6, 45.7]	7.07	-1.68	$\theta_{3}$	40.3			0.296
TVKA	$\theta_{3}$	1.24	[1.02, 1.47]	9.12	$\theta_{3}$	1.21	[0.997, 1.43]	9.06	-2.59	$\theta_{4}$	1.22			0.490
WT-on-CL										$\theta_{2}$	0.545
Interindividual variance parameters
OM1 TVCL	$\Omega_{(1,1)}$	0.130	[0.0125, 0.248]	46.1	$\Omega_{(1,1)}$	0.122	[0.0236, 0.221]	41.2	-6.19	$\Omega_{(1,1)}$	0.123			0.756
OM2 TVV	$\Omega_{(2,2)}$	0.136	[0.0585, 0.214]	29.1	$\Omega_{(2,2)}$	0.124	[0.0519, 0.196]	29.7	-9.14	$\Omega_{(2,2)}$	0.125			0.587
OM3 TVKA	$\Omega_{(3,3)}$	0.114	[-0.00602, 0.235]	53.7	$\Omega_{(3,3)}$	0.122	[0.0121, 0.233]	46.0	7.00	$\Omega_{(3,3)}$	0.124			1.20
Interindividual covariance parameters
OM1,2 TVCL, TVV					$\Omega_{(2,1)}$	0.0745	[0.0131, 0.136]	42.0		$\Omega_{(2,1)}$	0.0722			-3.17
Residual error
SIG1	$\Sigma_{(1,1)}$	0.0372	[0.0145, 0.0600]	31.2	$\Sigma_{(1,1)}$	0.0375	[0.0257, 0.0494]	16.1	0.820	$\Sigma_{(1,1)}$	0.0374			-0.496
SIG2	$\Sigma_{(2,2)}$	0.00661	[-0.0481, 0.0613]	423	$\Sigma_{(2,2)}$	0.00527	[-0.0128, 0.0233]	175	-20.2	$\Sigma_{(2,2)}$	0.00589			11.8
Condition Number: 29.6 (run002), 6.17 (run003)
No. of Observations: 210 (run002), 210 (run003)
OFV: -103.468 (run002), -109.826 (run003)
Condition Number: 6.17 (run003), N/A (run003b1)
No. of Observations: 210 (run003), 210 (run003b1)
OFV: -109.826 (run003), -108.889 (run003b1)
95% CI: $\mathrm{Estimate} \pm z_{0.025} \cdot \mathrm{SE}$
% Change: $\frac{\mathrm{Estimate}_{\mathrm{model}} - \mathrm{Estimate}_{\mathrm{ref}}}{\mathrm{Estimate}_{\mathrm{ref}}} \cdot 100$
Abbreviations:
CI = confidence intervals; RSE = relative standard error; SE = standard error;
OFV = Objective Function Value

Structural model comparison

spec <- TableSpec() |>
  set_spec_transforms(omega = "cv") |>
  set_spec_sections(
    kind == "THETA" ~ "Structural model parameters",
    kind == "OMEGA" & diagonal ~ "Interindividual variance parameters",
    kind == "OMEGA" & !diagonal ~ "Interindividual covariance parameters",
    kind == "SIGMA" ~ "Residual error",
    TRUE ~ "Other"
  ) |>
  set_spec_sigfig(3) |>
  set_spec_columns("symbol", "fixed", "estimate") |>
  set_spec_title("Structural Model Parameter Comparison")

mod1 <- read_model(file.path(model_dir, "run001.mod"))
mod_sum1 <- summary(mod1)
info1 <- get_model_parameter_info(mod1)

mod2 <- read_model(file.path(model_dir, "run002.mod"))
mod_sum2 <- summary(mod2)
info2 <- get_model_parameter_info(mod2)

mod3 <- read_model(file.path(model_dir, "run003.mod"))
mod_sum3 <- summary(mod3)
info3 <- get_model_parameter_info(mod3)

mod4 <- read_model(file.path(model_dir, "run003b1.mod"))
mod_sum4 <- summary(mod4)
info4 <- get_model_parameter_info(mod4)

comp <- get_parameters(mod1) |>
  apply_table_spec(spec, info1) |>
  add_summary_info(mod_sum1) |>
  compare_with(
    get_parameters(mod2) |>
      apply_table_spec(spec, info2) |>
      add_summary_info(mod_sum2),
    labels = c("run001", "run002")
   ) |>
  compare_with(
    get_parameters(mod3) |>
      apply_table_spec(spec, info3) |>
      add_summary_info(mod_sum3),
    labels = c("run003")
  ) |>
  compare_with(
    get_parameters(mod4) |>
      apply_table_spec(spec, info4) |>
      add_summary_info(mod_sum4),
    labels = c("run004")
  )
comp |>
  make_comparison_table()
#> LRT suppressed for run001 vs run002: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.
#> LRT suppressed for run002 vs run003: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.
#> LRT suppressed for run003 vs run004: no lineage attached
#> ℹ Both OFVs and matching observation counts are present, but LRT conditions are not met.

Parameter	run001			run002			run003			run004
Structural Model Parameter Comparison
Parameter	Symbol	Fixed	Estimate	Symbol	Fixed	Estimate	Symbol	Fixed	Estimate	Symbol	Fixed	Estimate
Structural model parameters
TVCL	$\theta_{1}$		1.24	$\theta_{1}$		1.25	$\theta_{1}$		1.33	$\theta_{1}$		1.25
TVV	$\theta_{2}$		40.9	$\theta_{2}$		40.8	$\theta_{2}$		40.2	$\theta_{3}$		40.3
TVKA	$\theta_{3}$		1.24	$\theta_{3}$		1.24	$\theta_{3}$		1.21	$\theta_{4}$		1.22
WT-on-CL										$\theta_{2}$		0.545
Interindividual variance parameters
OM1 TVCL	$\Omega_{(1,1)}$		0.131	$\Omega_{(1,1)}$		0.130	$\Omega_{(1,1)}$		0.122	$\Omega_{(1,1)}$		0.123
OM2 TVV	$\Omega_{(2,2)}$		0.136	$\Omega_{(2,2)}$		0.136	$\Omega_{(2,2)}$		0.124	$\Omega_{(2,2)}$		0.125
OM3 TVKA	$\Omega_{(3,3)}$	Fixed	0.100	$\Omega_{(3,3)}$		0.114	$\Omega_{(3,3)}$		0.122	$\Omega_{(3,3)}$		0.124
Interindividual covariance parameters
OM1,2 TVCL, TVV							$\Omega_{(2,1)}$		0.0745	$\Omega_{(2,1)}$		0.0722
Residual error
Proportional	$\Sigma_{(1,1)}$		0.0364
Additive	$\Sigma_{(2,2)}$	Fixed	0.0100
SIG1				$\Sigma_{(1,1)}$		0.0372	$\Sigma_{(1,1)}$		0.0375	$\Sigma_{(1,1)}$		0.0374
SIG2				$\Sigma_{(2,2)}$		0.00661	$\Sigma_{(2,2)}$		0.00527	$\Sigma_{(2,2)}$		0.00589
Condition Number: 1.98 (run001), 29.6 (run002)
No. of Observations: 210 (run001), 210 (run002)
OFV: -103.299 (run001), -103.468 (run002)
Condition Number: 29.6 (run002), 6.17 (run003)
No. of Observations: 210 (run002), 210 (run003)
OFV: -103.468 (run002), -109.826 (run003)
Condition Number: 6.17 (run003), N/A (run004)
No. of Observations: 210 (run003), 210 (run004)
OFV: -109.826 (run003), -108.889 (run004)
% Change: $\frac{\mathrm{Estimate}_{\mathrm{model}} - \mathrm{Estimate}_{\mathrm{ref}}}{\mathrm{Estimate}_{\mathrm{ref}}} \cdot 100$
Abbreviations:
OFV = Objective Function Value