Format bootstrap parameter estimate values and output selected columns to be shown in the bootstrap parameter table.
Left join this output bootstrap data.frame with the formatted output of non-bootstrap parameter estimates
parameter estimates output from define_boot_table with modifications ready for formatting
columns to select for output. Default selects "abb", "desc", "boot_value", "boot_ci". To return all columns, specify "all" for .select_cols.
set significant digits for output (optional). Default is three digits
set maxex for computation (optional). Default is NULL
#Using output from `define_boot_table` (defineBootOut),
boot_paramEst <- utils::read.csv(system.file("model/nonmem/boot/data/boot-106.csv",
package = "pmparams"))
nonboot_paramEst <- utils::read.csv(system.file("model/nonmem/nonboot_param_est.csv",
package = "pmparams"))
paramKey <- system.file("model/nonmem/pk-parameter-key-new.yaml", package = "pmparams")
defineBootOut <- define_boot_table(.boot_estimates = boot_paramEst,
.nonboot_estimates = nonboot_paramEst,
.key = paramKey)
#> [1] "Parameter table yaml path provided: /data/pmparams/inst/model/nonmem/pk-parameter-key-new.yaml"
format_boot_table(.boot_df = defineBootOut)
#> abb desc boot_value boot_ci_95
#> 1 KA (1/h) First order absorption rate constant 1.57 1.39, 1.78
#> 2 V2/F (L) Apparent central volume 61.5 58.3, 65.1
#> 3 CL/F (L/h) Apparent clearance 3.23 3.07, 3.42
#> 4 V3/F (L) Apparent peripheral volume 67.3 65.0, 69.8
#> 5 Q/F (L/h) Apparent intercompartmental clearance 3.61 3.37, 3.86
#> 6 CL/F ~ eGFR eGFR effect on CL/F 0.484 0.408, 0.558
#> 7 CL/F ~ Age Age effect on CL/F -0.0386 -0.167, 0.0878
#> 8 CL/F ~ ALB Serum albumin effect on CL/F 0.420 0.294, 0.587
#> 9 IIV-KA Variance of absorption 0.218 <NA>
#> 10 IIV-V2/F Variance of central volume 0.0821 <NA>
#> 11 IIV-CL/F Variance of clearance 0.112 <NA>
#> 12 V2/F-KA Covariance of V2/F - KA 0.0656 <NA>
#> 13 CL/F-KA Covariance of CL/F - KA 0.121 <NA>
#> 14 CL/F-V2/F Covariance of CL/F - V2/F 0.0696 <NA>
#> 15 Proportional Variance 0.0400 <NA>
#To include all columns:
format_boot_table(.boot_df = defineBootOut, .select_cols="all")
#> parameter_names estimate lower upper name abb
#> 1 THETA1 0.44880350 1.38806751 1.78221206 THETA1 KA (1/h)
#> 2 THETA2 4.11949000 58.28377484 65.05317419 THETA2 V2/F (L)
#> 3 THETA3 1.17220500 3.06673660 3.41684975 THETA3 CL/F (L/h)
#> 4 THETA4 4.20983500 64.99289784 69.82682512 THETA4 V3/F (L)
#> 5 THETA5 1.28442500 3.37292139 3.86409016 THETA5 Q/F (L/h)
#> 6 THETA6 0.48368700 0.40819383 0.55820400 THETA6 CL/F ~ eGFR
#> 7 THETA7 -0.03861535 -0.16724268 0.08782413 THETA7 CL/F ~ Age
#> 8 THETA8 0.42044750 0.29365133 0.58652035 THETA8 CL/F ~ ALB
#> 9 OMEGA.1.1. 0.21791200 0.12965965 0.33063635 OMEGA11 IIV-KA
#> 10 OMEGA.2.2. 0.08210580 0.06432011 0.10123122 OMEGA22 IIV-V2/F
#> 11 OMEGA.3.3. 0.11213300 0.08956925 0.14029418 OMEGA33 IIV-CL/F
#> 12 OMEGA.2.1. 0.06564225 0.03282125 0.10749465 OMEGA21 V2/F-KA
#> 13 OMEGA.3.1. 0.12131700 0.08049071 0.17341253 OMEGA31 CL/F-KA
#> 14 OMEGA.3.2. 0.06963290 0.05252801 0.08823306 OMEGA32 CL/F-V2/F
#> 15 SIGMA.1.1. 0.03996855 0.03760094 0.04238123 SIGMA11 Proportional
#> desc panel trans fixed value
#> 1 First order absorption rate constant struct logTrans FALSE 1.56643682
#> 2 Apparent central volume struct logTrans FALSE 61.52785506
#> 3 Apparent clearance struct logTrans FALSE 3.22910497
#> 4 Apparent peripheral volume struct logTrans FALSE 67.34542690
#> 5 Apparent intercompartmental clearance struct logTrans FALSE 3.61259012
#> 6 eGFR effect on CL/F cov none FALSE 0.48368700
#> 7 Age effect on CL/F cov none FALSE -0.03861535
#> 8 Serum albumin effect on CL/F cov none FALSE 0.42044750
#> 9 Variance of absorption IIV lognormalOm NA 0.21791200
#> 10 Variance of central volume IIV lognormalOm NA 0.08210580
#> 11 Variance of clearance IIV lognormalOm NA 0.11213300
#> 12 Covariance of V2/F - KA IIV none NA 0.06564225
#> 13 Covariance of CL/F - KA IIV none NA 0.12131700
#> 14 Covariance of CL/F - V2/F IIV none NA 0.06963290
#> 15 Variance RV propErr NA 0.03996855
#> transTHETA THETAERR TH OM S LOG LOGIT lognormO Osd logitOsd
#> 1 NA FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> 2 NA FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> 3 NA FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> 4 NA FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> 5 NA FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> 6 NA FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 7 NA FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 8 NA FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 9 NA FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
#> 10 NA FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
#> 11 NA FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
#> 12 NA FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 13 NA FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 14 NA FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 15 NA FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
#> propErr addErr addErrLogDV boot_ci_95 boot_value
#> 1 FALSE FALSE FALSE 1.39, 1.78 1.57
#> 2 FALSE FALSE FALSE 58.3, 65.1 61.5
#> 3 FALSE FALSE FALSE 3.07, 3.42 3.23
#> 4 FALSE FALSE FALSE 65.0, 69.8 67.3
#> 5 FALSE FALSE FALSE 3.37, 3.86 3.61
#> 6 FALSE FALSE FALSE 0.408, 0.558 0.484
#> 7 FALSE FALSE FALSE -0.167, 0.0878 -0.0386
#> 8 FALSE FALSE FALSE 0.294, 0.587 0.420
#> 9 FALSE FALSE FALSE <NA> 0.218
#> 10 FALSE FALSE FALSE <NA> 0.0821
#> 11 FALSE FALSE FALSE <NA> 0.112
#> 12 FALSE FALSE FALSE <NA> 0.0656
#> 13 FALSE FALSE FALSE <NA> 0.121
#> 14 FALSE FALSE FALSE <NA> 0.0696
#> 15 TRUE FALSE FALSE <NA> 0.0400