Format parameter estimate values and output selected columns to be shown in the parameter table.
There are four main steps of this function:
When necessary, back transform parameters and their CIs, round parameters using pmtables::sig, and combine columns.
Format the THETA/OMEGA/SIGMA values to display as greek letters in Latex, with subscript numbers, and where necessary, the transformation applied to that parameter.
Determine which panel of the final table the parameter should be displayed in. This is informed by the panel argument you defined in your parameter key. Note that there are a finite number of options included by default (see below) but you can include additional panels as needed. Panel types include:
Residual variance
Interindividual covariance parameters
Interindividual variance parameters
Interoccasion variance parameters
Covariate effect parameters
Structural model parameters
Select columns for final tables.
parameter estimates output from define_param_table with modifications ready for formatting
columns to select for output. Default selects "type", "abb", "greek", "desc", "value", "ci", "shrinkage". To return all columns, specify "all" for .select_cols
output pRSE. Default is FALSE
set significant digits for output (optional). Default is three digits
set maxex for computation (optional). Default is NULL
#Using output from `define_param_table` (defineOut),
paramEst <- utils::read.csv(system.file("model/nonmem/param_est.csv", package = "pmparams"))
paramKey <- system.file("model/nonmem/pk-parameter-key-new.yaml", package = "pmparams")
defineOut <- define_param_table(.estimates = paramEst, .key = paramKey, .ci = 95, .zscore = NULL)
#> [1] "Parameter table yaml path provided: /data/pmparams/inst/model/nonmem/pk-parameter-key-new.yaml"
format_param_table(.df = defineOut)
#> type abb greek
#> 1 Structural model parameters KA (1/h) $\\exp(\\theta_{1})$
#> 2 Structural model parameters V2/F (L) $\\exp(\\theta_{2})$
#> 3 Structural model parameters CL/F (L/h) $\\exp(\\theta_{3})$
#> 4 Structural model parameters V3/F (L) $\\exp(\\theta_{4})$
#> 5 Structural model parameters Q/F (L/h) $\\exp(\\theta_{5})$
#> 6 Interindividual variance parameters IIV-KA $\\Omega_{(1,1)}$
#> 7 Interindividual variance parameters IIV-V2/F $\\Omega_{(2,2)}$
#> 8 Interindividual variance parameters IIV-CL/F $\\Omega_{(3,3)}$
#> 9 Interindividual covariance parameters V2/F-KA $\\Omega_{(2,1)}$
#> 10 Interindividual covariance parameters CL/F-KA $\\Omega_{(3,1)}$
#> 11 Interindividual covariance parameters CL/F-V2/F $\\Omega_{(3,2)}$
#> 12 Residual variance Proportional $\\Sigma_{(1,1)}$
#> desc value ci_95
#> 1 First order absorption rate constant 1.54 1.36, 1.75
#> 2 Apparent central volume 61.5 58.2, 64.9
#> 3 Apparent clearance 3.05 2.86, 3.25
#> 4 Apparent peripheral volume 67.4 64.9, 69.9
#> 5 Apparent intercompartmental clearance 3.62 3.38, 3.88
#> 6 Variance of absorption 0.221 [CV\\%=49.7] 0.117, 0.324
#> 7 Variance of central volume 0.0827 [CV\\%=29.4] 0.0634, 0.102
#> 8 Variance of clearance 0.169 [CV\\%=42.9] 0.130, 0.208
#> 9 Covariance of V2/F - KA 0.0690 [Corr=0.511] 0.0299, 0.108
#> 10 Covariance of CL/F - KA 0.134 [Corr=0.694] 0.0878, 0.180
#> 11 Covariance of CL/F - V2/F 0.0735 [Corr=0.622] 0.0528, 0.0942
#> 12 Variance 0.0399 [CV\\%=20.0] 0.0375, 0.0423
#> shrinkage
#> 1 -
#> 2 -
#> 3 -
#> 4 -
#> 5 -
#> 6 17.9
#> 7 6.02
#> 8 0.587
#> 9 -
#> 10 -
#> 11 -
#> 12 5.28
#To include all columns:
format_param_table(.df = defineOut, .select_cols="all")
#> X.1 X num2 estimate stderr random_effect_sd random_effect_sdse fixed
#> 1 1 1 1 0.4335920 0.06287440 NA NA FALSE
#> 2 2 2 2 4.1187600 0.02762730 NA NA FALSE
#> 3 3 3 3 1.1150300 0.03284750 NA NA FALSE
#> 4 4 4 4 4.2099100 0.01924850 NA NA FALSE
#> 5 5 5 5 1.2863100 0.03542620 NA NA FALSE
#> 6 6 6 (1,1) 0.2206060 0.05297990 0.469687 0.05639920 FALSE
#> 7 8 8 (2,2) 0.0826922 0.00982547 0.287563 0.01708410 FALSE
#> 8 11 11 (3,3) 0.1691160 0.01972890 0.411237 0.02398730 FALSE
#> 9 7 7 (2,1) 0.0690088 0.01996170 0.510933 0.09746980 FALSE
#> 10 9 9 (3,1) 0.1340090 0.02358740 0.693796 0.06860550 FALSE
#> 11 10 10 (3,2) 0.0735027 0.01054810 0.621554 0.05238880 FALSE
#> 12 12 12 (1,1) 0.0399167 0.00122595 0.199792 0.00306807 FALSE
#> diag shrinkage name abb desc
#> 1 NA - THETA1 KA (1/h) First order absorption rate constant
#> 2 NA - THETA2 V2/F (L) Apparent central volume
#> 3 NA - THETA3 CL/F (L/h) Apparent clearance
#> 4 NA - THETA4 V3/F (L) Apparent peripheral volume
#> 5 NA - THETA5 Q/F (L/h) Apparent intercompartmental clearance
#> 6 TRUE 17.9 OMEGA11 IIV-KA Variance of absorption
#> 7 TRUE 6.02 OMEGA22 IIV-V2/F Variance of central volume
#> 8 TRUE 0.587 OMEGA33 IIV-CL/F Variance of clearance
#> 9 FALSE - OMEGA21 V2/F-KA Covariance of V2/F - KA
#> 10 FALSE - OMEGA31 CL/F-KA Covariance of CL/F - KA
#> 11 FALSE - OMEGA32 CL/F-V2/F Covariance of CL/F - V2/F
#> 12 TRUE 5.28 SIGMA11 Proportional Variance
#> panel trans transTHETA THETAERR TH OM S LOG LOGIT
#> 1 struct logTrans NA FALSE TRUE FALSE FALSE TRUE FALSE
#> 2 struct logTrans NA FALSE TRUE FALSE FALSE TRUE FALSE
#> 3 struct logTrans NA FALSE TRUE FALSE FALSE TRUE FALSE
#> 4 struct logTrans NA FALSE TRUE FALSE FALSE TRUE FALSE
#> 5 struct logTrans NA FALSE TRUE FALSE FALSE TRUE FALSE
#> 6 IIV lognormalOm NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 7 IIV lognormalOm NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 8 IIV lognormalOm NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 9 IIV none NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 10 IIV none NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 11 IIV none NA FALSE FALSE TRUE FALSE FALSE FALSE
#> 12 RV propErr NA FALSE FALSE FALSE TRUE FALSE FALSE
#> lognormO Osd logitOsd propErr addErr addErrLogDV value
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE 1.54
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE 61.5
#> 3 FALSE FALSE FALSE FALSE FALSE FALSE 3.05
#> 4 FALSE FALSE FALSE FALSE FALSE FALSE 67.4
#> 5 FALSE FALSE FALSE FALSE FALSE FALSE 3.62
#> 6 TRUE FALSE FALSE FALSE FALSE FALSE 0.221 [CV\\%=49.7]
#> 7 TRUE FALSE FALSE FALSE FALSE FALSE 0.0827 [CV\\%=29.4]
#> 8 TRUE FALSE FALSE FALSE FALSE FALSE 0.169 [CV\\%=42.9]
#> 9 FALSE FALSE FALSE FALSE FALSE FALSE 0.0690 [Corr=0.511]
#> 10 FALSE FALSE FALSE FALSE FALSE FALSE 0.134 [Corr=0.694]
#> 11 FALSE FALSE FALSE FALSE FALSE FALSE 0.0735 [Corr=0.622]
#> 12 FALSE FALSE FALSE TRUE FALSE FALSE 0.0399 [CV\\%=20.0]
#> se corr_SD lower upper ci_level cv pRSE sd text
#> 1 0.06287440 - 1.36391355 1.74512437 95 - 6.29 - theta
#> 2 0.02762730 - 58.24221829 64.90401641 95 - 2.76 - theta
#> 3 0.03284750 - 2.85950605 3.25245827 95 - 3.29 - theta
#> 4 0.01924850 - 64.85687636 69.93995303 95 - 1.93 - theta
#> 5 0.03542620 - 3.37661811 3.87965159 95 - 3.54 - theta
#> 6 0.05297990 - 0.11676540 0.32444660 95 49.7 24.0 - Omega
#> 7 0.00982547 - 0.06343428 0.10195012 95 29.4 11.9 - Omega
#> 8 0.01972890 - 0.13044736 0.20778464 95 42.9 11.7 - Omega
#> 9 0.01996170 0.511 0.02988387 0.10813373 95 - - - Omega
#> 10 0.02358740 0.694 0.08777770 0.18024030 95 - - - Omega
#> 11 0.01054810 0.622 0.05282842 0.09417698 95 - - - Omega
#> 12 0.00122595 - 0.03751384 0.04231956 95 20.0 3.07 - Sigma
#> greek type type_f
#> 1 $\\exp(\\theta_{1})$ Structural model parameters 1
#> 2 $\\exp(\\theta_{2})$ Structural model parameters 1
#> 3 $\\exp(\\theta_{3})$ Structural model parameters 1
#> 4 $\\exp(\\theta_{4})$ Structural model parameters 1
#> 5 $\\exp(\\theta_{5})$ Structural model parameters 1
#> 6 $\\Omega_{(1,1)}$ Interindividual variance parameters 3
#> 7 $\\Omega_{(2,2)}$ Interindividual variance parameters 3
#> 8 $\\Omega_{(3,3)}$ Interindividual variance parameters 3
#> 9 $\\Omega_{(2,1)}$ Interindividual covariance parameters 5
#> 10 $\\Omega_{(3,1)}$ Interindividual covariance parameters 5
#> 11 $\\Omega_{(3,2)}$ Interindividual covariance parameters 5
#> 12 $\\Sigma_{(1,1)}$ Residual variance 6
#> ci_95
#> 1 1.36, 1.75
#> 2 58.2, 64.9
#> 3 2.86, 3.25
#> 4 64.9, 69.9
#> 5 3.38, 3.88
#> 6 0.117, 0.324
#> 7 0.0634, 0.102
#> 8 0.130, 0.208
#> 9 0.0299, 0.108
#> 10 0.0878, 0.180
#> 11 0.0528, 0.0942
#> 12 0.0375, 0.0423