DMP Publication 2024

Dosing and LATIN

Author

Affiliation

Eric

Ultragenyx

1 Quarto

Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see https://quarto.org.

2 Running Code

Code

cat('$$
\\small{
CHG = \\beta_0 + \\beta_1 \\times TRT01PN + \\beta_2 \\times AVISITN + \\beta_3 \\times (TRT01PN \\times AVISITN) + \\beta_4 \\times STRATAGN + \\beta_5 \\times STRATGLN + \\beta_6 \\times BASE + \\epsilon
}
$$')

\small{ CHG = \beta_0 + \beta_1 \times TRT01PN + \beta_2 \times AVISITN + \beta_3 \times (TRT01PN \times AVISITN) + \beta_4 \times STRATAGN + \beta_5 \times STRATGLN + \beta_6 \times BASE + \epsilon }

Code

cat('$$
\\begin{align*}
\\text{CHG Contrast} = & -1 \\times \\beta_{\\text{TRT01PN=DTX401}} + 1 \\times \\beta_{\\text{TRT01PN=Placebo}} + 
0 \\times \\beta_{\\text{TRT01PN=DTX401, AVISITN=Week 36 }} - 1 \\times \\beta_{\\text{TRT01PN=DTX401, AVISITN=Week 48}} + \\\\&
+0 \\times \\beta_{\\text{TRT01PN=Placebo, AVISITN=Week 36 }} + 1 \\times \\beta_{\\text{TRT01PN=Placebo, AVISITN=Week 48}}
\\end{align*}
$$')

\begin{align*} \text{CHG Contrast} = & -1 \times \beta_{\text{TRT01PN=DTX401}} + 1 \times \beta_{\text{TRT01PN=Placebo}} + 0 \times \beta_{\text{TRT01PN=DTX401, AVISITN=Week 36 }} - 1 \times \beta_{\text{TRT01PN=DTX401, AVISITN=Week 48}} + \\& +0 \times \beta_{\text{TRT01PN=Placebo, AVISITN=Week 36 }} + 1 \times \beta_{\text{TRT01PN=Placebo, AVISITN=Week 48}} \end{align*}

Code

cat('$$
\\begin{align*}
Improvement = & \\beta_0 + \\beta_1 \\times \\text{TRTGRPCD} + \\beta_2 \\times \\text{SEX} + \\beta_3 \\times \\text{AGE} + \\beta_4 \\times \\text{age.diag} + \\beta_5 \\times \\text{AAGEPHOS} + \\beta_6 \\times \\text{AAGEVITD} + \\beta_7 \\times \\text{age.first.burmb} + \\beta_8 \\times \\text{HEIGHT} \\\\&
+ \\beta_9 \\times \\text{WEIGHT} + \\beta_{10} \\times \\text{HTZ\\_MONTH\\_0\\_DMDlnk} + \\beta_{11} \\times \\text{HTZ\\_diff} + \\beta_{12} \\times \\text{BMI\\_MONTH\\_0} + \\beta_{13} \\times \\text{BMI\\_diff} + \\beta_{14} \\times \\text{RSS\\_glb\\_bs\\_cat} +\\\\& \\beta_{15} \\times \\text{RSS\\_kne\\_bs\\_cat} 
+ \\beta_{16} \\times \\text{phos\\_AVALZ\\_MONTH\\_0\\_DMDlnk} + \\beta_{17} \\times \\text{phosZ\\_diff} + \\beta_{18} \\times \\text{ALPS\\_MONTH\\_0\\_DMDlnk} \\\\& + \\beta_{19} \\times \\text{ALPS\\_diff} + \\beta_{20} \\times \\text{PTHI\\_MONTH\\_0\\_DMDlnk} + \\beta_{21} \\times \\text{VD1\\_25\\_MONTH\\_0} 
+ \\beta_{22} \\times \\text{AverageDose\\_DMP} +\\\\& \\beta_{23} \\times \\text{TRTDURW.month} + \\beta_{24} \\times \\text{PHEXBL\\_BL\\_dlnk} + \\epsilon
\\end{align*}
$$')

\begin{align*} Improvement = & \beta_0 + \beta_1 \times \text{TRTGRPCD} + \beta_2 \times \text{SEX} + \beta_3 \times \text{AGE} + \beta_4 \times \text{age.diag} + \beta_5 \times \text{AAGEPHOS} + \beta_6 \times \text{AAGEVITD} + \beta_7 \times \text{age.first.burmb} + \beta_8 \times \text{HEIGHT} \\& + \beta_9 \times \text{WEIGHT} + \beta_{10} \times \text{HTZ\_MONTH\_0\_DMDlnk} + \beta_{11} \times \text{HTZ\_diff} + \beta_{12} \times \text{BMI\_MONTH\_0} + \beta_{13} \times \text{BMI\_diff} + \beta_{14} \times \text{RSS\_glb\_bs\_cat} +\\& \beta_{15} \times \text{RSS\_kne\_bs\_cat} + \beta_{16} \times \text{phos\_AVALZ\_MONTH\_0\_DMDlnk} + \beta_{17} \times \text{phosZ\_diff} + \beta_{18} \times \text{ALPS\_MONTH\_0\_DMDlnk} \\& + \beta_{19} \times \text{ALPS\_diff} + \beta_{20} \times \text{PTHI\_MONTH\_0\_DMDlnk} + \beta_{21} \times \text{VD1\_25\_MONTH\_0} + \beta_{22} \times \text{AverageDose\_DMP} +\\& \beta_{23} \times \text{TRTDURW.month} + \beta_{24} \times \text{PHEXBL\_BL\_dlnk} + \epsilon \end{align*}

Code

cat('$$
\\begin{align*}
\\text{Normalized difference} = & \\beta_0 + \\beta_1 \\times \\text{TRTGRPCD} +  \\beta_2 \\times \\text{age.first.burmb} + \\beta_{3} \\times \\text{HTZ\\_MONTH\\_0\\_DMDlnk} + \\beta_{4} \\times \\text{HTZ\\_diff} + \\beta_{5} \\times \\text{PHEXBL\\_BL\\_dlnk} + \\epsilon
\\end{align*}
$$')

\begin{align*} \text{Normalized difference} = & \beta_0 + \beta_1 \times \text{TRTGRPCD} + \beta_2 \times \text{age.first.burmb} + \beta_{3} \times \text{HTZ\_MONTH\_0\_DMDlnk} + \beta_{4} \times \text{HTZ\_diff} + \beta_{5} \times \text{PHEXBL\_BL\_dlnk} + \epsilon \end{align*}

Code

library(tern)

Warning: package 'tern' was built under R version 4.2.3

Loading required package: rtables

Warning: package 'rtables' was built under R version 4.2.3

Loading required package: formatters

Warning: package 'formatters' was built under R version 4.2.3

Loading required package: magrittr

Warning: package 'magrittr' was built under R version 4.2.3

Attaching package: 'rtables'

The following object is masked from 'package:utils':

    str

Registered S3 method overwritten by 'tern':
  method   from 
  tidy.glm broom

Code

library(nestcolor)

Warning: package 'nestcolor' was built under R version 4.2.3

Code

adsl <- tern_ex_adsl
adlb <- tern_ex_adlb %>% dplyr::filter(ANL01FL == "Y", PARAMCD == "ALT", AVISIT != "SCREENING")
adlb$AVISIT <- droplevels(adlb$AVISIT)
adlb <- dplyr::mutate(adlb, AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min))

# Mean with CI
g_lineplot(adlb, adsl, subtitle = "Laboratory Test:")

Code

# Mean with CI, no stratification with group_var
g_lineplot(adlb, variables = control_lineplot_vars(group_var = NA,x = "AVISIT",
  y = "AVAL"))

Code

# Mean, upper whisker of CI, no group_var(strata) counts N
g_lineplot(
  adlb,
  whiskers = "mean_ci_upr",
  title = "Plot of Mean and Upper 95% Confidence Limit by Visit"
)

Code

# Median with CI
g_lineplot(
  adlb,
  adsl,
  mid = "median",
  interval = "median_ci",
  whiskers = c("median_ci_lwr", "median_ci_upr"),
  title = "Plot of Median and 95% Confidence Limits by Visit"
)

Code

# Mean, +/- SD
g_lineplot(adlb, adsl,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = "Plot of Median +/- SD by Visit"
)

Code

# Mean with CI plot with stats table
g_lineplot(adlb, adsl, table = c("n", "mean", "mean_ci"))

Code

# Mean with CI, table and customized confidence level
g_lineplot(
  adlb,
  adsl,
  table = c("n", "mean", "mean_ci"),
  control = control_analyze_vars(conf_level = 0.80),
  title = "Plot of Mean and 80% Confidence Limits by Visit"
)

Code

# Mean with CI, table, filtered data
adlb_f <- dplyr::filter(adlb, ARMCD != "ARM A" | AVISIT == "BASELINE")
g_lineplot(adlb_f, table = c("n", "mean"))

Code

adsl<-pharmaverseadam::adsl
admh<-pharmaverseadam::admh
adcm<-pharmaverseadam::adcm
adex<-pharmaverseadam::adex
adae<-pharmaverseadam::adae
adlb<-pharmaverseadam::adlb

Code

library(dataxray)
adsl %>% make_xray() %>%  view_xray()

Citation

BibTeX citation:

@online{eric2024,
  author = {Eric},
  title = {DMP {Publication} 2024},
  date = {2024-05-30},
  langid = {en}
}

For attribution, please cite this work as:

Eric. 2024. “DMP Publication 2024.” Analysis. May 30, 2024.