From 547d3accd6084d42e68ec8ae942e1e32c1ac3646 Mon Sep 17 00:00:00 2001 From: John Harrold Date: Fri, 25 Oct 2024 20:13:19 -0700 Subject: [PATCH] Fixed broken initial conditions in rxode2/nlmixr2 output. --- docs/articles/Deployment.html | 2 +- docs/articles/In_Vitro.html | 117 +++++----- docs/articles/Language.html | 30 +-- docs/articles/NCA.html | 224 +++++++++---------- docs/articles/Reporting.html | 234 ++++++++++---------- docs/pkgdown.yml | 2 +- docs/reference/build_system.html | 2 +- docs/reference/system_fetch_iiv.html | 2 +- docs/reference/system_fetch_parameters.html | 2 +- docs/reference/system_fetch_set.html | 2 +- docs/reference/system_fetch_template.html | 4 +- docs/reference/system_log_debug_save.html | 2 +- docs/reference/system_log_entry.html | 2 +- docs/reference/system_log_init.html | 2 +- docs/reference/system_select_set.html | 2 +- docs/reference/system_set_bolus.html | 2 +- docs/reference/system_set_covariate.html | 2 +- docs/reference/system_set_iiv.html | 2 +- docs/reference/system_set_rate.html | 2 +- docs/reference/system_view.html | 6 +- docs/reference/system_zero_inputs.html | 2 +- docs/reference/tic.html | 2 +- docs/reference/toc.html | 2 +- docs/reference/vp.html | 2 +- docs/reference/workshop_fetch.html | 28 +-- docs/search.json | 2 +- inst/ubinc/perl/build_system.pl | 10 + inst/ubinc/systems/system-in_vitro.txt | 3 + inst/ubinc/templates/r_nlmixr.R | 2 +- vignettes/Language.Rmd | 12 +- 30 files changed, 362 insertions(+), 346 deletions(-) diff --git a/docs/articles/Deployment.html b/docs/articles/Deployment.html index ff410c5..4bf03c8 100644 --- a/docs/articles/Deployment.html +++ b/docs/articles/Deployment.html @@ -93,7 +93,7 @@

John Harrold & Anson K Abraham

-

2024-10-23

+

2024-10-25

Source: vignettes/Deployment.Rmd
Deployment.Rmd
diff --git a/docs/articles/In_Vitro.html b/docs/articles/In_Vitro.html index 6881eed..ba9a245 100644 --- a/docs/articles/In_Vitro.html +++ b/docs/articles/In_Vitro.html @@ -193,85 +193,85 @@

The dataset: in_vitro_er_data.cs

This table contains a snapshot of the relevant columns of the dataset:

- - + +
- - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + +

C_A0

C_B0

Effect

treat

samp_time

C_A0

C_B0

Effect

treat

samp_time

0.001

0.1

102.15401

A_0_001_B_0_1

1

0.001

0.1

102.15401

A_0_001_B_0_1

1

0.001

0.1

100.78589

A_0_001_B_0_1

1

0.001

0.1

100.78589

A_0_001_B_0_1

1

0.001

0.1

91.14621

A_0_001_B_0_1

1

0.001

0.1

91.14621

A_0_001_B_0_1

1

0.001

100

93.38012

A_0_001_B_100

1

0.001

100

93.38012

A_0_001_B_100

1

0.001

100

91.03467

A_0_001_B_100

1

0.001

100

91.03467

A_0_001_B_100

1

0.001

100

86.20118

A_0_001_B_100

1

0.001

100

86.20118

A_0_001_B_100

1

0.001

500

51.76744

A_0_001_B_500

1

0.001

500

51.76744

A_0_001_B_500

1

0.001

500

48.95016

A_0_001_B_500

1

0.001

500

48.95016

A_0_001_B_500

1

0.001

500

52.68611

A_0_001_B_500

1

0.001

500

52.68611

A_0_001_B_500

1

0.001

1000

28.46122

A_0_001_B_1000

1

0.001

1000

28.46122

A_0_001_B_1000

1
@@ -473,6 +473,9 @@

Contents of system-in_vitro.txtVariance parameters <VP>

Parameter estimation information <EST:?>?

-

Currently applies only to nlmixr2/rxode2. Essentially all the -parameters not listed here will be fixed.

+

Currently applies only to nlmixr2/rxode +. Essentially all the parameters not listed here will be +fixed.

This descriptor specifies information about parameters for estimation. Sometimes it is necessary to estimate parameters in the log space. Here you can specify the parmaeters to log transform (LT). If you @@ -485,8 +486,9 @@

Model inputs

Bolus dosing <B:times>, <B:events> @@ -636,7 +638,6 @@

Model outputs

Output error model <OE:?> ?

-

Current applies only to nlmixr2/rxode2 output.

This links parameters defined using <VP:?> to specific outputs defined using . You can define either add for additive and/or prop for proportional error:

@@ -654,17 +655,18 @@

Output error model <OE:?> ? 
<OE:Cp> add=add_err; prop=prop_err

There are certain target-specific considerations. For example if you -are using Matlab or R and you just wanted to do a weighted least squares -estimation proportional to the prediction squared you would use the -following but fix prop_err as 1.

+are using Matlab or R and you just +wanted to do a weighted least squares estimation proportional to the +prediction squared you would use the following but fix +prop_err as 1.

<OE:Cp> prop=prop_err

To do least squares estimation you could do the following and fix add_err as 1.

<OE:Cp> add=add_err

These represent the default values though it’s possible to overwrite -them. In the Matlab and R workflows if you define the variance at the -cohort level, the error models in the system file will be overwritten. -## Functions and operators

+them. In the Matlab and R workflows if +you define the variance at the cohort level, the error models in the +system file will be overwritten. ## Functions and operators

Most of the standard operators behave as expected (+, -, *, & /) because most languages use these consistently. There are however certain operators @@ -1007,9 +1009,9 @@

Concentrations vs amountssystem.txt to tell ubiquity to generate perform this conversion on the differential equations.

For example, if you defined the state Cc but want it to -be Ac within the nlmixr2 model target. These are related by -Cc = Ac/Vc and Vc is a parameter the following -would be used:

+be Ac within the nlmixr2 model target. +These are related by Cc = Ac/Vc and Vc is a +parameter the following would be used:

<AMTIFY> Cc; Ac; Vc

diff --git a/docs/articles/NCA.html b/docs/articles/NCA.html index cff4a39..40bd547 100644 --- a/docs/articles/NCA.html +++ b/docs/articles/NCA.html @@ -451,166 +451,166 @@

Summarizing Datacomponents field.

- - + +
- - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + +

ID

Cmax

Tmax

Half-life

AUC last

ID

Cmax

Tmax

Half-life

AUC last

(ng/ml)

(ng/ml)

1

9,950

1

423

1,760,000

1

9,950

1

423

1,760,000

2

11,300

1

477

2,510,000

2

11,300

1

477

2,510,000

3

7,420

1

500

2,320,000

3

7,420

1

500

2,320,000

4

5,760

1

589

1,650,000

4

5,760

1

589

1,650,000

5

6,460

1

574

1,890,000

5

6,460

1

574

1,890,000

6

9,460

1

526

2,450,000

6

9,460

1

526

2,450,000

7

13,800

1

627

3,230,000

7

13,800

1

627

3,230,000

8

7,160

1

567

1,970,000

8

7,160

1

567

1,970,000

9

9,180

1

561

2,180,000

9

9,180

1

561

2,180,000

10

4,760

1

500

1,250,000

10

4,760

1

500

1,250,000

11

4,670

1

599

1,630,000

11

4,670

1

599

1,630,000

12

12,100

1

546

2,620,000

12

12,100

1

546

2,620,000

13

6,380

1

581

2,010,000

13

6,380

1

581

2,010,000

14

5,130

1

549

1,620,000

14

5,130

1

549

1,620,000

15

4,910

1

751

1,890,000

15

4,910

1

751

1,890,000

16

7,580

1

619

1,640,000

16

7,580

1

619

1,640,000

17

10,200

1

507

2,500,000

17

10,200

1

507

2,500,000

18

10,600

1

639

2,900,000

18

10,600

1

639

2,900,000

Mean (Std Dev)

563 (73.1)

2110000 (517000)

Mean (Std Dev)

563 (73.1)

2110000 (517000)

Median

1

Median

1
diff --git a/docs/articles/Reporting.html b/docs/articles/Reporting.html index 4661b78..827f4bf 100644 --- a/docs/articles/Reporting.html +++ b/docs/articles/Reporting.html @@ -650,153 +650,153 @@

PowerPoint - - + +
- - - + + + - - - + + + - - - + + + - - + + - - - + + + - - + + - - - + + + - - - + + + - - + + - - + + - - - + + + - - + + - - + + - - - + + + - - + + - - + + - - + + - - + + - - + + - - - + + + - - + + - - + + - - + + - - + + - - + + - - - + + + - - + + - - + + - - + + - - - + + + - - + + - - + + - - + +

Master/Template

onbrand

Content

Master/Template

onbrand

Content

Name

Placeholder

Type

Name

Placeholder

Type

title_slide

title

text

title_slide

title

text

sub_title

text

sub_title

text

section_slide

title

text

section_slide

title

text

sub_title

text

sub_title

text

title_only

title

text

title_only

title

text

content_text

title

text

content_text

title

text

sub_title

text

sub_title

text

content_body

text

content_body

text

content_list

title

text

content_list

title

text

sub_title

text

sub_title

text

content_body

list

content_body

list

two_content_header_list

title

text

two_content_header_list

title

text

sub_title

text

sub_title

text

content_left_header

text

content_left_header

text

content_left

list

content_left

list

content_right_header

text

content_right_header

text

content_right

list

content_right

list

two_content_header_text

title

text

two_content_header_text

title

text

sub_title

text

sub_title

text

content_left_header

text

content_left_header

text

content_left

text

content_left

text

content_right_header

text

content_right_header

text

content_right

text

content_right

text

two_content_list

title

text

two_content_list

title

text

sub_title

text

sub_title

text

content_left

list

content_left

list

content_right

list

content_right

list

two_content_text

title

text

two_content_text

title

text

sub_title

text

sub_title

text

content_left

text

content_left

text

content_right

text

content_right

text
@@ -809,70 +809,70 @@

Word following styles defined. When you create the onbrand mapping file you will need to use the onbrand Style name listed.

- - + +
- - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + +

onbrand

Word

Style

onbrand

Word

Style

Style

Style

Type

Style

Style

Type

Code

Code

paragraph

Code

Code

paragraph

Figure_Caption

graphic title

paragraph

Figure_Caption

graphic title

paragraph

Heading_1

heading 1

paragraph

Heading_1

heading 1

paragraph

Heading_2

heading 2

paragraph

Heading_2

heading 2

paragraph

Heading_3

heading 3

paragraph

Heading_3

heading 3

paragraph

Normal

Normal

paragraph

Normal

Normal

paragraph

Notes

Notes

paragraph

Notes

Notes

paragraph

TOC

toc 1

paragraph

TOC

toc 1

paragraph

Table_Caption

table title

paragraph

Table_Caption

table title

paragraph

Table

Table Grid

table

Table

Table Grid

table
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 76d9ccd..f0556bb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: Reporting: Reporting.html Simulation: Simulation.html Titration: Titration.html -last_built: 2024-10-24T04:17Z +last_built: 2024-10-26T03:10Z urls: reference: https://r.ubiquity.tools/reference article: https://r.ubiquity.tools/articles diff --git a/docs/reference/build_system.html b/docs/reference/build_system.html index b0ae5c5..21b4b11 100644 --- a/docs/reference/build_system.html +++ b/docs/reference/build_system.html @@ -134,7 +134,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Creating output directory diff --git a/docs/reference/system_fetch_iiv.html b/docs/reference/system_fetch_iiv.html index 8848c55..017461a 100644 --- a/docs/reference/system_fetch_iiv.html +++ b/docs/reference/system_fetch_iiv.html @@ -112,7 +112,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_fetch_parameters.html b/docs/reference/system_fetch_parameters.html index 8944653..7441d6e 100644 --- a/docs/reference/system_fetch_parameters.html +++ b/docs/reference/system_fetch_parameters.html @@ -100,7 +100,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_fetch_set.html b/docs/reference/system_fetch_set.html index dd166fd..46a13d4 100644 --- a/docs/reference/system_fetch_set.html +++ b/docs/reference/system_fetch_set.html @@ -101,7 +101,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_fetch_template.html b/docs/reference/system_fetch_template.html index 50ff6ed..6c243df 100644 --- a/docs/reference/system_fetch_template.html +++ b/docs/reference/system_fetch_template.html @@ -137,7 +137,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system @@ -152,7 +152,7 @@

Examplesfr = system_fetch_template(cfg, template = "Simulation", output_directory = tempdir()) -#> → Creating file: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwEhjBf/analysis_simulate.R +#> → Creating file: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz9swW/analysis_simulate.R # }

diff --git a/docs/reference/system_log_debug_save.html b/docs/reference/system_log_debug_save.html index 47869a9..c326f4c 100644 --- a/docs/reference/system_log_debug_save.html +++ b/docs/reference/system_log_debug_save.html @@ -111,7 +111,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_log_entry.html b/docs/reference/system_log_entry.html index 86fe84d..00d3717 100644 --- a/docs/reference/system_log_entry.html +++ b/docs/reference/system_log_entry.html @@ -101,7 +101,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_log_init.html b/docs/reference/system_log_init.html index 3828347..cd95cb7 100644 --- a/docs/reference/system_log_init.html +++ b/docs/reference/system_log_init.html @@ -97,7 +97,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_select_set.html b/docs/reference/system_select_set.html index b3af472..d2b3008 100644 --- a/docs/reference/system_select_set.html +++ b/docs/reference/system_select_set.html @@ -114,7 +114,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_set_bolus.html b/docs/reference/system_set_bolus.html index 1f2fd19..531219e 100644 --- a/docs/reference/system_set_bolus.html +++ b/docs/reference/system_set_bolus.html @@ -113,7 +113,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_set_covariate.html b/docs/reference/system_set_covariate.html index 0607136..606f177 100644 --- a/docs/reference/system_set_covariate.html +++ b/docs/reference/system_set_covariate.html @@ -115,7 +115,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_set_iiv.html b/docs/reference/system_set_iiv.html index 8797fe5..7af6ba0 100644 --- a/docs/reference/system_set_iiv.html +++ b/docs/reference/system_set_iiv.html @@ -116,7 +116,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_set_rate.html b/docs/reference/system_set_rate.html index b02b482..6e74aaf 100644 --- a/docs/reference/system_set_rate.html +++ b/docs/reference/system_set_rate.html @@ -113,7 +113,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/system_view.html b/docs/reference/system_view.html index c340063..2ea3e11 100644 --- a/docs/reference/system_view.html +++ b/docs/reference/system_view.html @@ -119,7 +119,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system @@ -159,8 +159,8 @@

Examples#> → field | values | scaling | units #> → -------------------------------------------------- #> → times | 0 7 14 | 1 | days -#> → At | 400 0 0 | 1e3/MW | mg #> → Cc | 0 0 0 | 1e3/MW/Vc | mg +#> → At | 400 0 0 | 1e3/MW | mg #> → -------------------------------------------------- #> → Infusion rate details #> → Rate | field | values | scaling | units @@ -193,9 +193,9 @@

Examples#> → On parameters #> → ka, ETAka(LN) #> → Vc, ETAVc(LN) +#> → Vp, ETAVp(LN) #> → CL, ETACL(LN) #> → Q, ETAQ(LN) -#> → Vp, ETAVp(LN) #> → #> → integrate_with c-file #> → output_times min = 0; max = 10.0; length = 101 diff --git a/docs/reference/system_zero_inputs.html b/docs/reference/system_zero_inputs.html index 7a74d31..b023542 100644 --- a/docs/reference/system_zero_inputs.html +++ b/docs/reference/system_zero_inputs.html @@ -115,7 +115,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpwE +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmprz #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system diff --git a/docs/reference/tic.html b/docs/reference/tic.html index 3ae1ef2..d0974d2 100644 --- a/docs/reference/tic.html +++ b/docs/reference/tic.html @@ -96,7 +96,7 @@

ExamplesSys.sleep(3) toc() #> elapsed -#> 3.011 +#> 3.016