From ad27c6f503a831216be15858677f57000d13c5ef Mon Sep 17 00:00:00 2001 From: John Harrold Date: Sat, 19 Oct 2024 20:29:30 -0700 Subject: [PATCH] Updated the documentation. --- docs/articles/Howto.html | 4 +- docs/articles/Language.html | 5 +- 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 +- vignettes/Language.Rmd | 7 +- 26 files changed, 277 insertions(+), 271 deletions(-) diff --git a/docs/articles/Howto.html b/docs/articles/Howto.html index de64230..87795ae 100644 --- a/docs/articles/Howto.html +++ b/docs/articles/Howto.html @@ -317,7 +317,7 @@

Models in different formats< # Outputs and error models Cc_mg_ml = Cc - Cc_mg_ml ~ prop(prop_err) + add(add_err) + Cc_mg_ml ~ add(add_err) + prop(prop_err) }) } @@ -370,7 +370,7 @@

Models in different formats< Cp)/Vc + Dinf/Vc) d/dt(Cp) = (+Q * (Cc - Cp)/Vt) Cc_mg_ml = Cc - Cc_mg_ml ~ prop(prop_err) + add(add_err) + Cc_mg_ml ~ add(add_err) + prop(prop_err) }) } diff --git a/docs/articles/Language.html b/docs/articles/Language.html index 872c460..d3ed069 100644 --- a/docs/articles/Language.html +++ b/docs/articles/Language.html @@ -220,6 +220,8 @@

Variance parameters <VP>

Parameter estimation information <EST:?>?

+

Currently applies only to nlmixr2/rxode2. 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 @@ -233,12 +235,11 @@

Parameter estimation information < want to estimate a subset of parameters (P), say P1 and P2, you can use the following:

<EST:P> P1; P2
-

Applies to nlmixr2. Essentially all the parameters not listed here -will be fixed.

Output error model <OE:?> ?

+

Current applies only to nlmixr2/rxode2 output.

This defines the output error model of the format:

`<OE:OUTPUT> expression`

The OUTPUT can be the name of any output defined with diff --git a/docs/articles/NCA.html b/docs/articles/NCA.html index a6d93d0..f2fc6de 100644 --- a/docs/articles/NCA.html +++ b/docs/articles/NCA.html @@ -448,166 +448,166 @@

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 dd0efb3..6d856e1 100644 --- a/docs/articles/Reporting.html +++ b/docs/articles/Reporting.html @@ -648,153 +648,153 @@

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
@@ -807,70 +807,70 @@

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 b9f6df8..9c311b6 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: Reporting: Reporting.html Simulation: Simulation.html Titration: Titration.html -last_built: 2024-10-20T00:02Z +last_built: 2024-10-20T03:26Z 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 6758676..f05bded 100644 --- a/docs/reference/build_system.html +++ b/docs/reference/build_system.html @@ -133,7 +133,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 610e938..5f074c9 100644 --- a/docs/reference/system_fetch_iiv.html +++ b/docs/reference/system_fetch_iiv.html @@ -111,7 +111,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 56bdc47..f050918 100644 --- a/docs/reference/system_fetch_parameters.html +++ b/docs/reference/system_fetch_parameters.html @@ -99,7 +99,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 da0c550..bac7163 100644 --- a/docs/reference/system_fetch_set.html +++ b/docs/reference/system_fetch_set.html @@ -100,7 +100,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 81b4eea..f213ec6 100644 --- a/docs/reference/system_fetch_template.html +++ b/docs/reference/system_fetch_template.html @@ -136,7 +136,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system @@ -151,7 +151,7 @@

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

diff --git a/docs/reference/system_log_debug_save.html b/docs/reference/system_log_debug_save.html index e38261b..fb69502 100644 --- a/docs/reference/system_log_debug_save.html +++ b/docs/reference/system_log_debug_save.html @@ -110,7 +110,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 c1bb7aa..0d5b614 100644 --- a/docs/reference/system_log_entry.html +++ b/docs/reference/system_log_entry.html @@ -100,7 +100,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 d12de8d..64fb657 100644 --- a/docs/reference/system_log_init.html +++ b/docs/reference/system_log_init.html @@ -96,7 +96,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 e74e037..50ddd3a 100644 --- a/docs/reference/system_select_set.html +++ b/docs/reference/system_select_set.html @@ -113,7 +113,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 266444a..e1450f0 100644 --- a/docs/reference/system_set_bolus.html +++ b/docs/reference/system_set_bolus.html @@ -112,7 +112,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 672cfad..636696d 100644 --- a/docs/reference/system_set_covariate.html +++ b/docs/reference/system_set_covariate.html @@ -114,7 +114,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 4be9600..5052fc1 100644 --- a/docs/reference/system_set_iiv.html +++ b/docs/reference/system_set_iiv.html @@ -115,7 +115,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 a218812..fb9218b 100644 --- a/docs/reference/system_set_rate.html +++ b/docs/reference/system_set_rate.html @@ -112,7 +112,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 d8db7c9..1a73b59 100644 --- a/docs/reference/system_view.html +++ b/docs/reference/system_view.html @@ -118,7 +118,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → ubiquity: https://r.ubiquity.tools #> → Distribution: package (2.0.4) #> → Compiling C version of system @@ -191,9 +191,9 @@

Examples#> → #> → On parameters #> → Vc, ETAVc(LN) -#> → CL, ETACL(LN) -#> → Vp, ETAVp(LN) #> → ka, ETAka(LN) +#> → Vp, ETAVp(LN) +#> → CL, ETACL(LN) #> → Q, ETAQ(LN) #> → #> → integrate_with c-file diff --git a/docs/reference/system_zero_inputs.html b/docs/reference/system_zero_inputs.html index b6c7603..85a4911 100644 --- a/docs/reference/system_zero_inputs.html +++ b/docs/reference/system_zero_inputs.html @@ -114,7 +114,7 @@

Examples output_directory = file.path(tempdir(), "output"), temporary_directory = tempdir()) #> -#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpHW +#> ── Building the system: /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmpYM #> → 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 6781b3c..4966680 100644 --- a/docs/reference/tic.html +++ b/docs/reference/tic.html @@ -95,7 +95,7 @@

ExamplesSys.sleep(3) toc() #> elapsed -#> 3.008 +#> 3.012