From b4c9db7af8f24255c073157c63134f3eb7b3de40 Mon Sep 17 00:00:00 2001 From: John Harrold Date: Wed, 18 Sep 2024 20:02:03 -0700 Subject: [PATCH] Doc update. --- .../Accessing_Figures_and_Tables.html | 80 +++--- .../Reporting_nlmixr_Fit_Results.html | 234 +++++++++--------- docs/pkgdown.yml | 2 +- docs/reference/build_figures.html | 4 +- docs/reference/fetch_option.html | 2 +- docs/reference/mk_error_tab.html | 2 +- docs/search.json | 2 +- 7 files changed, 161 insertions(+), 165 deletions(-) diff --git a/docs/articles/Accessing_Figures_and_Tables.html b/docs/articles/Accessing_Figures_and_Tables.html index 9648284..0f55a4e 100644 --- a/docs/articles/Accessing_Figures_and_Tables.html +++ b/docs/articles/Accessing_Figures_and_Tables.html @@ -133,71 +133,67 @@

Using report objects in RMarkdownfig_title = bfres$rptfigs$dv_vs_pred$title_proc

And you can include them in RMarkdown using the following:

![`r fig_title`](`r fig_path`){width=80%}
-
-if(file.exists(fig_path)){
-  file.copy(fig_path, "vignettes/", overwrite=TRUE)
-}
dv_vs_pred title
dv_vs_pred title

Tables are used in a similiar fashion. This code will extract the flextable object and title for the pest_table. Then it attaches the title as a caption and displays it below.

-
+
 tab_ft    = btres$rpttabs$pest_table$table$ft[[1]]
 tab_title = btres$rpttabs$pest_table$title_proc
 tab_ft_knit = flextable::set_caption(tab_ft, caption = tab_title)
 
 tab_ft_knit

 

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 Parameter Estimates
 
Parameter
Est.
SE
%RSE
Back-transformed(95%CI)
BSV(CV%)
Shrink(SD)%
Parameter
Est.
SE
%RSE
Back-transformed(95%CI)
BSV(CV%)
Shrink(SD)%

 

 
 
Log Ka
0.476
0.203
42.7
1.61 (1.08, 2.39)
69.8
1.23%<
Log Ka
0.476
0.203
42.7
1.61 (1.08, 2.39)
69.8
1.23%<

 

 
Log Cl
1.02
0.0754
7.42
2.76 (2.38, 3.2)
26.1
2.36%<
Log Cl
1.02
0.0754
7.42
2.76 (2.38, 3.2)
26.1
2.36%<

 

 
Log V
3.46
0.0632
1.83
31.8 (28.1, 36)
13.8
9.71%<
Log V
3.46
0.0632
1.83
31.8 (28.1, 36)
13.8
9.71%<

 

 
add.sd
0.696
0.696
 
 
add.sd
0.696
0.696
 
 

 

 
 

diff --git a/docs/articles/Reporting_nlmixr_Fit_Results.html b/docs/articles/Reporting_nlmixr_Fit_Results.html
index e5e2362..252bd02 100644
--- a/docs/articles/Reporting_nlmixr_Fit_Results.html
+++ b/docs/articles/Reporting_nlmixr_Fit_Results.html
@@ -514,153 +514,153 @@ 
PowerPoint
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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

 

 
 

@@ -672,70 +672,70 @@ 
Word
 
Similarly, to create an onbrand Word template you will
 need to the following onbrand styles defined.

 

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onbrand
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onbrand
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Style
Type
Style
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Type

 

 
 
 
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paragraph
Code
Code
paragraph

 

 
Figure_Caption
graphic title
paragraph
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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
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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 3d601b5..41cad7a 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,4 +4,4 @@ pkgdown_sha: ~
 articles:
   Accessing_Figures_and_Tables: Accessing_Figures_and_Tables.html
   Reporting_nlmixr_Fit_Results: Reporting_nlmixr_Fit_Results.html
-last_built: 2024-09-19T02:48Z
+last_built: 2024-09-19T02:59Z
diff --git a/docs/reference/build_figures.html b/docs/reference/build_figures.html
index 09e11b4..98d186a 100644
--- a/docs/reference/build_figures.html
+++ b/docs/reference/build_figures.html
@@ -136,7 +136,7 @@ 
Examples#> `geom_smooth()` using formula = 'y ~ x'
 #> `geom_smooth()` using formula = 'y ~ x'
 #>   •
-#>   /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN/dv_vs_pred-Word.png
+#>   /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN/dv_vs_pred-Word.png
 #> → bad_figure
 #> 
 #> ── Figure generation failed 
@@ -147,7 +147,7 @@ 
Examples#> → command run:
 #> → bad_figure_command
 #>   •
-#>   /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN/bad_figure-Word.png
+#>   /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN/bad_figure-Word.png
 #> → skip_figure
diff --git a/docs/reference/fetch_option.html b/docs/reference/fetch_option.html index dec6d7b..2501914 100644 --- a/docs/reference/fetch_option.html +++ b/docs/reference/fetch_option.html @@ -110,7 +110,7 @@

Examples#> NULL #> #> $value -#> [1] "/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN" +#> [1] "/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN" #> diff --git a/docs/reference/mk_error_tab.html b/docs/reference/mk_error_tab.html index 0d50ecc..410ae5b 100644 --- a/docs/reference/mk_error_tab.html +++ b/docs/reference/mk_error_tab.html @@ -70,7 +70,7 @@

Value

Examples

error_tab = mk_error_tab("This is an error")
 error_tab$ft[[1]]
-
Error
This is an error
+

Error

This is an error

diff --git a/docs/search.json b/docs/search.json index d88e315..8fff69a 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Accessing Figures and Tables","text":"create report_fit.yaml file defined figures tables reporting. However may want reuse report objects outside Word PowerPoint. example may want use inside Shiny Apps RMarkdown document. vignette outlines can build objects outside nlmixr2rpt workflow.","code":""},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"creating-figures-and-tables","dir":"Articles","previous_headings":"","what":"Creating figures and tables","title":"Accessing Figures and Tables","text":"First need load appropriate libraries. need onbrand library tables figures generated based type report. Specifically default figure dimensions change based report type. initialize empty Word report onbrand. report type extracted object functions . nlmixr2 fit object analysis. load example package. Next read yaml file using yaml_read_fit(). using stripped example testing. contents yaml file stored rptdetails list element returned. Now can use rptdetails object just created create figures tables using build_figures() build_tables() functions respectively.","code":"library(nlmixr2rpt) library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) fit = fetch_fit_example() rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails bfres = build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) btres = build_tables(obnd = obnd, fit = fit, rptdetails = rptdetails)"},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"using-report-objects-in-rmarkdown","dir":"Articles","previous_headings":"","what":"Using report objects in RMarkdown","title":"Accessing Figures and Tables","text":"can look help two build functions . objects create contain information figures tables defined report_fit.yaml file. access figure just need specify figure ID. example path title figure containing dv_vs_pred figure can found : can include RMarkdown using following: Tables used similiar fashion. code extract flextable object title pest_table. attaches title caption displays . Parameter Estimates Parameter Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)% Log Ka 0.476 0.203 42.7 1.61 (1.08, 2.39) 69.8 1.23%< Log Cl 1.02 0.0754 7.42 2.76 (2.38, 3.2) 26.1 2.36%< Log V 3.46 0.0632 1.83 31.8 (28.1, 36) 13.8 9.71%< add.sd 0.696 0.696","code":"fig_path = bfres$rptfigs$dv_vs_pred$figure[[1]] fig_title = bfres$rptfigs$dv_vs_pred$title_proc ![`r fig_title`](`r fig_path`){width=80%} if(file.exists(fig_path)){ file.copy(fig_path, \"vignettes/\", overwrite=TRUE) } tab_ft = btres$rpttabs$pest_table$table$ft[[1]] tab_title = btres$rpttabs$pest_table$title_proc tab_ft_knit = flextable::set_caption(tab_ft, caption = tab_title) tab_ft_knit"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Reporting nlmixr2 Fit Results","text":"purpose nlmixr2rpt automate reporting nlmixr2 analyses. accomplished creating yaml file contains reporting options, figure table generation code, general content Word PowerPoint files.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"general-workflow","dir":"Articles","previous_headings":"","what":"General workflow","title":"Reporting nlmixr2 Fit Results","text":"First need nlmixr2 fit object. ’re going load fit example stored package: Next need create onbrand report objects. create report objects PowerPoint (obnd_pptx) Word (obnd_docx). Next add report elements report objects using report_fit() function. function can used types report. contents different depending document type. function append report elements supplied fit object supplied report. multiple fit objects can added sequentially. can also add report content using onbrand officer functions. ’re done just need save reports: contents report type defined yaml file. commands use default value found nlmixr2rpt package. customize report elements can make copy file current working directory: can edit my_report.yaml file call report_fit() provide yaml file rptyaml argument. following section describe elements yaml report format.","code":"library(nlmixr2rpt) library(onbrand) # This will create an example fit object to use in the examples below fit = fetch_fit_example() obnd_pptx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_docx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_pptx = report_fit( fit = fit, obnd = obnd_pptx) obnd_docx = report_fit( fit = fit, obnd = obnd_docx) save_report(obnd_pptx, \"report.pptx\") save_report(obnd_docx, \"report.docx\") file.copy(system.file(package=\"nlmixr2rpt\", \"templates\", \"report_fit.yaml\"), \"my_report.yaml\")"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"the-yaml-report-file-structure","dir":"Articles","previous_headings":"","what":"The yaml report file structure","title":"Reporting nlmixr2 Fit Results","text":"core nlmixr2rpt yaml reporting file. outline main sections describe expected elements sections.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"placeholders","dir":"Articles","previous_headings":"The yaml report file structure","what":"placeholders","title":"Reporting nlmixr2 Fit Results","text":"may wish create report template placeholders. example want create generic template population PK analysis, may useful label figures generically. can use section define placeholders applied report created. example consider yaml code : create report can label y-axis generically : \"===CMPD=== (===CUNITS===)\" report built, become: \"Compound Name (Conc Units)\" Notice OBJ placeholder contains R Code. default reporting process try evaluate placeholders R Code. fails revert back string supplied. run problems can quote placeholder value double single quotes. example: ISSTR field just result string \"ls()\" ISCMD field return list objects environment string evaluated. also possible overwrite contents file runtime providing placeholders (placeholder) argument report_fit(). Note: Fields support placeholders indicated [PH] fields evaluable code indicated [EV].","code":"placeholders: CMPD: Compound Name CUNITS: Conc Units OBJ: sprintf(\"%3g\", fit$objf) ISSTR:\"'ls()'\" ISCMD: ls()"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"parameters","dir":"Articles","previous_headings":"The yaml report file structure","what":"parameters","title":"Reporting nlmixr2 Fit Results","text":"certain reporting elements may better present parameters differently parameter names used model. nlmixr can use comment parameter definition specify alternate text. function gen_pest_table() use alternate text present. parameters section flexability parameters reported. can define parameters want whether present model . used present. tables Word PowerPoint can specify names using markdown (md), otherwise can specify handled text environments (txt). example intrinsic clearance may called lCLint model. can specify : also possible overwrite contents file runtime providing parameters argument report_fit(). Note: specify parameter name overwrite alternate text specified model ini().","code":"parameters: lCLint: md: \"CL~int~ (L/hr)\" txt: \"CLint (L/hr)\""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"covariates","dir":"Articles","previous_headings":"The yaml report file structure","what":"covariates","title":"Reporting nlmixr2 Fit Results","text":"figure table generation can useful covariates defined. can define either categorical (cat) continuous (cont). example define categorical covariates SEX ROUTE continuous covariate WT following: don’t need covariates can set NULL. want overwrite runtime can specify different values calling report_fit(). available figure table runtime environments objects cat_covars categorical covariates cont_covars continuous covariates.","code":"covariates: cat: [\"SEX\", \"ROUTE\"] cont: [\"WT\"]"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"options","dir":"Articles","previous_headings":"The yaml report file structure","what":"options","title":"Reporting nlmixr2 Fit Results","text":"section allows control general report options. element can either explicit value. identified evaluable [EV] first attempt evaluate R code. fails explicit value used. following options supported expected data type parentheses: output_dir[PH,EV] - location figures generated (character) resolution[EV] - Resolution figures generated (numeric) figenv_preamble tabenv_preamble - User-defined code evaluated figures tables built (specify libraries needed, source files containing user defined code, etc.) fig_stamp[PH] - set string stamp contents string lower left portion figure writing. applies figures p_res object either vanilla ggplot object, paginated ggforce object, result ggarrage ggpubr package. Along regular placeholders, option can also contain ===FILE=== placeholder. replaced full path figure file generated.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"building-figures-tables","dir":"Articles","previous_headings":"The yaml report file structure","what":"Building figures & tables","title":"Reporting nlmixr2 Fit Results","text":"Figures tables defined terms R code evaluated. several objects available environment can used creating report elements. following objects defined: fid - current figure ID (figure environment ) tid - current table ID (table environment ) fit - nlmixr2 fit object cat_covars - character object containing categorical covariates cont_covars - character object containing continuous covariates height - figure height inches (figure environment ) obnd - onbrand object report document output_dir - directory figures stored resolution - resolution figure (figure environment ) rptdetails - result reading report yaml file rpttype - either “Word” “PowerPoint” width - figure width inches (figure environment ) xpdb - default yaml file contains code preamble create object running xpose_data_nlmixr(fit) (figure environment )","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"figures","dir":"Articles","previous_headings":"The yaml report file structure","what":"figures","title":"Reporting nlmixr2 Fit Results","text":"figures section consists figure IDs. IDs used defining Word PowerPoint report contents. Consider example: creates figure ID dv_vs_pred. following elements: orientation - Orientation used Word report, can either “portrait” “landscape”. caption[PH] - Figure caption Word reports. caption_format - element optional can either \"text\"(default plain text) \"md\" (Markdown). title[PH] - Slide title figure used PowerPoint. cmd[PH] - Command generate figure. Note: cmd evaluated needs create variable called p_res. can either ggplot object, paginated object ggforce, result ggarrage ggpubr package, vector file names containing image files created code cmd. want conditionally skip reporting figure, can instead set value p_res NA. generate message prevent inclusion build error final document. also include libraries want relevant preamble section ensure functions available .","code":"figures: dv_vs_pred: orientation: \"portrait\" caption: \"dv_vs_pred caption\" caption_format: \"text\" title: \"dv_vs_pred title\" cmd: |- p_res <- dv_vs_pred(xpdb, caption=NULL, title=NULL) + xlab(\"Observed ===CMPD=== Concentrations (===CUNITS===)\") + ylab(\"Population Predicted ===CMPD=== Concentrations (===CUNITS===)\")"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"tables","dir":"Articles","previous_headings":"The yaml report file structure","what":"tables","title":"Reporting nlmixr2 Fit Results","text":"Tables behave similarly figures. tables section create table ID following options specified. orientation - Orientation used Word report, can either “portrait” “landscape”. caption[PH] - Table caption Word reports. caption_format - element optional can either \"text\"(default plain text) \"md\" (Markdown). title[PH] - Slide title table used PowerPoint. cmd[PH] - Command generate table. example create table parameter estimates. Note: cmd evaluated needs create variable called t_res. list can contain following elements: df - List data frames containing tabular information. ft - List flextables containing tabular information supply data frames list element, converted flextables internally. Flextables span multiple pages automatically. prefer caption page can split tables manually multiple data frames/flextables. reporting functionality written support table spanning multiple pages. define separate table page need add sequential list elements df ft elements. example: single table want span multiple pages automatically simply specify first element listed (e.g. t_res$df[[1]]). want conditionally skip generation table, simply set t_res NA. Like figures , signal reporting functions want generate table current fit object. also prevent generation build error.","code":"tables: pest_table: orientation: \"portrait\" caption: \"Parameter Estimates\" caption_format: \"text\" title: \"Parameter Estimates\" cmd: |- t_res <- gen_pest_table( fit = fit, obnd = obnd, rptdetails = rptdetails) t_res$df = list() t_res$df[[1]] = data.frame() t_res$df[[2]] = data.frame() etc t_res$ft = list() t_res$ft[[1]] = flextable::flextable() t_res$ft[[2]] = flextable::flextable() etc"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"pptx","dir":"Articles","previous_headings":"The yaml report file structure","what":"pptx","title":"Reporting nlmixr2 Fit Results","text":"section defines general aspects PowerPoint reports also contents report relating fitting results. figures tables sections contain onbrand slide master names (\"content_text\") used hold objects. slides created title specified figure table IDs. placeholder name title (\"title\") must specified well placeholder name content (\"content_body\"). Figures PowerPoint reports must generated dimensions placeholder, important width height elements specified inches. actual content specified content section. list keywords followed value. table keyword followed table ID defined tables section. Similarly figure keyworld followed figure ID defined figures section:","code":"pptx: figures: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" width: 9.5 height: 5.0 tables: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" content: - table: pest_table - figure: ind_plots - figure: dv_vs_pred - figure: dv_vs_ipred - figure: res_vs_pred - figure: res_vs_idv - figure: prm_vs_iteration - figure: absval_res_vs_pred"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"docx","dir":"Articles","previous_headings":"The yaml report file structure","what":"docx","title":"Reporting nlmixr2 Fit Results","text":"section starts general information word documents. figures section defines height width figures landscape portrait orientations. units inches. Just like PowerPoint content defined content section. can defined figure table PowerPoint. Content can also include text elements well. Just specify onbrand style control general formatting.","code":"docx: figures: landscape: width: 8.0 height: 4.2 portrait: width: 6.5 height: 6.0 content: - text: text: \"Figures\" style: Heading_1 - figure: dv_vs_pred - figure: ind_plots - figure: dv_vs_ipred - figure: res_vs_pred - figure: res_vs_idv - figure: prm_vs_iteration - figure: absval_res_vs_pred - text: text: \"Tables\" style: Heading_1 - table: pest_table"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"customizing-reports-for-your-organization","dir":"Articles","previous_headings":"","what":"Customizing reports for your organization","title":"Reporting nlmixr2 Fit Results","text":"reporting done using onbrand package. provides abstraction layer officer package. benefit can use organization Word PowerPoint templates. Simply create appropriate masters PowerPoint styles Word, create brand mapping file. initialize report objects can just provide organizational template mapping files. details create templates mapping files, see vignette onbrand package.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"powerpoint","dir":"Articles","previous_headings":"Customizing reports for your organization","what":"PowerPoint","title":"Reporting nlmixr2 Fit Results","text":"create onbrand PowerPoint template organization need following master slide names define corresponding elements. Master/Template onbrand Content Name Placeholder Type title_slide title text sub_title text section_slide title text sub_title text title_only title text content_text title text sub_title text content_body text content_list title text sub_title text content_body list two_content_header_list title text sub_title text content_left_header text content_left list content_right_header text content_right list two_content_header_text title text sub_title text content_left_header text content_left text content_right_header text content_right text two_content_list title text sub_title text content_left list content_right list two_content_text title text sub_title text content_left text content_right text","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"word","dir":"Articles","previous_headings":"Customizing reports for your organization","what":"Word","title":"Reporting nlmixr2 Fit Results","text":"Similarly, create onbrand Word template need following onbrand styles defined. onbrand Word Style Style Style Type Code Code paragraph Figure_Caption graphic title paragraph Heading_1 heading 1 paragraph Heading_2 heading 2 paragraph Heading_3 heading 3 paragraph Normal Normal paragraph Notes Notes paragraph TOC toc 1 paragraph Table_Caption table title paragraph Table Table Grid table","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"report-configuration-file-report_fit-yaml","dir":"Articles","previous_headings":"","what":"Report configuration file report_fit.yaml","title":"Reporting nlmixr2 Fit Results","text":"","code":"placeholders: CMPD: Compound Name CUNITS: Conc Units TUNITS: Time Units RUN: RUNN OBJ: sprintf(\"%3g\", fit$objf) parameters: lVp: md: \"V~p~\" txt: \"Vp\" add_err: md: \"Add Err\" txt: \"Add Err\" prop_err: md: \"Prop Err\" txt: \"Prop Err\" covariates: cat: NULL cont: NULL options: output_dir: \"file.path(getwd(), '===RUN===')\" resolution: 300 fig_stamp: \"source: ===FILE===\" figenv_preamble: |- library(\"ggplot2\") library(\"xpose\") library(\"ggforce\") if(system.file(package=\"ggPMX\") != \"\"){ library(\"ggPMX\") } xpdb = xpose.nlmixr2::xpose_data_nlmixr(fit) tabenv_preamble: NULL figures: dv_vs_pred_ipred: orientation: \"portrait\" caption: \"Observed vs Predicted\" title: \"Observed vs Predicted\" cmd: |- p_pred <- dv_vs_pred(xpdb, caption=NULL, title=NULL, subtitle=NULL) + ggtitle(\"===CMPD=== (===CUNITS===)\") + coord_fixed()+ ylab(\"Observed\") + xlab(\"Population Predicted\") + theme_light() yrange = layer_scales(p_pred)$y$range$range xrange = layer_scales(p_pred)$x$range$range lb = min(c(yrange,xrange)) ub = max(c(yrange,xrange)) p_pred = p_pred + xlim(c(lb, ub)) + ylim(c(lb,ub)) p_ipred <- dv_vs_ipred(xpdb, caption=NULL, title=NULL, subtitle=NULL) + ggtitle(\"===CMPD=== (===CUNITS===)\") + coord_fixed()+ ylab(\"Observed\") + xlab(\"Individual Predicted\") + theme_light() yrange = layer_scales(p_ipred)$y$range$range xrange = layer_scales(p_ipred)$x$range$range lb = min(c(yrange,xrange)) ub = max(c(yrange,xrange)) p_ipred = p_ipred + xlim(c(lb, ub)) + ylim(c(lb,ub)) p_res <- ggpubr::ggarrange(p_pred, p_ipred, ncol=2, nrow=1 ) res_vs_pred_idv: orientation: \"portrait\" caption: \"CWRES vs Pred and Time\" title: \"CWRES vs Pred and Time\" cmd: |- if(\"CWRES\" %in% names(fit)){ p_pred <- res_vs_pred(xpdb, caption=NULL, title=NULL, res=\"CWRES\") + ggtitle(\"===CMPD=== (===CUNITS===)\") + ylab(\"CWRES\") + xlab(\"Population Predicted\") + theme_light() p_idv <- res_vs_idv(xpdb, caption=NULL, title=NULL, res=\"CWRES\") + ggtitle(\"Time (===CUNITS===)\") + ylab(\"CWRES\") + xlab(\"Time (===TUNITS===)\") + theme_light() p_res <- ggpubr::ggarrange(p_pred, p_idv, ncol=2, nrow=1 ) } else { p_res <- NA } eta_cat: orientation: \"landscape\" caption: \"Effect of categorical covariates\" title: \"Effect of categorical covariates\" cmd: |- if(!is.null(cat_covars)){ if(system.file(package=\"ggPMX\") != \"\"){ ctr = ggPMX::pmx_nlmixr(fit, vpc = FALSE, conts = cont_covars, cats = cat_covars) p_res <- ggPMX::pmx_plot_eta_cats(ctr) + theme_light() } else { p_res <- mk_error_fig(\"ggPMX is not installed\") } } else { p_res <- NA } eta_cont: orientation: \"landscape\" caption: \"Effect of continuous covariates\" title: \"Effect of continuous covariates\" cmd: |- if(!is.null(cont_covars)){ if(system.file(package=\"ggPMX\") != \"\"){ ctr = ggPMX::pmx_nlmixr(fit, vpc = FALSE, conts = cont_covars, cats = cat_covars) p_res <- ggPMX::pmx_plot_eta_conts(ctr) + theme_light() } else { p_res = mk_error_fig(\"ggPMX is not installed\") } } else { p_res <- NA } prm_vs_iteration: orientation: \"landscape\" caption: \"SAEM Stabilization\" title: \"SAEM Stabilization\" cmd: |- p_res <- prm_vs_iteration(xpdb, caption=NULL, title=NULL) + theme_light() ind_plots: orientation: \"landscape\" caption: \"Individual and population prediction overlay\" title: \"Individual and population prediction overlay\" cmd: |- p_res <- ind_plots(xpdb, nrow=3, ncol=4, caption=NULL, title=NULL) + ylab(\" ===CMPD=== (===CUNITS===)\") + xlab(\"Time (===TUNITS===)\") + theme_light() skip_figure: orientation: \"landscape\" caption: \"ind_plots caption\" title: \"ind_plots title\" cmd: |- p_res <- NA tables: skip_table: orientation: \"portrait\" caption: \"Parameter Estimates\" title: \"Parameter Estimates\" cmd: |- t_res <- NA pest_table: orientation: \"portrait\" caption: \"Parameter Estimates\" title: \"Parameter Estimates\" cmd: |- t_res <- gen_pest_table( fit = fit, obnd = obnd, rptdetails = rptdetails) pptx: figures: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" width: 9.5 height: 5.0 tables: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" content: - table: pest_table - table: skip_table - figure: ind_plots - figure: dv_vs_pred_ipred - figure: res_vs_pred_idv - figure: prm_vs_iteration - figure: eta_cont - figure: eta_cat - figure: skip_figure docx: figures: landscape: width: 8.0 height: 4.2 portrait: width: 6.5 height: 6.0 content: - text: text: \"Tables\" style: Heading_1 - table: pest_table - text: text: \"Figures\" style: Heading_1 - figure: ind_plots - figure: dv_vs_pred_ipred - figure: res_vs_pred_idv - figure: prm_vs_iteration - figure: skip_figure - figure: eta_cont - figure: eta_cat"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Harrold. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Harrold J (2024). nlmixr2rpt: Templated Word PowerPoint Reporting 'nlmixr2' Fitting Results. R package version 0.2.1, https://nlmixr2.github.io/nlmixr2rpt/.","code":"@Manual{, title = {nlmixr2rpt: Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results}, author = {John Harrold}, year = {2024}, note = {R package version 0.2.1}, url = {https://nlmixr2.github.io/nlmixr2rpt/}, }"},{"path":"/index.html","id":"nlmixr2rpt-","dir":"","previous_headings":"","what":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"Templated Word PowerPoint reporting nlmixr2","code":""},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"purpose package automate reporting analyses performed nlmixr2 package PowerPoint Word. accomplished yaml file contains specifications report elements (figures tables) well contents Word PowerPoint documents. Internal templates documents report yaml file included. can customized: format document templates can customized organization using onbrand package. report contents can customized creating copy included yaml file modifying suite needs (see vignette ).","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"install CRAN: install development version GitHub","code":"install.packages(\"nlmixr2rpt\", dependencies = TRUE) #install.packages(\"devtools\") devtools::install_github(\"nlmixr2/nlmixr2rpt\", dependencies=TRUE)"},{"path":[]},{"path":"/index.html","id":"powerpoint","dir":"","previous_headings":"Getting Started","what":"PowerPoint","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"Assuming results nlmixr analysis object fit can dump results PowerPoint document following: creates onbrand reporting object obnd_pptx. can add reporting elements using onbrand officer. Next command report_fit() append results fit object onbrand report. calling report_fit() can append reporting elements. Finally just need save document using save_report().","code":"obnd_pptx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_pptx = report_fit( fit = fit, obnd = obnd_pptx) save_report(obnd_pptx, \"report.pptx\")"},{"path":"/index.html","id":"word","dir":"","previous_headings":"Getting Started","what":"Word","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"process Word document . simply need use Word onbrand template instead PowerPoint.","code":"obnd_docx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_docx = report_fit( fit = fit, obnd = obnd_docx) save_report(obnd_docx, \"report.docx\")"},{"path":"/index.html","id":"further-reading","dir":"","previous_headings":"","what":"Further reading","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"want learn customizing outputs using organizational templates reporting, sure browse documentation check vignettes: Reporting nlmixr Fit Results Accessing Figures Tables","code":""},{"path":"/reference/build_figures.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates Figures for an nlmixr2 Report — build_figures","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"Creates figures specified rptyaml file","code":""},{"path":"/reference/build_figures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"","code":"build_figures( obnd = NULL, fit = NULL, rptdetails = NULL, cat_covars = NULL, cont_covars = NULL, verbose = TRUE )"},{"path":"/reference/build_figures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails Object created reading rptyaml file cat_covars character vector categorical covariates overwrite defaults yaml file cont_covars character vector continuous covariates overwrite defaults yaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/build_figures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"List containing figures following structure: \"rptfigs\" - List figures names corresponding figure ids yaml file. figure ID contains following elements: \"figure\" - list figure file names current fid \"orientation\" - Figure orientation (\"portrait\" \"landscape\") \"isgood\" - Boolean variable indicating success failure \"skip\" - Boolean variable indicating whether figure skipped reporting \"fmsgs\" - Vector messages \"cmd\" - Original plot generation command \"cmd_proc\" - Plot generation command processing placeholders \"height\" - Figure height \"width\" - Figure width \"caption\" - Caption Word \"caption_proc\" - Caption Word processing placeholders \"title\" - Slide title PowerPoint \"title_proc\" - Slide title PowerPoint processing placeholders \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/build_figures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"","code":"# We need an onbrand object to use below library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails # Now we will build the figures bfres = build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) #> #> Attaching package: ‘xpose’ #> The following object is masked from ‘package:stats’: #> #> filter #> #> ── Building report figures #> → dv_vs_pred #> `geom_smooth()` using formula = 'y ~ x' #> `geom_smooth()` using formula = 'y ~ x' #> • #> /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN/dv_vs_pred-Word.png #> → bad_figure #> #> ── Figure generation failed #> → figure id: bad_figure #> → Unable to generate figure #> → -> call: eval, parse(text = finfo[[\"cmd_proc\"]]) #> → -> message: object 'bad_figure_command' not found #> → command run: #> → bad_figure_command #> • #> /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN/bad_figure-Word.png #> → skip_figure"},{"path":"/reference/build_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates Tables for an nlmixr2 Report — build_tables","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"Creates tables specified rptyaml file","code":""},{"path":"/reference/build_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"","code":"build_tables( obnd = NULL, fit = NULL, rptdetails = NULL, cat_covars = NULL, cont_covars = NULL, verbose = TRUE )"},{"path":"/reference/build_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails object creating reading rptyaml file cat_covars character vector categorical covariates overwrite defaults yaml file cont_covars character vector continuous covariates overwrite defaults yaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/build_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"List containing tables following structure: \"rpttabs\" - List tables names corresponding table ids yaml file. contains elements yamle file following elements: \"table\" - Result build (t_res object) \"orientation\" - Table orientation (\"portrait\" \"landscape\") \"isgood\" - Boolean variable indicating success failure \"skip\" - Boolean variable indicating whether table skipped reporting \"tmsgs\" - Vector messages \"cmd\" - Original plot generation command \"cmd_proc\" - Plot generation command processing placeholders \"height\" - Table height \"width\" - Table width \"caption\" - Caption Word \"caption_proc\" - Caption Word processing placeholders \"title\" - Slide title PowerPoint \"title_proc\" - Slide title PowerPoint processing placeholders \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/build_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"","code":"# We need an onbrand object to use below # \\donttest{ library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails # Now we will build the tables btres = build_tables(obnd = obnd, fit = fit, rptdetails = rptdetails) #> #> ── Building report tables #> → pest_table #> → bad_table #> #> ── Table generation failed #> → Unable to generate table #> → -> call: eval, parse(text = tinfo[[\"cmd_proc\"]]) #> → -> message: object 'bad_table_command' not found #> → table id: bad_table #> → command run: #> → bad_table_command #> → skip_table # }"},{"path":"/reference/eval_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate R Code in String — eval_str","title":"Evaluate R Code in String — eval_str","text":"Attempts evaluate string chunk R code.","code":""},{"path":"/reference/eval_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate R Code in String — eval_str","text":"","code":"eval_str(estr = \"\", fit = NULL)"},{"path":"/reference/eval_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate R Code in String — eval_str","text":"estr Object creating reading rptyaml file fit nlmixr2 fit object reported","code":""},{"path":"/reference/eval_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate R Code in String — eval_str","text":"String containing evaled character original string","code":""},{"path":"/reference/eval_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate R Code in String — eval_str","text":"","code":"res = eval_str(estr=\"ls()\")"},{"path":"/reference/fetch_fdim.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets Figure Dimensions — fetch_fdim","title":"Gets Figure Dimensions — fetch_fdim","text":"given figure id report type pull dimensions figure.","code":""},{"path":"/reference/fetch_fdim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets Figure Dimensions — fetch_fdim","text":"","code":"fetch_fdim(obnd = NULL, fid = NULL, fdim = \"width\", rptdetails = NULL)"},{"path":"/reference/fetch_fdim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets Figure Dimensions — fetch_fdim","text":"obnd onbrand report object report elements appended fid Figure ID used figures section yaml file fdim Dimension fetch either \"width\" \"height\" rptdetails Object creating reading rptyaml file","code":""},{"path":"/reference/fetch_fdim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets Figure Dimensions — fetch_fdim","text":"ggplot object","code":""},{"path":"/reference/fetch_fdim.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gets Figure Dimensions — fetch_fdim","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails fetch_fdim(obnd=obnd, fid=\"bad_figure\", fdim=\"width\", rptdetails=rptdetails) #> [1] 9.5 fetch_fdim(obnd=obnd, fid=\"bad_figure\", fdim=\"height\", rptdetails=rptdetails) #> [1] 5"},{"path":"/reference/fetch_fit_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Fit Example — fetch_fit_example","title":"Fetch Fit Example — fetch_fit_example","text":"Creates nlmixr2 fit example using posthoc estimation method testing purposes. displayed terminal following:","code":""},{"path":"/reference/fetch_fit_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Fit Example — fetch_fit_example","text":"","code":"fetch_fit_example(use_cache = TRUE)"},{"path":"/reference/fetch_fit_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Fit Example — fetch_fit_example","text":"use_cache Boolean variable used cache fit process current R session.","code":""},{"path":"/reference/fetch_fit_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Fit Example — fetch_fit_example","text":"Example nlmixr2 fit object","code":""},{"path":"/reference/fetch_fit_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Fit Example — fetch_fit_example","text":"","code":"fit = fetch_fit_example()"},{"path":"/reference/fetch_option.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Analysis Options — fetch_option","title":"Fetch Analysis Options — fetch_option","text":"Fetches analysis options report yaml applies strings.","code":""},{"path":"/reference/fetch_option.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Analysis Options — fetch_option","text":"","code":"fetch_option(rptdetails, option = NULL, fit = NULL, verbose = TRUE)"},{"path":"/reference/fetch_option.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Analysis Options — fetch_option","text":"rptdetails Object creating reading rptyaml file option String containing option fetch (see ) fit nlmixr2 fit object reported verbose Boolean variable set TRUE (default) messages displayed terminal following:","code":""},{"path":"/reference/fetch_option.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Analysis Options — fetch_option","text":"List containing following information output directory \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"value\" - value option default specified","code":""},{"path":"/reference/fetch_option.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fetch Analysis Options — fetch_option","text":"option can one following (default: NULL): \"output_dir\" - Directory place figures generated (default: tempdir()) \"resolution\" - Resolution figure files (default: 300)","code":""},{"path":"/reference/fetch_option.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Analysis Options — fetch_option","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails fetch_option(rptdetails, option=\"output_dir\", fit=fit) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> #> $value #> [1] \"/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//Rtmp6gI0dV/RUNN\" #>"},{"path":"/reference/gen_pest_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"Generates flextable containting parameter estimates.","code":""},{"path":"/reference/gen_pest_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"","code":"gen_pest_table(obnd = NULL, fit = NULL, rptdetails = NULL, verbose = TRUE)"},{"path":"/reference/gen_pest_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails object creating reading rptyaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/gen_pest_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"List following elements \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"ft\" - Parameter estimates flextable object \"df\" - Parameter estimates data.frame","code":""},{"path":"/reference/gen_pest_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() #'# This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails gen_pest_table(obnd = obnd, fit = fit, rptdetails = rptdetails, verbose = TRUE) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> #> $ft #> $ft[[1]] #> #> #> $df #> $df[[1]] #> Parameter Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)% #> tka Log Ka 0.476 0.203 42.7 1.61 (1.08, 2.39) 69.8 1.23%< #> tcl Log Cl 1.02 0.0754 7.42 2.76 (2.38, 3.2) 26.1 2.36%< #> tv Log V 3.46 0.0632 1.83 31.8 (28.1, 36) 13.8 9.71%< #> add.sd add.sd 0.696 0.696 #> #>"},{"path":"/reference/mk_error_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates ggplot Object with Error Message — mk_error_fig","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"Takes vector messages returns ggplot object text figure. can used automated figure generation cascade error message end user.","code":""},{"path":"/reference/mk_error_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"","code":"mk_error_fig(msgs)"},{"path":"/reference/mk_error_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"msgs Vector error messages","code":""},{"path":"/reference/mk_error_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"ggplot object","code":""},{"path":"/reference/mk_error_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"","code":"mk_error_fig(\"This is an error\")"},{"path":"/reference/mk_error_tab.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a flextable Object with Error Message — mk_error_tab","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"Takes vector messages returns flextable object text table. can used automated table generation cascade error message end user.","code":""},{"path":"/reference/mk_error_tab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"","code":"mk_error_tab(msgs)"},{"path":"/reference/mk_error_tab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"msgs Vector error messages","code":""},{"path":"/reference/mk_error_tab.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"list single flextable object","code":""},{"path":"/reference/mk_error_tab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"Error error","code":"error_tab = mk_error_tab(\"This is an error\") error_tab$ft[[1]] .cl-b25435c6{}.cl-b2506ba8{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-b2525684{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-b25262be{width:1.304in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-b25262c8{width:1.304in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}ErrorThis is an error"},{"path":"/reference/process_ph.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitutes Placehodlers in Strings — process_ph","title":"Substitutes Placehodlers in Strings — process_ph","text":"Takes placeholder information rptyaml file applies strings.","code":""},{"path":"/reference/process_ph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitutes Placehodlers in Strings — process_ph","text":"","code":"process_ph(str, rptdetails)"},{"path":"/reference/process_ph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitutes Placehodlers in Strings — process_ph","text":"str String process rptdetails Object creating reading rptyaml file (default: NULL)","code":""},{"path":"/reference/process_ph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitutes Placehodlers in Strings — process_ph","text":"processed string","code":""},{"path":"/reference/process_ph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Substitutes Placehodlers in Strings — process_ph","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails str = \"This is ===CMPD===\" process_ph(str, rptdetails) #> [1] \"This is Compound Name\""},{"path":"/reference/report_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"Appends nlmixr2 fit results onbrand report object content format report supplied yaml file","code":""},{"path":"/reference/report_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"","code":"report_fit( obnd = NULL, fit = NULL, placeholders = NULL, cat_covars = NULL, cont_covars = NULL, parameters = NULL, rptyaml = system.file(package = \"nlmixr2rpt\", \"templates\", \"report_fit.yaml\"), verbose = FALSE )"},{"path":"/reference/report_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"obnd onbrand report object report elements appended . fit nlmixr2 fit object reported. placeholders Manual placeholders, see yaml_read_fit . cat_covars character vector categorical covariates overwrite defaults yaml file. cont_covars character vector continuous covariates overwrite defaults yaml file. parameters list element names parameter overwrite defaults yaml file. rptyaml yaml file containing report elements structure. verbose Boolean variable set TRUE messages .","code":""},{"path":"/reference/report_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"onbrand object report elements added.","code":""},{"path":"/reference/report_fit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"","code":"# \\donttest{ library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # Appening fit results obnd_pptx = report_fit( fit = fit, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), obnd = obnd) #> ! Suggested package: ggPMX was not found #> `geom_smooth()` using formula = 'y ~ x' #> `geom_smooth()` using formula = 'y ~ x' # Writing the report to a file save_report(obnd, file.path(tempdir(), \"report.pptx\")) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> # }"},{"path":"/reference/write_figure.html","id":null,"dir":"Reference","previous_headings":"","what":"Writes Figures to File — write_figure","title":"Writes Figures to File — write_figure","text":"Takes figure object, optionally stamps image, writes file dimensions figure.","code":""},{"path":"/reference/write_figure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Writes Figures to File — write_figure","text":"","code":"write_figure( p_res = NULL, page = NULL, width = 3, height = 3, resolution = NULL, fig_file = NULL, fig_stamp = NULL, verbose = TRUE )"},{"path":"/reference/write_figure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Writes Figures to File — write_figure","text":"p_res ggplot, ggforce paginated object, ggarrange object. page Page number write NULL ggplot object. width Width inches. height Height inches. resolution resolution dpi. fig_file File name write figure . fig_stamp Character object containing text stamp figure optional ===file=== placeholder. verbose Boolean variable set TRUE (default) messages . displayed terminal","code":""},{"path":"/reference/write_figure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Writes Figures to File — write_figure","text":"list following \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/write_figure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Writes Figures to File — write_figure","text":"","code":"library(ggplot2) write_figure( p_res = ggplot(), page = NULL, width = 3, height = 3, resolution = 200, fig_file = file.path(tempdir(), \"write_figure_example.png\"), fig_stamp = \"stamp\", verbose = TRUE) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #>"},{"path":"/reference/yaml_read_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads and Checks report_fit.yaml File — yaml_read_fit","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"Reads report yaml file looks make sure necessary fields given report.","code":""},{"path":"/reference/yaml_read_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"","code":"yaml_read_fit( obnd = NULL, rptyaml = NULL, placeholders = NULL, parameters = NULL, fit = NULL )"},{"path":"/reference/yaml_read_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"obnd onbrand report object report elements appended . rptyaml yaml file containing report elements structure. placeholders list placeholders overwrite defaults yaml file. parameters list element names parameter overwrite runtime. named list example RUN may \"RUNN\" yaml file. overwrite just provide list(RUN=\"RUN_1\") (default: NULL) fit nlmixr2 fit object reported.","code":""},{"path":"/reference/yaml_read_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"List containing following information report \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"rpttype\" - Type onbrand report (\"Word\" \"PowerPoint\") \"rptfigfmt\" - Default figure formatting (orientation dimensions) \"rpttabfmt\" - Default table formatting (orientation dimensions) \"rptdetails\" - Contents yaml file \"rptcont\" - Contents report generate","code":""},{"path":"/reference/yaml_read_fit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"","code":"# We need an onbrand object to use below library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details yaml_read_res = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)"},{"path":"/news/index.html","id":"nlmixr2rpt-021-development-version","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.2.1 (development version)","title":"nlmixr2rpt 0.2.1 (development version)","text":"NA","code":""},{"path":"/news/index.html","id":"nlmixr2rpt-020","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.2.0","title":"nlmixr2rpt 0.2.0","text":"CRAN release: 2023-06-06 Fixing error CRAN","code":""},{"path":"/news/index.html","id":"nlmixr2rpt-010","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.1.0","title":"nlmixr2rpt 0.1.0","text":"CRAN release: 2022-12-05 Initial release","code":""}] +[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Accessing Figures and Tables","text":"create report_fit.yaml file defined figures tables reporting. However may want reuse report objects outside Word PowerPoint. example may want use inside Shiny Apps RMarkdown document. vignette outlines can build objects outside nlmixr2rpt workflow.","code":""},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"creating-figures-and-tables","dir":"Articles","previous_headings":"","what":"Creating figures and tables","title":"Accessing Figures and Tables","text":"First need load appropriate libraries. need onbrand library tables figures generated based type report. Specifically default figure dimensions change based report type. initialize empty Word report onbrand. report type extracted object functions . nlmixr2 fit object analysis. load example package. Next read yaml file using yaml_read_fit(). using stripped example testing. contents yaml file stored rptdetails list element returned. Now can use rptdetails object just created create figures tables using build_figures() build_tables() functions respectively.","code":"library(nlmixr2rpt) library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) fit = fetch_fit_example() rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails bfres = build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) btres = build_tables(obnd = obnd, fit = fit, rptdetails = rptdetails)"},{"path":"/articles/Accessing_Figures_and_Tables.html","id":"using-report-objects-in-rmarkdown","dir":"Articles","previous_headings":"","what":"Using report objects in RMarkdown","title":"Accessing Figures and Tables","text":"can look help two build functions . objects create contain information figures tables defined report_fit.yaml file. access figure just need specify figure ID. example path title figure containing dv_vs_pred figure can found : can include RMarkdown using following: Tables used similiar fashion. code extract flextable object title pest_table. attaches title caption displays . Parameter Estimates Parameter Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)% Log Ka 0.476 0.203 42.7 1.61 (1.08, 2.39) 69.8 1.23%< Log Cl 1.02 0.0754 7.42 2.76 (2.38, 3.2) 26.1 2.36%< Log V 3.46 0.0632 1.83 31.8 (28.1, 36) 13.8 9.71%< add.sd 0.696 0.696","code":"fig_path = bfres$rptfigs$dv_vs_pred$figure[[1]] fig_title = bfres$rptfigs$dv_vs_pred$title_proc ![`r fig_title`](`r fig_path`){width=80%} tab_ft = btres$rpttabs$pest_table$table$ft[[1]] tab_title = btres$rpttabs$pest_table$title_proc tab_ft_knit = flextable::set_caption(tab_ft, caption = tab_title) tab_ft_knit"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Reporting nlmixr2 Fit Results","text":"purpose nlmixr2rpt automate reporting nlmixr2 analyses. accomplished creating yaml file contains reporting options, figure table generation code, general content Word PowerPoint files.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"general-workflow","dir":"Articles","previous_headings":"","what":"General workflow","title":"Reporting nlmixr2 Fit Results","text":"First need nlmixr2 fit object. ’re going load fit example stored package: Next need create onbrand report objects. create report objects PowerPoint (obnd_pptx) Word (obnd_docx). Next add report elements report objects using report_fit() function. function can used types report. contents different depending document type. function append report elements supplied fit object supplied report. multiple fit objects can added sequentially. can also add report content using onbrand officer functions. ’re done just need save reports: contents report type defined yaml file. commands use default value found nlmixr2rpt package. customize report elements can make copy file current working directory: can edit my_report.yaml file call report_fit() provide yaml file rptyaml argument. following section describe elements yaml report format.","code":"library(nlmixr2rpt) library(onbrand) # This will create an example fit object to use in the examples below fit = fetch_fit_example() obnd_pptx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_docx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_pptx = report_fit( fit = fit, obnd = obnd_pptx) obnd_docx = report_fit( fit = fit, obnd = obnd_docx) save_report(obnd_pptx, \"report.pptx\") save_report(obnd_docx, \"report.docx\") file.copy(system.file(package=\"nlmixr2rpt\", \"templates\", \"report_fit.yaml\"), \"my_report.yaml\")"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"the-yaml-report-file-structure","dir":"Articles","previous_headings":"","what":"The yaml report file structure","title":"Reporting nlmixr2 Fit Results","text":"core nlmixr2rpt yaml reporting file. outline main sections describe expected elements sections.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"placeholders","dir":"Articles","previous_headings":"The yaml report file structure","what":"placeholders","title":"Reporting nlmixr2 Fit Results","text":"may wish create report template placeholders. example want create generic template population PK analysis, may useful label figures generically. can use section define placeholders applied report created. example consider yaml code : create report can label y-axis generically : \"===CMPD=== (===CUNITS===)\" report built, become: \"Compound Name (Conc Units)\" Notice OBJ placeholder contains R Code. default reporting process try evaluate placeholders R Code. fails revert back string supplied. run problems can quote placeholder value double single quotes. example: ISSTR field just result string \"ls()\" ISCMD field return list objects environment string evaluated. also possible overwrite contents file runtime providing placeholders (placeholder) argument report_fit(). Note: Fields support placeholders indicated [PH] fields evaluable code indicated [EV].","code":"placeholders: CMPD: Compound Name CUNITS: Conc Units OBJ: sprintf(\"%3g\", fit$objf) ISSTR:\"'ls()'\" ISCMD: ls()"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"parameters","dir":"Articles","previous_headings":"The yaml report file structure","what":"parameters","title":"Reporting nlmixr2 Fit Results","text":"certain reporting elements may better present parameters differently parameter names used model. nlmixr can use comment parameter definition specify alternate text. function gen_pest_table() use alternate text present. parameters section flexability parameters reported. can define parameters want whether present model . used present. tables Word PowerPoint can specify names using markdown (md), otherwise can specify handled text environments (txt). example intrinsic clearance may called lCLint model. can specify : also possible overwrite contents file runtime providing parameters argument report_fit(). Note: specify parameter name overwrite alternate text specified model ini().","code":"parameters: lCLint: md: \"CL~int~ (L/hr)\" txt: \"CLint (L/hr)\""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"covariates","dir":"Articles","previous_headings":"The yaml report file structure","what":"covariates","title":"Reporting nlmixr2 Fit Results","text":"figure table generation can useful covariates defined. can define either categorical (cat) continuous (cont). example define categorical covariates SEX ROUTE continuous covariate WT following: don’t need covariates can set NULL. want overwrite runtime can specify different values calling report_fit(). available figure table runtime environments objects cat_covars categorical covariates cont_covars continuous covariates.","code":"covariates: cat: [\"SEX\", \"ROUTE\"] cont: [\"WT\"]"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"options","dir":"Articles","previous_headings":"The yaml report file structure","what":"options","title":"Reporting nlmixr2 Fit Results","text":"section allows control general report options. element can either explicit value. identified evaluable [EV] first attempt evaluate R code. fails explicit value used. following options supported expected data type parentheses: output_dir[PH,EV] - location figures generated (character) resolution[EV] - Resolution figures generated (numeric) figenv_preamble tabenv_preamble - User-defined code evaluated figures tables built (specify libraries needed, source files containing user defined code, etc.) fig_stamp[PH] - set string stamp contents string lower left portion figure writing. applies figures p_res object either vanilla ggplot object, paginated ggforce object, result ggarrage ggpubr package. Along regular placeholders, option can also contain ===FILE=== placeholder. replaced full path figure file generated.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"building-figures-tables","dir":"Articles","previous_headings":"The yaml report file structure","what":"Building figures & tables","title":"Reporting nlmixr2 Fit Results","text":"Figures tables defined terms R code evaluated. several objects available environment can used creating report elements. following objects defined: fid - current figure ID (figure environment ) tid - current table ID (table environment ) fit - nlmixr2 fit object cat_covars - character object containing categorical covariates cont_covars - character object containing continuous covariates height - figure height inches (figure environment ) obnd - onbrand object report document output_dir - directory figures stored resolution - resolution figure (figure environment ) rptdetails - result reading report yaml file rpttype - either “Word” “PowerPoint” width - figure width inches (figure environment ) xpdb - default yaml file contains code preamble create object running xpose_data_nlmixr(fit) (figure environment )","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"figures","dir":"Articles","previous_headings":"The yaml report file structure","what":"figures","title":"Reporting nlmixr2 Fit Results","text":"figures section consists figure IDs. IDs used defining Word PowerPoint report contents. Consider example: creates figure ID dv_vs_pred. following elements: orientation - Orientation used Word report, can either “portrait” “landscape”. caption[PH] - Figure caption Word reports. caption_format - element optional can either \"text\"(default plain text) \"md\" (Markdown). title[PH] - Slide title figure used PowerPoint. cmd[PH] - Command generate figure. Note: cmd evaluated needs create variable called p_res. can either ggplot object, paginated object ggforce, result ggarrage ggpubr package, vector file names containing image files created code cmd. want conditionally skip reporting figure, can instead set value p_res NA. generate message prevent inclusion build error final document. also include libraries want relevant preamble section ensure functions available .","code":"figures: dv_vs_pred: orientation: \"portrait\" caption: \"dv_vs_pred caption\" caption_format: \"text\" title: \"dv_vs_pred title\" cmd: |- p_res <- dv_vs_pred(xpdb, caption=NULL, title=NULL) + xlab(\"Observed ===CMPD=== Concentrations (===CUNITS===)\") + ylab(\"Population Predicted ===CMPD=== Concentrations (===CUNITS===)\")"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"tables","dir":"Articles","previous_headings":"The yaml report file structure","what":"tables","title":"Reporting nlmixr2 Fit Results","text":"Tables behave similarly figures. tables section create table ID following options specified. orientation - Orientation used Word report, can either “portrait” “landscape”. caption[PH] - Table caption Word reports. caption_format - element optional can either \"text\"(default plain text) \"md\" (Markdown). title[PH] - Slide title table used PowerPoint. cmd[PH] - Command generate table. example create table parameter estimates. Note: cmd evaluated needs create variable called t_res. list can contain following elements: df - List data frames containing tabular information. ft - List flextables containing tabular information supply data frames list element, converted flextables internally. Flextables span multiple pages automatically. prefer caption page can split tables manually multiple data frames/flextables. reporting functionality written support table spanning multiple pages. define separate table page need add sequential list elements df ft elements. example: single table want span multiple pages automatically simply specify first element listed (e.g. t_res$df[[1]]). want conditionally skip generation table, simply set t_res NA. Like figures , signal reporting functions want generate table current fit object. also prevent generation build error.","code":"tables: pest_table: orientation: \"portrait\" caption: \"Parameter Estimates\" caption_format: \"text\" title: \"Parameter Estimates\" cmd: |- t_res <- gen_pest_table( fit = fit, obnd = obnd, rptdetails = rptdetails) t_res$df = list() t_res$df[[1]] = data.frame() t_res$df[[2]] = data.frame() etc t_res$ft = list() t_res$ft[[1]] = flextable::flextable() t_res$ft[[2]] = flextable::flextable() etc"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"pptx","dir":"Articles","previous_headings":"The yaml report file structure","what":"pptx","title":"Reporting nlmixr2 Fit Results","text":"section defines general aspects PowerPoint reports also contents report relating fitting results. figures tables sections contain onbrand slide master names (\"content_text\") used hold objects. slides created title specified figure table IDs. placeholder name title (\"title\") must specified well placeholder name content (\"content_body\"). Figures PowerPoint reports must generated dimensions placeholder, important width height elements specified inches. actual content specified content section. list keywords followed value. table keyword followed table ID defined tables section. Similarly figure keyworld followed figure ID defined figures section:","code":"pptx: figures: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" width: 9.5 height: 5.0 tables: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" content: - table: pest_table - figure: ind_plots - figure: dv_vs_pred - figure: dv_vs_ipred - figure: res_vs_pred - figure: res_vs_idv - figure: prm_vs_iteration - figure: absval_res_vs_pred"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"docx","dir":"Articles","previous_headings":"The yaml report file structure","what":"docx","title":"Reporting nlmixr2 Fit Results","text":"section starts general information word documents. figures section defines height width figures landscape portrait orientations. units inches. Just like PowerPoint content defined content section. can defined figure table PowerPoint. Content can also include text elements well. Just specify onbrand style control general formatting.","code":"docx: figures: landscape: width: 8.0 height: 4.2 portrait: width: 6.5 height: 6.0 content: - text: text: \"Figures\" style: Heading_1 - figure: dv_vs_pred - figure: ind_plots - figure: dv_vs_ipred - figure: res_vs_pred - figure: res_vs_idv - figure: prm_vs_iteration - figure: absval_res_vs_pred - text: text: \"Tables\" style: Heading_1 - table: pest_table"},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"customizing-reports-for-your-organization","dir":"Articles","previous_headings":"","what":"Customizing reports for your organization","title":"Reporting nlmixr2 Fit Results","text":"reporting done using onbrand package. provides abstraction layer officer package. benefit can use organization Word PowerPoint templates. Simply create appropriate masters PowerPoint styles Word, create brand mapping file. initialize report objects can just provide organizational template mapping files. details create templates mapping files, see vignette onbrand package.","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"powerpoint","dir":"Articles","previous_headings":"Customizing reports for your organization","what":"PowerPoint","title":"Reporting nlmixr2 Fit Results","text":"create onbrand PowerPoint template organization need following master slide names define corresponding elements. Master/Template onbrand Content Name Placeholder Type title_slide title text sub_title text section_slide title text sub_title text title_only title text content_text title text sub_title text content_body text content_list title text sub_title text content_body list two_content_header_list title text sub_title text content_left_header text content_left list content_right_header text content_right list two_content_header_text title text sub_title text content_left_header text content_left text content_right_header text content_right text two_content_list title text sub_title text content_left list content_right list two_content_text title text sub_title text content_left text content_right text","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"word","dir":"Articles","previous_headings":"Customizing reports for your organization","what":"Word","title":"Reporting nlmixr2 Fit Results","text":"Similarly, create onbrand Word template need following onbrand styles defined. onbrand Word Style Style Style Type Code Code paragraph Figure_Caption graphic title paragraph Heading_1 heading 1 paragraph Heading_2 heading 2 paragraph Heading_3 heading 3 paragraph Normal Normal paragraph Notes Notes paragraph TOC toc 1 paragraph Table_Caption table title paragraph Table Table Grid table","code":""},{"path":"/articles/Reporting_nlmixr_Fit_Results.html","id":"report-configuration-file-report_fit-yaml","dir":"Articles","previous_headings":"","what":"Report configuration file report_fit.yaml","title":"Reporting nlmixr2 Fit Results","text":"","code":"placeholders: CMPD: Compound Name CUNITS: Conc Units TUNITS: Time Units RUN: RUNN OBJ: sprintf(\"%3g\", fit$objf) parameters: lVp: md: \"V~p~\" txt: \"Vp\" add_err: md: \"Add Err\" txt: \"Add Err\" prop_err: md: \"Prop Err\" txt: \"Prop Err\" covariates: cat: NULL cont: NULL options: output_dir: \"file.path(getwd(), '===RUN===')\" resolution: 300 fig_stamp: \"source: ===FILE===\" figenv_preamble: |- library(\"ggplot2\") library(\"xpose\") library(\"ggforce\") if(system.file(package=\"ggPMX\") != \"\"){ library(\"ggPMX\") } xpdb = xpose.nlmixr2::xpose_data_nlmixr(fit) tabenv_preamble: NULL figures: dv_vs_pred_ipred: orientation: \"portrait\" caption: \"Observed vs Predicted\" title: \"Observed vs Predicted\" cmd: |- p_pred <- dv_vs_pred(xpdb, caption=NULL, title=NULL, subtitle=NULL) + ggtitle(\"===CMPD=== (===CUNITS===)\") + coord_fixed()+ ylab(\"Observed\") + xlab(\"Population Predicted\") + theme_light() yrange = layer_scales(p_pred)$y$range$range xrange = layer_scales(p_pred)$x$range$range lb = min(c(yrange,xrange)) ub = max(c(yrange,xrange)) p_pred = p_pred + xlim(c(lb, ub)) + ylim(c(lb,ub)) p_ipred <- dv_vs_ipred(xpdb, caption=NULL, title=NULL, subtitle=NULL) + ggtitle(\"===CMPD=== (===CUNITS===)\") + coord_fixed()+ ylab(\"Observed\") + xlab(\"Individual Predicted\") + theme_light() yrange = layer_scales(p_ipred)$y$range$range xrange = layer_scales(p_ipred)$x$range$range lb = min(c(yrange,xrange)) ub = max(c(yrange,xrange)) p_ipred = p_ipred + xlim(c(lb, ub)) + ylim(c(lb,ub)) p_res <- ggpubr::ggarrange(p_pred, p_ipred, ncol=2, nrow=1 ) res_vs_pred_idv: orientation: \"portrait\" caption: \"CWRES vs Pred and Time\" title: \"CWRES vs Pred and Time\" cmd: |- if(\"CWRES\" %in% names(fit)){ p_pred <- res_vs_pred(xpdb, caption=NULL, title=NULL, res=\"CWRES\") + ggtitle(\"===CMPD=== (===CUNITS===)\") + ylab(\"CWRES\") + xlab(\"Population Predicted\") + theme_light() p_idv <- res_vs_idv(xpdb, caption=NULL, title=NULL, res=\"CWRES\") + ggtitle(\"Time (===CUNITS===)\") + ylab(\"CWRES\") + xlab(\"Time (===TUNITS===)\") + theme_light() p_res <- ggpubr::ggarrange(p_pred, p_idv, ncol=2, nrow=1 ) } else { p_res <- NA } eta_cat: orientation: \"landscape\" caption: \"Effect of categorical covariates\" title: \"Effect of categorical covariates\" cmd: |- if(!is.null(cat_covars)){ if(system.file(package=\"ggPMX\") != \"\"){ ctr = ggPMX::pmx_nlmixr(fit, vpc = FALSE, conts = cont_covars, cats = cat_covars) p_res <- ggPMX::pmx_plot_eta_cats(ctr) + theme_light() } else { p_res <- mk_error_fig(\"ggPMX is not installed\") } } else { p_res <- NA } eta_cont: orientation: \"landscape\" caption: \"Effect of continuous covariates\" title: \"Effect of continuous covariates\" cmd: |- if(!is.null(cont_covars)){ if(system.file(package=\"ggPMX\") != \"\"){ ctr = ggPMX::pmx_nlmixr(fit, vpc = FALSE, conts = cont_covars, cats = cat_covars) p_res <- ggPMX::pmx_plot_eta_conts(ctr) + theme_light() } else { p_res = mk_error_fig(\"ggPMX is not installed\") } } else { p_res <- NA } prm_vs_iteration: orientation: \"landscape\" caption: \"SAEM Stabilization\" title: \"SAEM Stabilization\" cmd: |- p_res <- prm_vs_iteration(xpdb, caption=NULL, title=NULL) + theme_light() ind_plots: orientation: \"landscape\" caption: \"Individual and population prediction overlay\" title: \"Individual and population prediction overlay\" cmd: |- p_res <- ind_plots(xpdb, nrow=3, ncol=4, caption=NULL, title=NULL) + ylab(\" ===CMPD=== (===CUNITS===)\") + xlab(\"Time (===TUNITS===)\") + theme_light() skip_figure: orientation: \"landscape\" caption: \"ind_plots caption\" title: \"ind_plots title\" cmd: |- p_res <- NA tables: skip_table: orientation: \"portrait\" caption: \"Parameter Estimates\" title: \"Parameter Estimates\" cmd: |- t_res <- NA pest_table: orientation: \"portrait\" caption: \"Parameter Estimates\" title: \"Parameter Estimates\" cmd: |- t_res <- gen_pest_table( fit = fit, obnd = obnd, rptdetails = rptdetails) pptx: figures: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" width: 9.5 height: 5.0 tables: master: name: \"content_text\" title_ph: \"title\" content_ph: \"content_body\" content: - table: pest_table - table: skip_table - figure: ind_plots - figure: dv_vs_pred_ipred - figure: res_vs_pred_idv - figure: prm_vs_iteration - figure: eta_cont - figure: eta_cat - figure: skip_figure docx: figures: landscape: width: 8.0 height: 4.2 portrait: width: 6.5 height: 6.0 content: - text: text: \"Tables\" style: Heading_1 - table: pest_table - text: text: \"Figures\" style: Heading_1 - figure: ind_plots - figure: dv_vs_pred_ipred - figure: res_vs_pred_idv - figure: prm_vs_iteration - figure: skip_figure - figure: eta_cont - figure: eta_cat"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Harrold. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Harrold J (2024). nlmixr2rpt: Templated Word PowerPoint Reporting 'nlmixr2' Fitting Results. R package version 0.2.1, https://nlmixr2.github.io/nlmixr2rpt/.","code":"@Manual{, title = {nlmixr2rpt: Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results}, author = {John Harrold}, year = {2024}, note = {R package version 0.2.1}, url = {https://nlmixr2.github.io/nlmixr2rpt/}, }"},{"path":"/index.html","id":"nlmixr2rpt-","dir":"","previous_headings":"","what":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"Templated Word PowerPoint reporting nlmixr2","code":""},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"purpose package automate reporting analyses performed nlmixr2 package PowerPoint Word. accomplished yaml file contains specifications report elements (figures tables) well contents Word PowerPoint documents. Internal templates documents report yaml file included. can customized: format document templates can customized organization using onbrand package. report contents can customized creating copy included yaml file modifying suite needs (see vignette ).","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"install CRAN: install development version GitHub","code":"install.packages(\"nlmixr2rpt\", dependencies = TRUE) #install.packages(\"devtools\") devtools::install_github(\"nlmixr2/nlmixr2rpt\", dependencies=TRUE)"},{"path":[]},{"path":"/index.html","id":"powerpoint","dir":"","previous_headings":"Getting Started","what":"PowerPoint","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"Assuming results nlmixr analysis object fit can dump results PowerPoint document following: creates onbrand reporting object obnd_pptx. can add reporting elements using onbrand officer. Next command report_fit() append results fit object onbrand report. calling report_fit() can append reporting elements. Finally just need save document using save_report().","code":"obnd_pptx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_pptx = report_fit( fit = fit, obnd = obnd_pptx) save_report(obnd_pptx, \"report.pptx\")"},{"path":"/index.html","id":"word","dir":"","previous_headings":"Getting Started","what":"Word","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"process Word document . simply need use Word onbrand template instead PowerPoint.","code":"obnd_docx = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) obnd_docx = report_fit( fit = fit, obnd = obnd_docx) save_report(obnd_docx, \"report.docx\")"},{"path":"/index.html","id":"further-reading","dir":"","previous_headings":"","what":"Further reading","title":"Templated Word and PowerPoint Reporting of nlmixr2 Fitting Results","text":"want learn customizing outputs using organizational templates reporting, sure browse documentation check vignettes: Reporting nlmixr Fit Results Accessing Figures Tables","code":""},{"path":"/reference/build_figures.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates Figures for an nlmixr2 Report — build_figures","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"Creates figures specified rptyaml file","code":""},{"path":"/reference/build_figures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"","code":"build_figures( obnd = NULL, fit = NULL, rptdetails = NULL, cat_covars = NULL, cont_covars = NULL, verbose = TRUE )"},{"path":"/reference/build_figures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails Object created reading rptyaml file cat_covars character vector categorical covariates overwrite defaults yaml file cont_covars character vector continuous covariates overwrite defaults yaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/build_figures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"List containing figures following structure: \"rptfigs\" - List figures names corresponding figure ids yaml file. figure ID contains following elements: \"figure\" - list figure file names current fid \"orientation\" - Figure orientation (\"portrait\" \"landscape\") \"isgood\" - Boolean variable indicating success failure \"skip\" - Boolean variable indicating whether figure skipped reporting \"fmsgs\" - Vector messages \"cmd\" - Original plot generation command \"cmd_proc\" - Plot generation command processing placeholders \"height\" - Figure height \"width\" - Figure width \"caption\" - Caption Word \"caption_proc\" - Caption Word processing placeholders \"title\" - Slide title PowerPoint \"title_proc\" - Slide title PowerPoint processing placeholders \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/build_figures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates Figures for an nlmixr2 Report — build_figures","text":"","code":"# We need an onbrand object to use below library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails # Now we will build the figures bfres = build_figures(obnd = obnd, fit = fit, rptdetails = rptdetails) #> #> Attaching package: ‘xpose’ #> The following object is masked from ‘package:stats’: #> #> filter #> #> ── Building report figures #> → dv_vs_pred #> `geom_smooth()` using formula = 'y ~ x' #> `geom_smooth()` using formula = 'y ~ x' #> • #> /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN/dv_vs_pred-Word.png #> → bad_figure #> #> ── Figure generation failed #> → figure id: bad_figure #> → Unable to generate figure #> → -> call: eval, parse(text = finfo[[\"cmd_proc\"]]) #> → -> message: object 'bad_figure_command' not found #> → command run: #> → bad_figure_command #> • #> /var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN/bad_figure-Word.png #> → skip_figure"},{"path":"/reference/build_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates Tables for an nlmixr2 Report — build_tables","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"Creates tables specified rptyaml file","code":""},{"path":"/reference/build_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"","code":"build_tables( obnd = NULL, fit = NULL, rptdetails = NULL, cat_covars = NULL, cont_covars = NULL, verbose = TRUE )"},{"path":"/reference/build_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails object creating reading rptyaml file cat_covars character vector categorical covariates overwrite defaults yaml file cont_covars character vector continuous covariates overwrite defaults yaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/build_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"List containing tables following structure: \"rpttabs\" - List tables names corresponding table ids yaml file. contains elements yamle file following elements: \"table\" - Result build (t_res object) \"orientation\" - Table orientation (\"portrait\" \"landscape\") \"isgood\" - Boolean variable indicating success failure \"skip\" - Boolean variable indicating whether table skipped reporting \"tmsgs\" - Vector messages \"cmd\" - Original plot generation command \"cmd_proc\" - Plot generation command processing placeholders \"height\" - Table height \"width\" - Table width \"caption\" - Caption Word \"caption_proc\" - Caption Word processing placeholders \"title\" - Slide title PowerPoint \"title_proc\" - Slide title PowerPoint processing placeholders \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/build_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates Tables for an nlmixr2 Report — build_tables","text":"","code":"# We need an onbrand object to use below # \\donttest{ library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails # Now we will build the tables btres = build_tables(obnd = obnd, fit = fit, rptdetails = rptdetails) #> #> ── Building report tables #> → pest_table #> → bad_table #> #> ── Table generation failed #> → Unable to generate table #> → -> call: eval, parse(text = tinfo[[\"cmd_proc\"]]) #> → -> message: object 'bad_table_command' not found #> → table id: bad_table #> → command run: #> → bad_table_command #> → skip_table # }"},{"path":"/reference/eval_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate R Code in String — eval_str","title":"Evaluate R Code in String — eval_str","text":"Attempts evaluate string chunk R code.","code":""},{"path":"/reference/eval_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate R Code in String — eval_str","text":"","code":"eval_str(estr = \"\", fit = NULL)"},{"path":"/reference/eval_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate R Code in String — eval_str","text":"estr Object creating reading rptyaml file fit nlmixr2 fit object reported","code":""},{"path":"/reference/eval_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate R Code in String — eval_str","text":"String containing evaled character original string","code":""},{"path":"/reference/eval_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate R Code in String — eval_str","text":"","code":"res = eval_str(estr=\"ls()\")"},{"path":"/reference/fetch_fdim.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets Figure Dimensions — fetch_fdim","title":"Gets Figure Dimensions — fetch_fdim","text":"given figure id report type pull dimensions figure.","code":""},{"path":"/reference/fetch_fdim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets Figure Dimensions — fetch_fdim","text":"","code":"fetch_fdim(obnd = NULL, fid = NULL, fdim = \"width\", rptdetails = NULL)"},{"path":"/reference/fetch_fdim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets Figure Dimensions — fetch_fdim","text":"obnd onbrand report object report elements appended fid Figure ID used figures section yaml file fdim Dimension fetch either \"width\" \"height\" rptdetails Object creating reading rptyaml file","code":""},{"path":"/reference/fetch_fdim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets Figure Dimensions — fetch_fdim","text":"ggplot object","code":""},{"path":"/reference/fetch_fdim.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gets Figure Dimensions — fetch_fdim","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails fetch_fdim(obnd=obnd, fid=\"bad_figure\", fdim=\"width\", rptdetails=rptdetails) #> [1] 9.5 fetch_fdim(obnd=obnd, fid=\"bad_figure\", fdim=\"height\", rptdetails=rptdetails) #> [1] 5"},{"path":"/reference/fetch_fit_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Fit Example — fetch_fit_example","title":"Fetch Fit Example — fetch_fit_example","text":"Creates nlmixr2 fit example using posthoc estimation method testing purposes. displayed terminal following:","code":""},{"path":"/reference/fetch_fit_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Fit Example — fetch_fit_example","text":"","code":"fetch_fit_example(use_cache = TRUE)"},{"path":"/reference/fetch_fit_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Fit Example — fetch_fit_example","text":"use_cache Boolean variable used cache fit process current R session.","code":""},{"path":"/reference/fetch_fit_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Fit Example — fetch_fit_example","text":"Example nlmixr2 fit object","code":""},{"path":"/reference/fetch_fit_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Fit Example — fetch_fit_example","text":"","code":"fit = fetch_fit_example()"},{"path":"/reference/fetch_option.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Analysis Options — fetch_option","title":"Fetch Analysis Options — fetch_option","text":"Fetches analysis options report yaml applies strings.","code":""},{"path":"/reference/fetch_option.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Analysis Options — fetch_option","text":"","code":"fetch_option(rptdetails, option = NULL, fit = NULL, verbose = TRUE)"},{"path":"/reference/fetch_option.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Analysis Options — fetch_option","text":"rptdetails Object creating reading rptyaml file option String containing option fetch (see ) fit nlmixr2 fit object reported verbose Boolean variable set TRUE (default) messages displayed terminal following:","code":""},{"path":"/reference/fetch_option.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Analysis Options — fetch_option","text":"List containing following information output directory \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"value\" - value option default specified","code":""},{"path":"/reference/fetch_option.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fetch Analysis Options — fetch_option","text":"option can one following (default: NULL): \"output_dir\" - Directory place figures generated (default: tempdir()) \"resolution\" - Resolution figure files (default: 300)","code":""},{"path":"/reference/fetch_option.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Analysis Options — fetch_option","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails fetch_option(rptdetails, option=\"output_dir\", fit=fit) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> #> $value #> [1] \"/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T//RtmparONJf/RUNN\" #>"},{"path":"/reference/gen_pest_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"Generates flextable containting parameter estimates.","code":""},{"path":"/reference/gen_pest_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"","code":"gen_pest_table(obnd = NULL, fit = NULL, rptdetails = NULL, verbose = TRUE)"},{"path":"/reference/gen_pest_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"obnd onbrand report object report elements appended fit nlmixr2 fit object reported rptdetails object creating reading rptyaml file verbose Boolean variable set TRUE (default) messages displayed terminal","code":""},{"path":"/reference/gen_pest_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"List following elements \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"ft\" - Parameter estimates flextable object \"df\" - Parameter estimates data.frame","code":""},{"path":"/reference/gen_pest_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Makes nlmixr2 Parameter Estimate Table for Reporting — gen_pest_table","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() #'# This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails gen_pest_table(obnd = obnd, fit = fit, rptdetails = rptdetails, verbose = TRUE) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> #> $ft #> $ft[[1]] #> #> #> $df #> $df[[1]] #> Parameter Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)% #> tka Log Ka 0.476 0.203 42.7 1.61 (1.08, 2.39) 69.8 1.23%< #> tcl Log Cl 1.02 0.0754 7.42 2.76 (2.38, 3.2) 26.1 2.36%< #> tv Log V 3.46 0.0632 1.83 31.8 (28.1, 36) 13.8 9.71%< #> add.sd add.sd 0.696 0.696 #> #>"},{"path":"/reference/mk_error_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates ggplot Object with Error Message — mk_error_fig","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"Takes vector messages returns ggplot object text figure. can used automated figure generation cascade error message end user.","code":""},{"path":"/reference/mk_error_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"","code":"mk_error_fig(msgs)"},{"path":"/reference/mk_error_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"msgs Vector error messages","code":""},{"path":"/reference/mk_error_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"ggplot object","code":""},{"path":"/reference/mk_error_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates ggplot Object with Error Message — mk_error_fig","text":"","code":"mk_error_fig(\"This is an error\")"},{"path":"/reference/mk_error_tab.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a flextable Object with Error Message — mk_error_tab","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"Takes vector messages returns flextable object text table. can used automated table generation cascade error message end user.","code":""},{"path":"/reference/mk_error_tab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"","code":"mk_error_tab(msgs)"},{"path":"/reference/mk_error_tab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"msgs Vector error messages","code":""},{"path":"/reference/mk_error_tab.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"list single flextable object","code":""},{"path":"/reference/mk_error_tab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates a flextable Object with Error Message — mk_error_tab","text":"Error error","code":"error_tab = mk_error_tab(\"This is an error\") error_tab$ft[[1]] .cl-417da132{}.cl-417a46ae{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-417bfb98{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-417c07fa{width:1.304in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-417c0804{width:1.304in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}ErrorThis is an error"},{"path":"/reference/process_ph.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitutes Placehodlers in Strings — process_ph","title":"Substitutes Placehodlers in Strings — process_ph","text":"Takes placeholder information rptyaml file applies strings.","code":""},{"path":"/reference/process_ph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitutes Placehodlers in Strings — process_ph","text":"","code":"process_ph(str, rptdetails)"},{"path":"/reference/process_ph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitutes Placehodlers in Strings — process_ph","text":"str String process rptdetails Object creating reading rptyaml file (default: NULL)","code":""},{"path":"/reference/process_ph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitutes Placehodlers in Strings — process_ph","text":"processed string","code":""},{"path":"/reference/process_ph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Substitutes Placehodlers in Strings — process_ph","text":"","code":"library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details as well rptdetails = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)$rptdetails str = \"This is ===CMPD===\" process_ph(str, rptdetails) #> [1] \"This is Compound Name\""},{"path":"/reference/report_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"Appends nlmixr2 fit results onbrand report object content format report supplied yaml file","code":""},{"path":"/reference/report_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"","code":"report_fit( obnd = NULL, fit = NULL, placeholders = NULL, cat_covars = NULL, cont_covars = NULL, parameters = NULL, rptyaml = system.file(package = \"nlmixr2rpt\", \"templates\", \"report_fit.yaml\"), verbose = FALSE )"},{"path":"/reference/report_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"obnd onbrand report object report elements appended . fit nlmixr2 fit object reported. placeholders Manual placeholders, see yaml_read_fit . cat_covars character vector categorical covariates overwrite defaults yaml file. cont_covars character vector continuous covariates overwrite defaults yaml file. parameters list element names parameter overwrite defaults yaml file. rptyaml yaml file containing report elements structure. verbose Boolean variable set TRUE messages .","code":""},{"path":"/reference/report_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"onbrand object report elements added.","code":""},{"path":"/reference/report_fit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report nlmixr2 Fit Results to PowerPoint and Word — report_fit","text":"","code":"# \\donttest{ library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.pptx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # This will create an example fit object to use in the examples below fit = fetch_fit_example() # Appening fit results obnd_pptx = report_fit( fit = fit, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), obnd = obnd) #> ! Suggested package: ggPMX was not found #> `geom_smooth()` using formula = 'y ~ x' #> `geom_smooth()` using formula = 'y ~ x' # Writing the report to a file save_report(obnd, file.path(tempdir(), \"report.pptx\")) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #> # }"},{"path":"/reference/write_figure.html","id":null,"dir":"Reference","previous_headings":"","what":"Writes Figures to File — write_figure","title":"Writes Figures to File — write_figure","text":"Takes figure object, optionally stamps image, writes file dimensions figure.","code":""},{"path":"/reference/write_figure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Writes Figures to File — write_figure","text":"","code":"write_figure( p_res = NULL, page = NULL, width = 3, height = 3, resolution = NULL, fig_file = NULL, fig_stamp = NULL, verbose = TRUE )"},{"path":"/reference/write_figure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Writes Figures to File — write_figure","text":"p_res ggplot, ggforce paginated object, ggarrange object. page Page number write NULL ggplot object. width Width inches. height Height inches. resolution resolution dpi. fig_file File name write figure . fig_stamp Character object containing text stamp figure optional ===file=== placeholder. verbose Boolean variable set TRUE (default) messages . displayed terminal","code":""},{"path":"/reference/write_figure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Writes Figures to File — write_figure","text":"list following \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages","code":""},{"path":"/reference/write_figure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Writes Figures to File — write_figure","text":"","code":"library(ggplot2) write_figure( p_res = ggplot(), page = NULL, width = 3, height = 3, resolution = 200, fig_file = file.path(tempdir(), \"write_figure_example.png\"), fig_stamp = \"stamp\", verbose = TRUE) #> $isgood #> [1] TRUE #> #> $msgs #> NULL #>"},{"path":"/reference/yaml_read_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads and Checks report_fit.yaml File — yaml_read_fit","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"Reads report yaml file looks make sure necessary fields given report.","code":""},{"path":"/reference/yaml_read_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"","code":"yaml_read_fit( obnd = NULL, rptyaml = NULL, placeholders = NULL, parameters = NULL, fit = NULL )"},{"path":"/reference/yaml_read_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"obnd onbrand report object report elements appended . rptyaml yaml file containing report elements structure. placeholders list placeholders overwrite defaults yaml file. parameters list element names parameter overwrite runtime. named list example RUN may \"RUNN\" yaml file. overwrite just provide list(RUN=\"RUN_1\") (default: NULL) fit nlmixr2 fit object reported.","code":""},{"path":"/reference/yaml_read_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"List containing following information report \"isgood\" - Boolean variable indicating success failure \"msgs\" - Vector messages \"rpttype\" - Type onbrand report (\"Word\" \"PowerPoint\") \"rptfigfmt\" - Default figure formatting (orientation dimensions) \"rpttabfmt\" - Default table formatting (orientation dimensions) \"rptdetails\" - Contents yaml file \"rptcont\" - Contents report generate","code":""},{"path":"/reference/yaml_read_fit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reads and Checks report_fit.yaml File — yaml_read_fit","text":"","code":"# We need an onbrand object to use below library(onbrand) obnd = read_template( template = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.docx\"), mapping = system.file(package=\"nlmixr2rpt\", \"templates\",\"nlmixr_obnd_template.yaml\")) # We also need an nlmixr fit object fit = fetch_fit_example() # This reads in the report details yaml_read_res = yaml_read_fit( obnd = obnd, rptyaml = system.file(package=\"nlmixr2rpt\", \"examples\", \"report_fit_test.yaml\"), fit = fit)"},{"path":"/news/index.html","id":"nlmixr2rpt-021-development-version","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.2.1 (development version)","title":"nlmixr2rpt 0.2.1 (development version)","text":"NA","code":""},{"path":"/news/index.html","id":"nlmixr2rpt-020","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.2.0","title":"nlmixr2rpt 0.2.0","text":"CRAN release: 2023-06-06 Fixing error CRAN","code":""},{"path":"/news/index.html","id":"nlmixr2rpt-010","dir":"Changelog","previous_headings":"","what":"nlmixr2rpt 0.1.0","title":"nlmixr2rpt 0.1.0","text":"CRAN release: 2022-12-05 Initial release","code":""}]