Added in vitro analysis examples to workshop and vignette.

DESCRIPTION

@@ -8,7 +8,7 @@ Authors@R: c(person("John", "Harrold",
                      comment = c(ORCID="0000-0003-2052-4373")))
 Maintainer: John Harrold <john.m.harrold@gmail.com>
 Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'. 
-URL: https://ubiquity.tools/rworkflow
+URL: https://r.ubiquity.tools
 SystemRequirements: Perl
 BugReports: https://github.com/john-harrold/ubiquity/issues
 License: BSD_2_clause + file LICENSE

R/ubiquity.r

@@ -292,7 +292,7 @@ return(cfg)}
 #'@param overwrite if \code{TRUE} the new workshop files will overwrite any existing files present (\code{FALSE})
 #'@param copy_files if \code{TRUE} the files will be written to the output_directory, if \code{FALSE} only the names and locations of the files will be returned (\code{TRUE})
 #'@param output_directory directory where workshop files will be placed (getwd())
-#'@details Valid sections are "Simulation", "Estimation", "Titration" "Reporting", and "NCA"
+#'@details Valid sections are "Simulation", "Estimation", "In Vitro", "Titration" "Reporting", and "NCA"
 #'
 #'@return list
 #'@examples
@@ -304,7 +304,7 @@ workshop_fetch <- function(section          = "Simulation",
                            copy_files       = TRUE,
                            output_directory = getwd()){
   res = list()
-  allowed = c("Simulation", "Estimation", "Titration", "Reporting", "Testing", "NCA")
+  allowed = c("Simulation", "Estimation", "In Vitro", "Titration", "Reporting", "Testing", "NCA")
 
   isgood = TRUE
   # This function only works if we're using the package
@@ -379,6 +379,16 @@ workshop_fetch <- function(section          = "Simulation",
                           "analysis_visit_infusion_dosing.r",                           
                           "system.txt")
          write_file   = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE)
+      } else if(section=="In Vitro") {
+         sources      = c(file.path(src_dir, "analysis_in_vitro.R"                          ),
+                          file.path(src_dir, "mk_data_in_vitro.R"                           ),
+                          file.path(csv_dir, "in_vitro_er_data.csv"                         ),
+                          file.path(sys_dir, "system-in_vitro.txt"                          ))
+         destinations = c("analysis_in_vitro.R",                    
+                          "mk_data_in_vitro.R",                          
+                          "in_vitro_er_data.csv",                       
+                          "system-in_vitro.txt")
+         write_file   = c(TRUE, TRUE, TRUE, TRUE)
       } else if(section=="Testing") {
          sources      = c(file.path(src_dir, "workshop_test.R"))
          destinations = c("workshop_test.R")

_pkgdown.yml

@@ -1,5 +1,7 @@
 url: https://r.ubiquity.tools
 template:
+  #math-rendering: mathjax
+  math-rendering: katex
   bootstrap: 5
   params:
     bootswatch: united 
@@ -105,6 +107,8 @@ navbar:
           href: articles/Deployment.html
         - text: "Trial/Rule-Based Simulations"
           href: articles/Titration.html
+        - text: "Estimation of In Vitro/Static Systems"
+          href: articles/In_Vitro.html
         - text: "Non-Compartmental Analysis"
           href: articles/NCA.html
         - text: "Integrated Word and PowerPoint Reporting"