minor tweaks to indentation

Author: shirewoman2

AUC user defined interval/AUCt for user defined interval.R

@@ -10,6 +10,7 @@ library(dplyr)
 library(pracma)
 
 
+
 if (exists("debugSource"))
    Simcyp::Initialise("C://Program files//Simcyp simulator v23//screens//systemfiles", 23)
 setwd("~/V23 Cobicistat")

Forest plot/Simcyp R package - forest plot example.R

@@ -5,6 +5,7 @@
 # 2. How to extract the necessary data for forest plots
 # 3. How to use those data to make a forest plot
 
+
 # Housekeeping ----------------------------------------------------------------
 library(Simcyp)
 library(RSQLite)

Summary Stats and Ribbon Plots/Summary Statistic and Ribbon Plots with Simcyp-R Package.R

@@ -2,7 +2,7 @@
 # Clear Global Environment ----
 rm(list=ls()) 
 
-# 1. Load Packages ----
+# 1. Load Packages -----
 # Required packages for Simcyp-R 
 library("Simcyp")
 library("RSQLite")

Tuning ODE Solver Parameters with R Package/e-learning.R

@@ -13,8 +13,8 @@ rtol     <- c(1e-1 ^ (1:3), 1e-1 ^ (1:3), 1e-1 ^ (1:3))
 atol     <- rtol * 1e-2
 
 res.df   <- data.frame(matrix(ncol = 6, nrow = Tot_iter,
-                       dimnames = list(NULL, c("method","rtol","atol",
-                                               "mean_time","sd_time","subjects_negC"))))
+                              dimnames = list(NULL, c("method","rtol","atol",
+                                                      "mean_time","sd_time","subjects_negC"))))
 
 res.df$method <- solvName[solv[1:Tot_iter]]
 res.df$rtol   <- rtol
@@ -29,12 +29,12 @@ SetWorkspace("V23_B305_minPBPK_ADAM_CLiv.wksz") # 10 x 10 workspace
 db_file  <- array( dim = Tot_iter )
 
 for( iter in 1 : Tot_iter ){
-  db_file[iter] <- paste0("sim_",sprintf("%004d",iter),".db")
-  
-  # Simcyp::SetSolver( solv[iter],
-  #                    rtol = rtol[iter], atol = atol[iter], maxsteps = 1e+07 )
-  # 
-  # Simulate( database = db_file[iter] )
+   db_file[iter] <- paste0("sim_",sprintf("%004d",iter),".db")
+   
+   # Simcyp::SetSolver( solv[iter],
+   #                    rtol = rtol[iter], atol = atol[iter], maxsteps = 1e+07 )
+   # 
+   # Simulate( database = db_file[iter] )
 }
 
 Simcyp::Uninitialise()
@@ -44,25 +44,26 @@ Simcyp::Uninitialise()
 Simcyp::Initialise(species = SpeciesID$Human, verbose = FALSE)
 
 for( iter in 1 : Tot_iter ){
-  conn <- RSQLite::dbConnect( SQLite(), db_file[iter] )
-  
-  # SIMULATION DURATIONS
-  PopResults    <- dbGetQuery( conn, "SELECT * FROM PopResults10" )
-  sim_duration  <- PopResults$SimulationDuration
-  
-  res.df$mean_time[iter] <- mean( sim_duration )
-  res.df$sd_time[  iter] <-   sd( sim_duration )
-  
-  # NO. OF SUBJECTS WITH A NEGATIVE CONC
-  negC <- vector()
-  for(k in 1:100){
-    Csys <- GetProfile_DB(ProfileID$Csys, compound = CompoundID$Substrate, individual = k, conn, inhibition = FALSE)
-    negC[k] <- as.numeric( 0 < sum( ( Csys < 0) ) ) # there is a neg conc or not
-  }
-  
-  res.df$subjects_negC[iter] <- sum( negC )
-  
-  RSQLite::dbDisconnect( conn )
+   conn <- RSQLite::dbConnect( SQLite(), db_file[iter] )
+   
+   # SIMULATION DURATIONS
+   PopResults    <- dbGetQuery( conn, "SELECT * FROM PopResults10" )
+   sim_duration  <- PopResults$SimulationDuration
+   
+   res.df$mean_time[iter] <- mean( sim_duration )
+   res.df$sd_time[  iter] <-   sd( sim_duration )
+   
+   # NO. OF SUBJECTS WITH A NEGATIVE CONC
+   negC <- vector()
+   for(k in 1:100){
+      Csys <- GetProfile_DB(ProfileID$Csys, compound = CompoundID$Substrate, individual = k, conn, inhibition = FALSE)
+      negC[k] <- as.numeric( 0 < sum( ( Csys < 0) ) ) # there is a neg conc or not
+   }
+   
+   res.df$subjects_negC[iter] <- sum( negC )
+   
+   RSQLite::dbDisconnect( conn )
 }
 
-Simcyp::Uninitialise()
+Simcyp::Uninitialise()
+