updated package entirely

.Rbuildignore

@@ -6,9 +6,8 @@
 ^.*\.sh$
 ^tests$
 ^data-raw$
-^packrat/
 ^\.Rprofile$
 ^README.*$
-^Figures$
-^rd2pdf\.sh$
+^assets$
+^Makefile$
 ^docs$

Makefile

@@ -0,0 +1,5 @@
+rd2pdf:
+	rm caffsim.pdf;R CMD rd2pdf ../caffsim
+
+pkgdown:
+	rm -rf docs;Rscript -e "Sys.setlocale('LC_ALL', 'C'); pkgdown::build_site()" 

NAMESPACE

@@ -1,11 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-export(ConcTime)
-export(ConcTimeMulti)
-export(Dataset)
-export(DatasetMulti)
-export(Plot)
-export(PlotMulti)
+export(caffConcTime)
+export(caffConcTimeMulti)
+export(caffDataset)
+export(caffDatasetMulti)
+export(caffPlot)
+export(caffPlotMulti)
 import(dplyr)
 import(ggplot2)
 importFrom(mgcv,rmvn)

R.Rproj

@@ -6,7 +6,7 @@ AlwaysSaveHistory: Yes
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
-NumSpacesForTab: 4
+NumSpacesForTab: 2
 Encoding: UTF-8
 
 RnwWeave: knitr

R/ConcTime.R

@@ -1,36 +1,36 @@
-#' Create a dataset of the concentration-time curve
+#' Create a dataset of the concentration-time curve of single oral administration of caffeine
 #'
-#' \code{ConcTime} will create a dataset of the concentration-time curve
+#' \code{caffConcTime} will create a dataset of the concentration-time curve
 #' 
 #' @param Weight Body weight (kg)
 #' @param Dose Dose of single caffeine (mg)
 #' @param N The number of simulated subjects
 #' @return The dataset of concentration and time of simulated subjects
 #' @export
 #' @examples 
-#' ConcTime(Weight = 20, Dose = 200, N = 20)
-#' ConcTime(20, 200)
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffConcTime(Weight = 20, Dose = 200, N = 20)
+#' caffConcTime(20, 200)
 #' @import dplyr
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-ConcTime <- function(Weight, Dose, N = 20){
-    #set.seed(Seed)
-    ggConc <- Dataset(Weight, Dose, N) %>% 
-        select(CL, V, Ka, Ke) %>% 
-        mutate(Subject = row_number()) %>% 
-        left_join(expand.grid(
-            x = seq(1, N, length.out = N),  #Subjecti
-            y = seq(0,24, by = 0.1)) %>% # Time
-                select(Subject=x, Time=y), by = "Subject") %>% 
-        mutate(Conc = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Time) - exp(-Ka * Time))) %>% 
-        select(Subject, Time, Conc)
-    return(ggConc)
+caffConcTime <- function(Weight, Dose, N = 20){
+  #set.seed(Seed)
+  ggConc <- caffDataset(Weight, Dose, N) %>% 
+    select(CL, V, Ka, Ke) %>% 
+    mutate(Subject = row_number()) %>% 
+    left_join(expand.grid(
+      x = seq(1, N, length.out = N),  #Subjecti
+      y = seq(0,24, by = 0.1)) %>% # Time
+        select(Subject=x, Time=y), by = "Subject") %>% 
+    mutate(Conc = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Time) - exp(-Ka * Time))) %>% 
+    select(Subject, Time, Conc)
+  return(ggConc)
 }
 
 
-#' Create a dataset of the concentration-time curve of multiple dosing
+#' Create a dataset of the concentration-time curve of multiple dosing of caffeine
 #'
-#' \code{ConcTimeMulti} will create a dataset of the concentration-time curve of multiple dosing
+#' \code{caffConcTimeMulti} will create a dataset of the concentration-time curve of multiple oral administrations of caffeine
 #' 
 #' @param Weight Body weight (kg)
 #' @param Dose Dose of single caffeine (mg)
@@ -40,31 +40,33 @@ ConcTime <- function(Weight, Dose, N = 20){
 #' @return The dataset of concentration and time of simulated subjects of multiple dosing
 #' @export
 #' @examples 
-#' ConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4)
-#' ConcTimeMulti(20, 200)
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4)
+#' caffConcTimeMulti(20, 200)
 #' @import dplyr
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-ConcTimeMulti <- function(Weight, Dose, N = 20, Tau = 8, Repeat = 4){
-    Subject <- seq(1, N, length.out = N) # 
-    Time <- seq(0, 96, length.out = 481) # 
-    Grid <- expand.grid(x = Subject, y = Time) %>% select(Subject=x, Time=y)
-
-    ggsuper <- Dataset(Weight, Dose, N) %>% select(CL, V, Ka, Ke) %>% 
-        mutate(Subject = row_number()) %>% 
-        left_join(Grid, by = "Subject") %>% 
-        mutate(Conc = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Time) - exp(-Ka * Time))) %>% 
-        group_by(Subject) %>% 
-        mutate(ConcOrig = Conc, 
-               ConcTemp = 0)
-    ## Superposition
-    for (i in 1:Repeat){
-        Frame <- Tau * 5 * i
-        ggsuper <- ggsuper %>% 
-            mutate(Conc = Conc + ConcTemp) %>% 
-            mutate(ConcTemp = lag(ConcOrig, n = Frame, default = 0))
-    }
-
-    ggsuper <- ggsuper %>% select(Subject, Time, Conc)
-    return(ggsuper)
+caffConcTimeMulti <- function(Weight, Dose, N = 20, Tau = 8, Repeat = 4){
+  Subject <- seq(1, N, length.out = N) # 
+  Time <- seq(0, 96, length.out = 481) # 
+  Grid <- expand.grid(x = Subject, y = Time) %>% select(Subject=x, Time=y)
+
+  ggsuper <- caffDataset(Weight, Dose, N) %>% 
+    select(CL, V, Ka, Ke) %>% 
+    mutate(Subject = row_number()) %>% 
+    left_join(Grid, by = "Subject") %>% 
+    mutate(Conc = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Time) - exp(-Ka * Time))) %>% 
+    group_by(Subject) %>% 
+    mutate(ConcOrig = Conc, 
+           ConcTemp = 0)
+
+  ## Superposition
+  for (i in 1:Repeat){
+    Frame <- Tau * 5 * i
+    ggsuper <- ggsuper %>% 
+      mutate(Conc = Conc + ConcTemp) %>% 
+      mutate(ConcTemp = lag(ConcOrig, n = Frame, default = 0))
+  }
+
+  ggsuper <- ggsuper %>% select(Subject, Time, Conc)
+  return(ggsuper)
 }

R/Dataset.R

@@ -1,21 +1,21 @@
 #' Create a dataset for simulation of single dose of caffeine 
 #'
-#' \code{Dataset} will create a dataset for simulation of single dose of caffeine 
+#' \code{caffDataset} will create a dataset for simulation of single dose of caffeine 
 #' 
 #' @param Weight Body weight (kg)
 #' @param Dose Dose of single caffeine (mg)
 #' @param N The number of simulated subjects
 #' @return The dataset of pharmacokinetic parameters of subjects after single caffeine dose following multivariate normal
 #' @export
 #' @examples 
-#' Dataset(Weight = 20, Dose = 200, N = 20)
-#' Dataset(20,500)
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffDataset(Weight = 20, Dose = 200, N = 20)
+#' caffDataset(20,500)
 #' @importFrom mgcv rmvn
 #' @import dplyr
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-Dataset <- function(Weight, Dose, N = 20){
-  MVN <- rmvn(N, CaffMu, CaffSigma);  
+caffDataset <- function(Weight, Dose, N = 20){
+  MVN <- mgcv::rmvn(N, CaffMu, CaffSigma)
   MVNdata <- data.frame(MVN, stringsAsFactors = FALSE) %>% 
     select(eta1 = X1, eta2 = X2, eta3 = X3) %>% 
     mutate(CL = 0.09792 * Weight * exp(eta1), # L/hr
@@ -31,7 +31,7 @@ Dataset <- function(Weight, Dose, N = 20){
 
 #' Create a dataset for simulation of multiple dose of caffeine 
 #'
-#' \code{DatasetMulti} will create a dataset for simulation of multiple dose of caffeine 
+#' \code{caffDatasetMulti} will create a dataset for simulation of multiple dose of caffeine 
 #'
 #' @param Weight Body weight (kg)
 #' @param Dose Dose of multiple caffeine (mg)
@@ -40,32 +40,31 @@ Dataset <- function(Weight, Dose, N = 20){
 #' @return The dataset of pharmacokinetic parameters of subjects after multiple caffeine dose following multivariate normal
 #' @export
 #' @examples 
-#' DatasetMulti(Weight = 20, Dose = 200, N = 20, Tau = 8)
-#' DatasetMulti(20,500)
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffDatasetMulti(Weight = 20, Dose = 200, N = 20, Tau = 8)
+#' caffDatasetMulti(20,500)
 #' @importFrom mgcv rmvn
 #' @import dplyr
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-DatasetMulti <- function(Weight, Dose, N = 20, Tau = 24){
-    #set.seed(20140523+1)
-    MVN <- rmvn(N, CaffMu, CaffSigma);  
-    MVNdata <- data.frame(MVN, stringsAsFactors = FALSE) %>% 
-        select(eta1 = X1, eta2 = X2, eta3 = X3) %>% 
-        mutate(CL = 0.09792 * Weight * exp(eta1), # L/hr
-               V  = 0.7219 * Weight * exp(eta2), # L, TVV =THETA[2] * (1 + ABST*THETA[7]) [1] 0.7218775
-               Ka = 4.268 * exp(eta3), # /hr
-               Ke = CL / V,
-               Half_life = 0.693 / Ke,
-               Tmax = (log(Ka) - log(Ke)) / (Ka - Ke),
-               Cmax = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Tmax) - exp(-Ka * Tmax)),
-               AUC  = Dose / CL
-               ) %>%  
-        mutate(AI = 1/(1-exp(-1*Ke*Tau)),
-               Aavss = 1.44 * Dose * Half_life / Tau,
-               Cavss = Dose / (CL * Tau), 
-               Cminss = Dose * exp(-Ke * Tau) / (V * (1 - exp(-Ke * Tau))),
-               Cmaxss = Dose / (V * (1 - exp(-Ke * Tau)))) %>% 
-        select(TmaxS = Tmax, CmaxS = Cmax, AUCS = AUC, AI, Aavss, Cavss, Cmaxss, Cminss)
-    return(MVNdata)
+caffDatasetMulti <- function(Weight, Dose, N = 20, Tau = 24){
+  #set.seed(20140523+1)
+  MVN <- mgcv::rmvn(N, CaffMu, CaffSigma)
+  MVNdata <- data.frame(MVN, stringsAsFactors = FALSE) %>% 
+    select(eta1 = X1, eta2 = X2, eta3 = X3) %>% 
+    mutate(CL = 0.09792 * Weight * exp(eta1), # L/hr
+           V  = 0.7219 * Weight * exp(eta2), # L, TVV =THETA[2] * (1 + ABST*THETA[7]) [1] 0.7218775
+           Ka = 4.268 * exp(eta3), # /hr
+           Ke = CL / V,
+           Half_life = 0.693 / Ke,
+           Tmax = (log(Ka) - log(Ke)) / (Ka - Ke),
+           Cmax = Dose / V * Ka / (Ka - Ke) * (exp(-Ke * Tmax) - exp(-Ka * Tmax)),
+           AUC  = Dose / CL
+    ) %>%  
+    mutate(AI = 1/(1-exp(-1*Ke*Tau)),
+           Aavss = 1.44 * Dose * Half_life / Tau,
+           Cavss = Dose / (CL * Tau), 
+           Cminss = Dose * exp(-Ke * Tau) / (V * (1 - exp(-Ke * Tau))),
+           Cmaxss = Dose / (V * (1 - exp(-Ke * Tau)))) %>% 
+    select(TmaxS = Tmax, CmaxS = Cmax, AUCS = AUC, AI, Aavss, Cavss, Cmaxss, Cminss)
+  return(MVNdata)
 }
-

R/Plot.R

@@ -7,25 +7,25 @@
 #' @return The concentration-time curve
 #' @export
 #' @examples 
-#' Plot(ConcTime(Weight = 20, Dose = 200, N = 20))
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffPlot(caffConcTime(Weight = 20, Dose = 200, N = 20))
 #' @import dplyr
 #' @import ggplot2
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-Plot <- function(ConcTime, log = FALSE){
-    p <- ggplot(ConcTime, aes(x=Time, y=Conc)) + 
-        xlab("Time (hour)") + ylab("Concentration (mg/L)") +
-        scale_x_continuous(breaks = seq(from = 0, to = 24, by = 4)) +
-        #scale_color_gradient2() +
-        #scale_colour_gradient(low="navy", high="red", space="Lab") +
-        geom_line(aes(group = Subject, colour = Conc)) + 
-        stat_summary(fun.y = "mean", colour = "#F0E442", size = 1, geom = "line") +
-        geom_hline(yintercept = 80, colour="red") + 
-        geom_hline(yintercept = 40, colour="blue") + 
-        geom_hline(yintercept = 10, colour="green") + theme_linedraw()
-    
-    if (log == TRUE) p <- p + scale_y_log10() #limits = c(0.1, max(80, ggConc$Conc))))
-    return(p)
+caffPlot <- function(caffConcTime, log = FALSE){
+  p <- ggplot(caffConcTime, aes(x=Time, y=Conc)) + 
+    xlab("Time (hour)") + ylab("Concentration (mg/L)") +
+    scale_x_continuous(breaks = seq(from = 0, to = 24, by = 4)) +
+    #scale_color_gradient2() +
+    #scale_colour_gradient(low="navy", high="red", space="Lab") +
+    geom_line(aes(group = Subject, colour = Conc)) + 
+    stat_summary(fun.y = "mean", colour = "#F0E442", size = 1, geom = "line") +
+    geom_hline(yintercept = 80, colour="red") + 
+    geom_hline(yintercept = 40, colour="blue") + 
+    geom_hline(yintercept = 10, colour="green") + theme_linedraw()
+
+  if (log == TRUE) p <- p + scale_y_log10() #limits = c(0.1, max(80, ggConc$Conc))))
+  return(p)
 }
 
 #' Create concentration-time curve after multiple doses of caffeine
@@ -37,22 +37,22 @@ Plot <- function(ConcTime, log = FALSE){
 #' @return The concentration-time curve
 #' @export
 #' @examples 
-#' PlotMulti(ConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4))
-#' @seealso \url{http://asancpt.github.io/CaffeineEdison}
+#' caffPlotMulti(ConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4))
 #' @import dplyr
 #' @import ggplot2
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
-PlotMulti <- function(ConcTimeMulti, log = FALSE){
-    p <- ggplot(ConcTimeMulti, aes(x=Time, y=Conc)) + #, group=Subject, colour = Conc)) + #Subject)) +
-        xlab("Time (hour)") + ylab("Concentration (mg/L)") +
-        scale_x_continuous(breaks = seq(0, 96, 12)) +
-        #scale_colour_gradient(low="navy", high="red", space="Lab") +
-        geom_line(aes(group = Subject, colour = Conc)) + 
-        stat_summary(fun.y = "mean", colour = "#F0E442", size = 1, geom = "line") +
-        geom_hline(yintercept = 80, colour="red") + 
-        geom_hline(yintercept = 40, colour="blue") + 
-        geom_hline(yintercept = 10, colour="green") + theme_linedraw()
-    
-    if (log == TRUE) p <- p + scale_y_log10() #limits = c(0.1, max(80, ggConc$Conc))))
-    return(p)
+caffPlotMulti <- function(caffConcTimeMulti, log = FALSE){
+  p <- ggplot(caffConcTimeMulti, aes(x=Time, y=Conc)) + #, group=Subject, colour = Conc)) + #Subject)) +
+    xlab("Time (hour)") + ylab("Concentration (mg/L)") +
+    scale_x_continuous(breaks = seq(0, 96, 12)) +
+    #scale_colour_gradient(low="navy", high="red", space="Lab") +
+    geom_line(aes(group = Subject, colour = Conc)) + 
+    stat_summary(fun.y = "mean", colour = "#F0E442", size = 1, geom = "line") +
+    geom_hline(yintercept = 80, colour="red") + 
+    geom_hline(yintercept = 40, colour="blue") + 
+    geom_hline(yintercept = 10, colour="green") + theme_linedraw()
+
+  if (log == TRUE) p <- p + scale_y_log10() #limits = c(0.1, max(80, ggConc$Conc))))
+  return(p)
 }

R/data.R

@@ -7,6 +7,6 @@
 #'   \item{Parameters}{Abbreviated pharmacokinetic parameters}
 #'   \item{Parameter}{Pharmacokinetic parameters in full name}
 #' }
-#' @source \url{http://asancpt.github.io/CaffeineEdison}
+#' @seealso \url{https://asancpt.github.io/caffsim}
 
 "UnitTable"