add absorption examples

absorption/README.md

@@ -1,4 +1,7 @@
 # Absorption models
 
 [Sequential zero-/first-order absorption](sequential.md)
+[Parallel-firstorder absorption](parallel-firstorder.md)
+[Mixed first order abs and zero order infusion](mixedzeroandfirst.md)
+[Weibull absorption](#)
 

absorption/mixedzeroandfirst.Rmd

@@ -0,0 +1,59 @@
+---
+title: "Mixed first order abs and zero order infusion"
+output: github_document
+---
+
+```{r,echo = FALSE, message = FALSE}
+knitr::opts_chunk$set(comment='.', 
+                      message = FALSE, warning = FALSE)
+```
+
+```{r}
+library(mrgsolve)
+library(tidyverse)
+```
+
+## Mixed first order abs into gut and zero order infusion
+
+```{r}
+code <- '
+$PARAM CL = 5, VC = 50, KA = 0.5, GUTBIOAV = 0.5, GUTLAGT=0
+BIOAV = 1, LAGT = 5, MODE = 0, DUR2 = 4, RAT2 = 10
+
+$CMT GUT CENT
+
+$MAIN
+F_GUT = GUTBIOAV;
+ALAG_GUT = GUTLAGT;
+
+F_CENT = 1-F_GUT;
+ALAG_CENT = LAGT;
+
+if(MODE==1) R_CENT = RAT2;
+if(MODE==2) D_CENT = DUR2;
+
+$ODE
+
+dxdt_GUT = -KA*GUT;
+dxdt_CENT = KA*GUT - (CL/VC)*CENT;
+
+$TABLE
+double CP = CENT/VC;
+
+$CAPTURE CP GUT CENT
+'
+
+mod <- mcode_cache("mixed", code)
+```
+
+```{r}
+mod <- update(mod, end=72)
+```
+
+### mixed zero and first-order events
+```{r}
+ev2 <- ev(ID=1,amt = 10, time=0, cmt=1) + ev(ID=1,time = 0, amt = 10, cmt=2, rate=-2, MODE=2)
+out <- mod %>% Req(GUT, CENT, CP) %>% mrgsim(ev2)
+plot(out)
+```
+

absorption/mixedzeroandfirst.md

@@ -0,0 +1,55 @@
+Mixed first order abs and zero order infusion
+================
+
+``` r
+library(mrgsolve)
+library(tidyverse)
+```
+
+Mixed first order abs into gut and zero order infusion
+------------------------------------------------------
+
+``` r
+code <- '
+$PARAM CL = 5, VC = 50, KA = 0.5, GUTBIOAV = 0.5, GUTLAGT=0
+BIOAV = 1, LAGT = 5, MODE = 0, DUR2 = 4, RAT2 = 10
+
+$CMT GUT CENT
+
+$MAIN
+F_GUT = GUTBIOAV;
+ALAG_GUT = GUTLAGT;
+
+F_CENT = 1-F_GUT;
+ALAG_CENT = LAGT;
+
+if(MODE==1) R_CENT = RAT2;
+if(MODE==2) D_CENT = DUR2;
+
+$ODE
+
+dxdt_GUT = -KA*GUT;
+dxdt_CENT = KA*GUT - (CL/VC)*CENT;
+
+$TABLE
+double CP = CENT/VC;
+
+$CAPTURE CP GUT CENT
+'
+
+mod <- mcode_cache("mixed", code)
+```
+
+``` r
+mod <- update(mod, end=72)
+```
+
+### mixed zero and first-order events
+
+``` r
+ev2 <- ev(ID=1,amt = 10, time=0, cmt=1) + ev(ID=1,time = 0, amt = 10, cmt=2, rate=-2, MODE=2)
+out <- mod %>% Req(GUT, CENT, CP) %>% mrgsim(ev2)
+plot(out)
+```
+
+![](mixedzeroandfirst_files/figure-markdown_github/unnamed-chunk-5-1.png)

absorption/parallel-firstorder.Rmd

@@ -0,0 +1,63 @@
+---
+title: "Parallel-firstorder absorption"
+output: 
+  github_document
+---
+
+```{r,echo = FALSE, message = FALSE}
+knitr::opts_chunk$set(comment='.', 
+                      message = FALSE, warning = FALSE)
+```
+
+```{r}
+library(mrgsolve)
+library(tidyverse)
+```
+
+## Two parallel first order absorption models
+
+```{r}
+code <- '
+$PARAM CL = 5, VC = 50, KA1 = 0.8, KA2=0.6
+GUT1BIOAV = 0.5, GUT1LAGT=0, GUT2BIOAV = 1, GUT2LAGT=5
+BIOAV = 1, LAGT = 0
+
+$CMT GUT1 GUT2 CENT
+
+$MAIN
+F_GUT1 = GUT1BIOAV;
+ALAG_GUT1 = GUT1LAGT;
+
+F_GUT2 = 1- GUT1BIOAV;
+ALAG_GUT2 = GUT2LAGT;
+
+F_CENT = BIOAV;
+ALAG_CENT = LAGT;
+
+$ODE
+
+dxdt_GUT1 = -KA1*GUT1;
+dxdt_GUT2 = -KA2*GUT2;
+dxdt_CENT = KA1*GUT1 + KA2*GUT2 - (CL/VC)*CENT;
+
+$TABLE
+double CP = CENT/VC;
+
+$CAPTURE CP
+'
+
+mod <- mcode_cache("parabs", code)
+```
+
+```{r}
+mod <- update(mod, end=72)
+```
+
+### two-parallel first-order events
+
+```{r}
+ev1 <- ev(ID=1, amt = 10, cmt=1) + ev(ID=1, amt = 10, cmt=2)
+out <- mod %>% Req(GUT1, GUT2, CP) %>% mrgsim(ev1)
+plot(out)
+```
+

absorption/parallel-firstorder.md

@@ -0,0 +1,57 @@
+Parallel-firstorder absorption
+================
+
+``` r
+library(mrgsolve)
+library(tidyverse)
+```
+
+Two parallel first order absorption models
+------------------------------------------
+
+``` r
+code <- '
+$PARAM CL = 5, VC = 50, KA1 = 0.8, KA2=0.6
+GUT1BIOAV = 0.5, GUT1LAGT=0, GUT2BIOAV = 1, GUT2LAGT=5
+BIOAV = 1, LAGT = 0
+
+$CMT GUT1 GUT2 CENT
+
+$MAIN
+F_GUT1 = GUT1BIOAV;
+ALAG_GUT1 = GUT1LAGT;
+
+F_GUT2 = 1- GUT1BIOAV;
+ALAG_GUT2 = GUT2LAGT;
+
+F_CENT = BIOAV;
+ALAG_CENT = LAGT;
+
+$ODE
+
+dxdt_GUT1 = -KA1*GUT1;
+dxdt_GUT2 = -KA2*GUT2;
+dxdt_CENT = KA1*GUT1 + KA2*GUT2 - (CL/VC)*CENT;
+
+$TABLE
+double CP = CENT/VC;
+
+$CAPTURE CP
+'
+
+mod <- mcode_cache("parabs", code)
+```
+
+``` r
+mod <- update(mod, end=72)
+```
+
+### two-parallel first-order events
+
+``` r
+ev1 <- ev(ID=1, amt = 10, cmt=1) + ev(ID=1, amt = 10, cmt=2)
+out <- mod %>% Req(GUT1, GUT2, CP) %>% mrgsim(ev1)
+plot(out)
+```
+
+![](parallel-firstorder_files/figure-markdown_github/unnamed-chunk-5-1.png)

absorption/weibull.Rmd

@@ -0,0 +1,61 @@
+---
+title: "Weibull absorption"
+output: github_document
+---
+
+```{r,echo = FALSE, message = FALSE}
+knitr::opts_chunk$set(comment='.', 
+                      message = FALSE, warning = FALSE)
+```
+
+```{r}
+library(mrgsolve)
+library(tidyverse)
+```
+
+## Weibull-type absorption
+
+```{r}
+code <- '
+$PARAM CL = 5, VC = 50, KA = 0.4, GUTBIOAV = 1, GUTLAGT=0, GAMA=4
+BIOAV = 1, LAGT = 0
+
+$CMT GUT CENT
+
+$MAIN
+// Weibull parameters
+double GAMA1 = GAMA;
+
+// Weibull function
+double WB = 1 - exp(pow((-KA*TIME),GAMA1));
+
+F_GUT = GUTBIOAV;
+ALAG_GUT = GUTLAGT;
+
+F_CENT = BIOAV;
+ALAG_CENT = LAGT;
+
+$ODE
+dxdt_GUT = -WB*GUT;
+dxdt_CENT = WB*GUT - (CL/VC)*CENT;
+
+$TABLE
+double CP = CENT/VC;
+
+$CAPTURE CP
+'
+
+mod <- mcode_cache("weibull", code)
+```
+
+```{r}
+mod <- update(mod, end=72)
+```
+
+### First order events
+
+```{r}
+ev3 <- ev(ID=1,amt = 10, cmt=1)
+out<- mod %>% Req(GUT, CENT, CP) %>% mrgsim(ev3)
+plot(out)
+```

topics.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX