First commit

Author: jasebailey

.gitignore

@@ -37,3 +37,8 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+
+# not images
+media/*.png
+
+.DS_Store

create-animations.R

@@ -0,0 +1,37 @@
+  # create-animations.R
+  # Script to create animated GIFs of
+  # specific tests
+  #
+  # jason bailey
+  # 20200120 first commit
+
+#install.packages("magick")
+library(magick)
+imagesPath <- ('/Users/jason/Source/RCode/zombie/media/')
+
+testsToAnimate<-c('Test 1', 'Test 21')
+
+for (testName in testsToAnimate){
+  
+  #print(testName)
+  
+  fileSearch<-paste("^",testName,'(.*).png$', sep="")
+  print(fileSearch)
+  # ^Product(.*)xlsx$
+  list <- list.files(imagesPath,pattern=fileSearch)
+  #print(list)
+  
+  imagesAll <- paste0(imagesPath, list)
+  images <- image_read(imagesAll)
+  #images
+  animation <- image_animate(images, fps = 0.8, loop = 5)
+  #animation
+  saveFileName<-paste(testName,".gif", sep="")
+  filePath<-paste0(imagesPath, saveFileName)
+  #saveFileName<-'gg.gif'
+  #print(filePath)
+  image_write(animation, filePath,format = "gif")
+  #imagesPath
+  
+  
+}

z-includes.R

@@ -0,0 +1,269 @@
+# z-includes.R
+# Include file for Main script
+#
+# jason bailey
+# 20200120 first commit
+
+
+# test data
+fn_initial_conditions<-function(){
+  
+  #iterations =15   #rows =10   #cols =10   #cells <- rows*cols
+  # numberOFZombies to start with   #zombieStart =1
+  # number of Immune  #immuneStart =250
+  a1<-c(15,10,10,1,1)
+  a2<-c(15,10,10,1,1)
+  a3<-c(15,10,10,1,1)
+  a4<-c(15,10,10,1,1)
+  a5<-c(15,10,10,1,1)
+  a6<-c(15,10,10,1,1)
+  a7<-c(15,10,10,1,1)
+  a8<-c(15,10,10,1,1)
+  a9<-c(15,10,10,1,1)
+  a10<-c(15,10,10,1,1)
+  a12<-c(15,10,10,1,1)
+  a11<-c(15,10,10,1,1)
+  a13<-c(15,10,10,1,1)
+  a14<-c(15,10,10,1,1)
+  a15<-c(15,10,10,1,1)
+  a16<-c(15,10,10,1,250)
+  a17<-c(15,10,10,1,250)
+  a18<-c(15,10,10,1,250)
+  a19<-c(15,10,10,1,250)
+  a20<-c(15,10,10,1,250)
+  a21<-c(15,10,10,1,299)
+  a22<-c(15,10,10,1,299)
+  a23<-c(15,10,10,1,299)
+  a24<-c(15,10,10,1,299)
+  a25<-c(15,10,10,1,299)
+  a26<-c(15,10,10,1,299)
+  a27<-c(15,10,10,1,250)
+  a28<-c(15,10,10,1,250)
+  a29<-c(15,10,10,1,250)
+  a30<-c(15,10,10,1,250)
+  a31<-c(15,10,10,1,50)
+  a32<-c(15,10,10,1,50)
+  a33<-c(15,10,10,1,50)
+  a34<-c(15,10,10,1,50)
+  a35<-c(15,10,10,1,60)
+  a36<-c(15,10,10,1,70)
+  a37<-c(15,10,10,1,80)
+  a38<-c(15,10,10,1,80)
+  a39<-c(15,10,10,1,70)
+  a40<-c(15,10,10,1,60)
+  a41<-c(25,100,100,1,1)
+  a42<-c(25,100,100,1,1)
+  a43<-c(25,100,100,1,1)
+  a44<-c(25,100,100,1,1)
+  a45<-c(25,100,100,1,1)
+  a46<-c(25,100,100,1,1000)
+  a47<-c(25,100,100,1,2000)
+  a48<-c(25,100,100,1,3000)
+  a49<-c(25,100,100,1,5000)
+  a50<-c(25,100,100,1,6000)
+  a51<-c(25,100,100,1,35000)
+  a52<-c(25,100,100,1,35000)
+  a53<-c(25,100,100,1,35000)
+  a54<-c(25,100,100,1,35000)
+  a55<-c(25,100,100,1,35000)
+  
+  d<-as.matrix( rbind(a1,a2,a3,a4,a5,a6,a7,a8,a9,a10,a11,a12,a13,a14,a15,a16,a17,a18,a19,a20,a21,a22,a23,a24,a25,a26,a27,a28,a29,a30,a31,a32,a33,a34,a35,a36,a37,a38,a39,a40,a41,a42,a43,a44,a45,a46,a47,a48,a49,a50,a51,a52,a53,a54,a55))
+  #d<-as.matrix( rbind(a1))
+  #matrix( c(1,2,3,), c(4,5,6), nrow = 2, byrow = TRUE)
+  return(d)
+}
+
+
+
+###########
+# Functions
+###########
+fn_doIterations <-function (testName,popMatrix, numRows,numCols){
+  cells = numRows*numCols
+  #print(popMatrix)
+  fn_plotZombie(testName,popMatrix,0, numRows,  numCols)
+  
+  #dfnamesR<-c( "test","step", "rows","cols","human","zombie","immune")
+  #iters0<-data.frame(testName0,0,0,0,0,0,0)
+  iters = fn_iterationStore(testName,popMatrix, 0, numRows,numCols)
+  infectionMatrix<-fn_resetInfections(0, cells, numRows)
+  for(step in 1:(iterations+1)){
+    # iterate over cells
+    for (rw in 1:(rows)){
+      for (col in 1:(cols)){
+        xy<-fn_checkPopulationCells(popMatrix[rw,col])
+        if(xy[1] ==FALSE){
+          #infectionMatrix[xy[1],xy[2]]<-1
+        } else {
+          #print(xy)
+          infectionMatrix[xy[1],xy[2]]<-1
+        }
+      } # end col
+    } # end row
+    
+    #infect humans!
+    popMatrix<-fn_infectPopulation(popMatrix, infectionMatrix)
+    fn_plotZombie(testName,popMatrix,step, numRows,  numCols)
+    iters2 = fn_iterationStore(testName,popMatrix, step, numRows,numCols)
+    iters<-rbind(iters,iters2)
+    #print(popMatrix)
+    # reset matrix after iteration
+    infectionMatrix<-fn_resetInfections(0, cells, rows)
+  }
+  #print(iters)
+  #return(popMatrix)
+  return(iters)
+}
+
+fn_plotZombie<-function(testName,population,step, numRows,  numCols){
+  #dev.off()
+  #print(as.vector(population))
+  
+  Is<-table(population)
+  numI<-Is[names(Is)=='I']
+  perI<-(numI/(numRows*numCols))*100
+  
+  gs <- lapply(as.vector(population), function(zhi){
+      if(zhi=="H"){
+        colr ="green"
+      } else if(zhi=="Z") {
+        colr="red"
+      } else{
+        colr="blue"
+      }
+      grobTree(rectGrob(gp=gpar(fill=colr, alpha=0.5)), textGrob(zhi, gp=gpar(fontsize=12,font=8)  ))
+    
+    }
+  )
+  #grid.arrange(grobs=gs, ncol=numCols, 
+  #             top="top label", bottom="bottom\nlabel", 
+  #             left="left label", right="right label")
+  #top=textGrob("Title", gp=gpar(fontsize=15,font=8)
+  title =paste(testName,"- ","Percentage Immune ",perI,"% - Step=", step,sep="")
+  
+  folder<-"/Users/jason/Source/RCode/zombie/media/"
+  pad<-sprintf("%02d", step)
+  path<-paste(folder,testName,"-",pad,".png", sep="")
+  png(filename=path)
+  grid.arrange(grobs=gs, ncol=numCols, 
+              top=textGrob(title, gp=gpar(fontsize=15,font=8)  ))
+  
+  
+  
+  dev.off()
+  
+  
+}
+
+fn_randomXY<-function(){
+  
+  randomRow <- sample(1:rows, 1)
+  randomCol <- sample(1:cols, 1)
+  xy <- c(randomRow, randomCol)
+  #xy <- c(1, 2)
+  return(xy)
+}
+
+fn_checkPopulationCells<-function(x){
+  isZombie<-fn_isZombie(x)
+  if (isZombie =="Y"){
+    randomXY<-fn_randomXY()
+  } else{
+    randomXY<-c(FALSE, FALSE)
+  }
+  
+  return(randomXY)
+} 
+
+
+
+
+fn_isZombie<-function(x){
+  if(x==zombie){
+    return("Y") 
+  } else{
+    return ("N")
+  }
+}
+
+fn_isHuman<-function(x){
+  if(x==human){
+    return("Y") 
+  } else{
+    return ("N")
+  }
+}
+
+
+fn_infectPopulation<-function(popM, infM){
+  for (rw in 1:(rows)){
+    for (col in 1:(cols)){
+      isHuman <-fn_isHuman(popM[rw, col])
+      infection <-infM[rw, col]
+      if(isHuman == "Y" && infection ==1){
+        popM[rw, col] <-zombie # turn human into zombie
+      }
+    } # end col
+  } # end row
+  return(popM)
+}
+
+# Create zombies and immunue
+fn_zombies_and_immune<-function(popData, immuneStart, zombieStart ){
+  # add some random imumune
+  for (iStep in 1:(immuneStart)){
+    xy =fn_randomXY()
+    popData[xy[1],xy[2]] <-immune
+  }
+  # add some random zombies
+  for (zStep in 1:(zombieStart)){
+    xy =fn_randomXY()
+    popData[xy[1],xy[2]] <-zombie
+    
+  }
+  
+  return(popData)
+}
+
+
+# reset infectionMatrix
+fn_resetInfections<-function(resetInfection, numcells, numrows){
+  infMatrix<-matrix( rep( resetInfection, len=numcells), nrow = numrows)
+  return(infMatrix)
+}
+
+# get numbers over 1 iteration
+fn_iterationStore<-function(testName,popMatrix, step, numRows,numCols){
+  
+  popData=table(popMatrix)
+  #print(postpopData[names(postpopData)=='H'])
+  if (length(popData[names(popData)=='H'])>0){
+    numH<-popData[names(popData)=='H']
+  } else{
+    numH<-0
+  }
+  
+  if (length(popData[names(popData)=='Z'])>0){
+    numZ<-popData[names(popData)=='Z']
+  } else{
+    numZ<-0
+  }
+  
+  if (length(popData[names(popData)=='I'])>0){
+    numI<-popData[names(popData)=='I']
+  } else{
+    numI<-0
+  }
+  #row1<-data.frame(iterations,rows,cols,prepopData[names(prepopData)=='Z'],prepopData[names(prepopData)=='H'],prepopData[names(prepopData)=='I'],postpopData[names(postpopData)=='Z'],postpopData[names(postpopData)=='H'],postpopData[names(postpopData)=='I'])
+  
+  dfnamesR<-c( "test","step", "rows","cols","human","zombie","immune")
+  rowStep<-data.frame(testName,step, numRows,numCols, numH, numZ, numI)
+  names(rowStep)<-dfnamesR
+  return(rowStep)
+  
+}
+
+# Test function -is include OK
+fn_test<-function(x){
+  return ("hello")
+}