get rid of "~/Desktop" in recipe file paths

Author: bhaller

QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file I.txt

@@ -11,5 +11,5 @@ initialize() {
 	sim.addSubpop("p1", 1000);
 }
 20000 late() {
-	p1.outputMSSample(2000, replace=F, filePath="~/Desktop/ms.txt");
+	p1.outputMSSample(2000, replace=F, filePath="ms.txt");
 }

QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt

@@ -11,7 +11,7 @@ initialize() {
 	sim.addSubpop("p1", 1000);
 
 	// READ MS FORMAT INITIAL STATE
-	lines = readFile("~/Desktop/ms.txt");
+	lines = readFile("ms.txt");
 	index = 0;
 
 	// skip lines until reaching the // line, then skip that line

QtSLiM/recipes/Recipe 15.10 - A simple biogeographic landscape model.txt

@@ -22,7 +22,7 @@ initialize() {
 	p1.setSpatialBounds(c(0.0, 0.0, 539.0, 216.0));
 
 	// this file is in the recipe archive at http://benhaller.com/slim/SLiM_Recipes.zip
-	mapImage = Image("~/Desktop/world_map_540x217.png");
+	mapImage = Image("world_map_540x217.png");
 	p1.defineSpatialMap("world", "xy", 1.0 - mapImage.floatK,
 		valueRange=c(0.0, 1.0), colors=c("#0000CC", "#55FF22"));
 

QtSLiM/recipes/Recipe 16.12 - Forcing a specific pedigree in a nonWF model I.txt

@@ -12,8 +12,8 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 
 	// delete any existing pedigree log files
-	deleteFile("~/Desktop/mating.txt");
-	deleteFile("~/Desktop/death.txt");
+	deleteFile("mating.txt");
+	deleteFile("death.txt");
 }
 reproduction() {
 	// choose a mate and generate an offspring
@@ -24,7 +24,7 @@ reproduction() {
 
 	// log the mating
 	line = paste(community.tick, individual.tag, mate.tag, child.tag);
-	writeFile("~/Desktop/mating.txt", line, append=T);
+	writeFile("mating.txt", line, append=T);
 }
 1 early() {
 	sim.addSubpop("p1", 10);
@@ -41,7 +41,7 @@ survival() {
 	if (!surviving) {
 		// log the death
 		line = community.tick + " " + individual.tag;
-		writeFile("~/Desktop/death.txt", line, append=T);
+		writeFile("death.txt", line, append=T);
 	}
 	return NULL;
 }

QtSLiM/recipes/Recipe 16.12 - Forcing a specific pedigree in a nonWF model II.txt

@@ -21,8 +21,8 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 
 	// read in the pedigree log files
-	defineConstant("M", readIntTable("~/Desktop/mating.txt"));
-	defineConstant("D", readIntTable("~/Desktop/death.txt"));
+	defineConstant("M", readIntTable("mating.txt"));
+	defineConstant("D", readIntTable("death.txt"));
 
 	// extract the ticks for quick lookup
 	defineConstant("Mt", drop(M[,0]));

QtSLiM/recipes/Recipe 16.19 - Range expansion in a stepping-stone model I.txt

@@ -33,7 +33,7 @@ reproduction() {
 }
 1 late() {
 	// set up a log file
-	log = community.createLogFile("~/Desktop/sim_log.txt", sep="\t", logInterval=10);
+	log = community.createLogFile("sim_log.txt", sep="\t", logInterval=10);
 	log.addCycle();
 	log.addPopulationSize();
 	log.addMeanSDColumns("size", "sim.subpopulations.individualCount;");

QtSLiM/recipes/Recipe 16.19 - Range expansion in a stepping-stone model II.txt

@@ -33,7 +33,7 @@ reproduction() {
 }
 1 late() {
 	// set up a log file
-	log = community.createLogFile("~/Desktop/sim_log.txt", sep="\t", logInterval=10);
+	log = community.createLogFile("sim_log.txt", sep="\t", logInterval=10);
 	log.addCycle();
 	log.addPopulationSize();
 	log.addMeanSDColumns("size", "sim.subpopulations.individualCount;");

QtSLiM/recipes/Recipe 16.20 - Logistic population growth with the Beverton-Holt model.txt

@@ -18,7 +18,7 @@ initialize() {
 	sim.addSubpop("p2", 50);   // Beverton-Holt influencing fecundity
 	sim.addSubpop("p3", 50);   // Beverton-Holt influencing survival
 
-	log = community.createLogFile("~/Desktop/sim_log.txt", logInterval=1);
+	log = community.createLogFile("sim_log.txt", logInterval=1);
 	log.addCycle();
 	log.addSubpopulationSize(p1);
 	log.addSubpopulationSize(p2);

QtSLiM/recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt

@@ -12,7 +12,7 @@ initialize() {
 	sim.addSubpop("p2", 1000);
 	p1.setMigrationRates(p2, 0.001);
 	p2.setMigrationRates(p1, 0.001);
-	log = community.createLogFile("~/Desktop/sim_log.txt", logInterval=10);
+	log = community.createLogFile("sim_log.txt", logInterval=10);
 	log.addCycle();
 	log.addCustomColumn("FST", "calcFST(p1.genomes, p2.genomes);");
 }

QtSLiM/recipes/Recipe 5.3.5 - Migration and admixture, Reading a migration matrix from a file.txt

@@ -13,7 +13,7 @@ initialize() {
 	subpops = sim.subpopulations;
 
 	// this file is in the recipe archive at http://benhaller.com/slim/SLiM_Recipes.zip
-	lines = readFile("~/Desktop/migration.csv");
+	lines = readFile("migration.csv");
 	lines = lines[substr(lines, 0, 1) != "//"];
 
 	for (line in lines)