visual inspection of data

REPRODUCEME.md

@@ -69,7 +69,9 @@ From here, you can continue to inspect the generated data or generate the plots
 
 ## 2. Inspection of provided data
 
-All produced data is in the folder _/data/_. For a detailed description of the data structure and contents see the file _/data/R_outputs/codebook.md_ (for outputs from R) and _/data/matlab_outputs/codebook.md_ (for outputs from matlab)
+All produced data is in the folder _/data/_. For a detailed description of the data structure and contents see the file _/data/R_outputs/codebook.md_ (for outputs from R) and _/data/matlab_outputs/codebook.md_ (for outputs from matlab).
+
+R outputs can be visualized using the scripts in _code/visualize_data.R_.
 
 ## 3. Reproduction of figures
 

code/visualize_data.R

@@ -0,0 +1,73 @@
+## Visualize Data ##
+
+#### Load packages ####
+require(paleoTS)
+
+#### Load R outputs ####
+load("data/R_outputs/results_modes_of_evolution.Rdata")
+load("data/R_outputs/ageDepthModelsScenariosAandB.Rdata")
+load("data/R_outputs/parameters_for_tests.Rdata")
+
+#### Age-Depth Models ####
+scenario = "A"
+dist = "1 km"
+
+stopifnot(scenario %in% scenarioNames)
+stopifnot( dist %in% all_dist )
+plot(x = ageDepthModels[[scenario]][[dist]]$time,
+     y = ageDepthModels[[scenario]][[dist]]$height,
+     xlab = "Time [Myr]",
+     ylab = "Height [m]",
+     main = paste0("Age-Depth Model, ", dist, " from shore, scenario ", scenario, sep = ""),
+     type = "l")
+
+#### Simulated lineages sampled in strat. domain ####
+scenario = "A"
+dist = "2 km"
+evo_mode = "Brownian motion"
+run_no = 10
+
+stopifnot(scenario %in% scenarioNames)
+stopifnot(dist %in% examinedBasinPositions)
+stopifnot(evo_mode %in% simulatedEvoModes)
+stopifnot(run_no <= noOfTests)
+
+## plot strat expression of trait evolution
+plot(x = testResultsStrat[[scenario]][[dist]][[evo_mode]][[run_no]]$inputData$height,
+     y = testResultsStrat[[scenario]][[dist]][[evo_mode]][[run_no]]$inputData$traitValue,
+     type = "l",
+     xlab = "Height [m]",
+     ylab = "Trait Value",
+     main = paste(evo_mode, "scenario", scenario, dist, "offshore ; run no. ", run_no))
+
+## plot time expression of trait evolution
+plot(x = testResultsStrat[[scenario]][[dist]][[evo_mode]][[run_no]]$inputData$time,
+     y = testResultsStrat[[scenario]][[dist]][[evo_mode]][[run_no]]$inputData$traitValue,
+     type = "l",
+     xlab = "Time [Myr]",
+     ylab = "Trait Value",
+     main = paste(evo_mode, "scenario", scenario, dist, "offshore ; run no. ", run_no))
+
+## plot paleoTS object derived from trait evolution in the section
+plot(testResultsStrat[[scenario]][[dist]][[evo_mode]][[run_no]]$paleots)
+
+#### Simulated lineages sampled only in the time domain ####
+scenario = "A"
+no_of_loc = "100"
+evo_mode = "Brownian motion"
+run_no = 100
+
+stopifnot(scenario %in% scenarioNames)
+stopifnot(dist %in% noOfSamplingLoc)
+stopifnot(evo_mode %in% simulatedEvoModes)
+stopifnot(run_no <= noOfTests)
+
+## Trait simulations
+plot(x = testResultsTime[[scenario]][[no_of_loc]][[evo_mode]][[run_no]]$inputData$time,
+     y = testResultsTime[[scenario]][[no_of_loc]][[evo_mode]][[run_no]]$inputData$traitValue,
+     xlab = "Time [Myr]",
+     ylab = "Trait Value",
+     main = paste0(evo_mode, "scenario", scenario, no_of_loc, "sampling locations, run no. ", run_no),
+     type = "l")
+## paleoTS objects
+plot(testResultsTime[[scenario]][[no_of_loc]][[evo_mode]][[run_no]]$paleots)