proceed implementing new parallel fct where several optimizsations ar…

…e conducted by one background process

Tests/IDA/temp.R

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+df <- read.csv("forKonrad-conc-vs-signal.csv",
+  sep = ";",
+  dec = ".",
+  header = TRUE
+)
+
+res <- tsf::opti(
+  case = "ida",
+  lowerBounds = c(
+    kG = 1000,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  ),
+  upperBounds = c(
+    kG = 10^8,
+    I0 = 100, # started at 10^7 but it ended always at 0...
+    IHD = 10^7,
+    ID = 10^7
+  ),
+  df,
+  additionalParameters = c(
+    host = 1e-6,
+    dye = 1e-6,
+    kHD = 3e6
+  ),
+  npop = 40,
+  ngen = 20,
+  Topology = "random",
+  errorThreshold = 0.7
+)
+
+res
+stop()
+
+tsf::sensitivity("ida", res[[2]], df, c(1e-6, 1e-6, 3e6), 20)
+
+stop()
+res <- tsf:::batch(
+  case = "ida",
+  lowerBounds = c(
+    kG = 1000,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  ),
+  upperBounds = c(
+    kG = 10^8,
+    I0 = 100, # started at 10^7 but it ended always at 0...
+    IHD = 10^7,
+    ID = 10^7
+  ),
+  "/home/konrad/Documents/GitHub/RProjects/Thermosimfit/Tests/IDA/idaBatch.csv",
+  additionalParameters = c(
+    host = 1.00E-06,
+    dye = 1.00E-06,
+    kHD = 3.00E+06
+  ),
+  npop = 40,
+  ngen = 20,
+  Topology = "random",
+  errorThreshold = 0.7,
+  num_rep = 2
+)
+
+plotStates <- function(list, num_rep = 1) {
+  list <- list[[1]]
+  num_data_sets <- length(list) / num_rep
+  repetitions <- (seq_len(length(list)) - 1) %% num_rep + 1
+  data_sets <- rep(1:num_data_sets, each = num_rep)
+  for (i in seq_along(list)) {
+    list[[i]]$dataset <- data_sets[i]
+    list[[i]]$repetition <- repetitions[i]
+  }
+  df <- Reduce(rbind, list)
+  # dye and host dye plot
+  data <- data.frame(
+    x = rep(df[, 1], 2),
+    y = c(df[, 4], df[, 5]),
+    names = c(
+      rep(names(df)[4], nrow(df)),
+      rep(names(df)[5], nrow(df))
+    ),
+    repetition = rep(df$repetition, 2),
+    dataset = rep(df$dataset, 2)
+  )
+  base_size <- 10
+  if (num_rep > 1) {
+    p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          x = interaction(dataset, x), y = y,
+          fill = factor(dataset),
+          group = interaction(dataset, x)
+        ),
+        width = 0.25,
+        size = 0.25
+      ) +
+      facet_wrap(. ~ names,
+        strip.position = "left",
+        scales = "free_y"
+      ) +
+      xlab(names(df)[1]) +
+      ylab(NULL) +
+      guides(fill = guide_legend(title = "Datasets")) +
+      scale_x_discrete(
+        labels = as.character(unique(rbind(data$x, "")))
+      )
+  } else {
+    p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          x = x,
+          y = y,
+          group = factor(x)
+        )
+      ) +
+      facet_wrap(~names,
+        strip.position = "left",
+        scales = "free_y"
+      ) +
+      ylab(NULL) +
+      xlab(names(df)[1])
+  }
+  p <- p + theme(
+    legend.position = "bottom",
+    axis.title = element_text(size = base_size * 1.2),
+    axis.text = element_text(size = base_size),
+    legend.text = element_text(size = base_size),
+    legend.title = element_text(size = base_size),
+    strip.text.x = element_text(size = base_size),
+    axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
+  )
+  # signal plot
+  data_signal_measured <- data.frame(
+    x = c(df[, 1], df[, 1]),
+    y = c(df[, 2], df[, 3]),
+    names = c(
+      rep(names(df)[2], nrow(df)),
+      rep(names(df)[3], nrow(df))
+    ),
+    repetition = rep(df$repetition, 2),
+    dataset = rep(df$dataset, 2)
+  )
+  p_signal <- ggplot(
+    data = data_signal_measured,
+    aes(
+      x = factor(x),
+      y = y,
+      colour = factor(dataset),
+      group = interaction(x, dataset, repetition)
+    )
+  ) +
+    geom_point(
+      data = subset(data_signal_measured, names != "Signal measured"),
+      aes(shape = factor(repetition))
+    ) +
+    geom_line(
+      data = subset(data_signal_measured, names == "Signal measured"),
+      aes(x = factor(x), y = y, group = 1)
+    ) +
+    xlab(names(df)[1]) +
+    ylab(NULL) +
+    theme(
+      legend.position = "bottom",
+      axis.title = element_text(size = base_size * 1.2),
+      axis.text = element_text(size = base_size),
+      legend.text = element_text(size = base_size),
+      legend.title = element_text(size = base_size),
+      strip.text.x = element_text(size = base_size),
+      axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
+    ) +
+    guides(
+      shape = guide_legend(title = "Repetitions"),
+      colour = guide_legend(title = "Datasets"),
+      linetype = guide_legend(title = "Repetitions")
+    ) +
+    facet_wrap(~names, strip.position = "left", scales = "free_y")
+
+  return(p_signal / p)
+}
+
+library(ggplot2)
+plotStates(res[[1]], 2)
+