Adds script to extract code from episodes and extracted code

code/01-intro.m

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+
+
+
+
+% ## Introduction to the MATLAB GUI
+% ## Working with variables
+  x = 55
+  y = 10
+  x + y
+  x - y
+  z = x * y
+  y = y/5
+  z = z - y^3 + 5*x
+% ### Logical operations
+  mass = 20
+  age = 2.5
+  frac = mass/age
+  c1 = frac < 10
+  c2 = frac > 10
+
+% ## Data types
+% !! Solution:
+  weight = 64.5
+  size3 = 'L'
+  patient_name = "Jane Doe"
+  alive_on_day_3 = true
+
+
+  c3 = frac == mass/age
+  c4 = frac < 10 && age > 5
+  c5 = frac < 10 || age > 5
+
+% ! Challenge:
+% ## Negating conditions and including the limits
+% !! Solution:
+
+
+% ### Arrays
+  A = [1, 2, 3]
+  B = [1, 2; 3, 4; 5, 6]
+  Names = ["John", "Abigail", "Bertrand", "Lucile"]
+  C = [true; false; false; true]
+  B > 3
+
+% ## Suppressing the output
+  x = 33;
+
+
+% ## Printing a variable's value
+  patient_name
+  disp(patient_name)
+
+
+% ## Keeping things tidy
+  clear alive_on_day_3
+  clc
+
+
+

code/02-arrays.m

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+
+
+
+
+% ## Initializing an Array
+  Z = zeros(3,5)
+  Z = zeros(3)
+  Z = zeros(1x5)
+  R = rand(8);
+  O = ones(10,10);
+
+
+  Fives = ones(3,6)*5;
+  M = magic(4)
+% ## Array indexing
+  M = magic(8)
+  M(5, 6)
+
+
+  M([4,5,6],[5,6,7])
+
+% ## The `:` operator
+  1:6
+  1:3:15
+
+  M(4:6, 5:7)
+
+% ! Challenge:
+% ## Checkerboard
+% !! Solution:
+  M(1:3:8, 2:2:8)
+
+
+% ### Selecting whole rows or columns
+  M(5, 1:8)
+
+% ## The key-word `end`
+  M(2,end)
+  M(5:end,3)
+
+  M(5, 1:end)
+
+% ## Using `:` as an index
+  M(5, :)
+
+  M(1:4, :)
+  M(:, 6:end)
+
+% ! Challenge:
+% ## Master indexing
+% !! Solution:
+  M(2:3:end, :)
+
+
+
+% ! Challenge:
+% ## Slicing character arrays
+  element = 'oxygen';
+  disp(['first three characters: ', element(1:3)])
+  disp(['last three characters: ', element(4:6)])
+% !! Solution:
+
+
+
+

code/03-loading_data.m

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+
+
+
+
+% ## Loading data to an array
+
+% ## Tip: Good Enough Practices for Scientific Computing
+
+  patient_data = readmatrix('data/base/inflammation-01.csv');
+  size(patient_data)
+  class(patient_data)
+% ## Initial exploration
+% #### **One patient at a time**
+  patient_5 = patient_data(5,:)
+  mean_p5=mean(patient_5)
+  max_p5 = max(patient_5)
+  min_p5 = min(patient_5)
+  std_p5 = std(patient_5)
+
+% ! Challenge:
+% ## All data points at once
+% !! Solution:
+  global_mean = mean(patient_data(:))
+  global_max = max(patient_data(:))
+  global_min = min(patient_data(:))
+  global_std = std(patient_data(:))
+
+
+  mean_p5 > global_mean
+  max_p5 == global_max
+  min_p5 == global_min
+  std_p5 < global_std
+
+% ! Challenge:
+% ## Food for thought
+
+% #### **One day at a time**
+  day_9 = patient_data(:,9);
+  mean_d9 = mean(day_9)
+  max_d9 = max(day_9)
+  min_d9 = min(day_9)
+  std_d9 = std(day_9)
+  mean_d9 > global_mean
+  max_d9 == global_max
+  min_d9 == global_min
+  std_d9 < global_std
+
+% ! Challenge:
+% ## Food for thought
+
+% #### **Whole array analysis**
+  x=mean(patient_data);
+  per_day_mean = mean(patient_data);
+  per_day_max = max(patient_data);
+  per_day_min = min(patient_data);
+  per_day_std = std(patient_data);
+  per_day_mean > global_mean
+  find(ans)
+  help mean
+  per_patient_mean = mean(patient_data,2);
+  per_patient_max = max(patient_data,[],2);
+  per_patient_min = min(patient_data,[],2);
+  per_patient_std = std(patient_data,[],2);
+
+% ! Challenge:
+% ## Most inflamed patients
+% !! Solution:
+  find(per_patient_max == global_max)
+
+
+
+

code/04-plotting.m

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+
+
+
+
+% ## Plotting
+  plot(1:40,per_day_mean)
+
+
+
+
+  title('Daily average inflammation')
+  xlabel('Day of trial')
+  ylabel('Inflammation')
+  plot(per_day_max)
+  title('Maximum inflammation per day')
+  ylabel('Inflammation')
+  xlabel('Day of trial')
+  plot(per_day_min)
+  title('Minimum inflammation per day')
+  ylabel('Inflammation')
+  xlabel('Day of trial')
+% ## Multiple lines in a plot
+  plot(per_day_mean,DisplayName="Mean")
+  legend
+  title('Daily average inflammation')
+  xlabel('Day of trial')
+  ylabel('Inflammation')
+  hold on
+  plot(patient_5,DisplayName="Patient 5")
+  hold off
+
+% ! Challenge:
+% ## Patients 3 & 4
+% !! Solution:
+  plot(per_day_mean,DisplayName="Mean")
+  legend
+  title('Daily average inflammation')
+  xlabel('Day of trial')
+  ylabel('Inflammation')
+  hold on
+  plot(patient_data(3,:),DisplayName="Patient 3")
+  plot(patient_data(4,:),DisplayName="Patient 4")
+  hold off
+
+
+% ## Multiple plots in a figure
+  tiledlayout(1, 2)
+  nexttile
+  plot(per_day_max)
+  title('Max')
+  xlabel('Day of trial')
+  ylabel('Inflamation')
+  nexttile
+  plot(per_day_min)
+  title('Min')
+  xlabel('Day of trial')
+  ylabel('Inflamation')
+  tlo=tiledlayout(1, 2)
+  title(tlo,'Per day data')
+  xlabel(tlo,'Day of trial')
+  ylabel(tlo,'Inflamation')
+  nexttile
+  plot(per_day_max)
+  title('Max')
+  nexttile
+  plot(per_day_min)
+  title('Min')
+
+% ## Clearing a figure
+
+% ## Heatmaps
+  heatmap(patient_data)
+  title('Inflammation')
+  xlabel('Day of trial')
+  ylabel('Patient number')
+  imagesc(patient_data)
+  title('Inflammation')
+  xlabel('Day of trial')
+  ylabel('Patient number')
+
+