piegy 1.1.4__py3-none-any.whl → 1.1.6__py3-none-any.whl

piegy/__version__.py

@@ -18,5 +18,7 @@ version history:
 1.1.2: fix text bad location in figure_tools, update labeling and titling in figures and test_var. Add dpi param to make_video in videos. Remove reset_data function in model.
 1.1.3: update README.
 1.1.4: changed name: ``model`` module to ``simulation``, and ``model.simulation`` class to ``simulation.model``. Bug fix in videos.
+1.1.5: update README.
+1.1.6: change name of variables in model class -- for compatability with the new C core. 1.1.6 is the last verion of v1. From v2 on, the piegy package has C core.
 
 '''

piegy/analysis.py

@@ -183,7 +183,7 @@ def combine_sim(mod1, mod2):
 
     Returns:
 
-    - sim3:     a new model object whose U, V, U_pi, V_pi are weighted averages of mod1 and mod2
+    - sim3:     a new model object whose U, V, Upi, Vpi are weighted averages of mod1 and mod2
                 (weighted by sim_time). 
                 sim3.print_pct is set to mod1's, seed set to None, sim_time set to sum of mod1's and mod2's. All other params same as mod1
     '''
@@ -213,8 +213,8 @@ def combine_sim(mod1, mod2):
             for k in range(sim3.max_record):
                 sim3.U[i][j][k] = (mod1.U[i][j][k] * mod1.sim_time + mod2.U[i][j][k] * mod2.sim_time) / combined_sim_time
                 sim3.V[i][j][k] = (mod1.V[i][j][k] * mod1.sim_time + mod2.V[i][j][k] * mod2.sim_time) / combined_sim_time
-                sim3.U_pi[i][j][k] = (mod1.U_pi[i][j][k] * mod1.sim_time + mod2.U_pi[i][j][k] * mod2.sim_time) / combined_sim_time
-                sim3.V_pi[i][j][k] = (mod1.V_pi[i][j][k] * mod1.sim_time + mod2.V_pi[i][j][k] * mod2.sim_time) / combined_sim_time
+                sim3.Upi[i][j][k] = (mod1.Upi[i][j][k] * mod1.sim_time + mod2.Upi[i][j][k] * mod2.sim_time) / combined_sim_time
+                sim3.Vpi[i][j][k] = (mod1.Vpi[i][j][k] * mod1.sim_time + mod2.Vpi[i][j][k] * mod2.sim_time) / combined_sim_time
 
     return sim3
 

piegy/data_tools.py

@@ -64,9 +64,9 @@ def save_data(mod, dirs = '', print_msg = True):
     outputs.append(mod.compress_itv)
     outputs.append(mod.U.tolist())
     outputs.append(mod.V.tolist())
-    outputs.append(mod.U_pi.tolist())
-    outputs.append(mod.V_pi.tolist())
-    # H&V_pi_total are not saved, will be calculated when reading the data
+    outputs.append(mod.Upi.tolist())
+    outputs.append(mod.Vpi.tolist())
+    # H&Vpi_total are not saved, will be calculated when reading the data
     data.append(outputs)
     
     data_json = json.dumps(data)
@@ -119,7 +119,7 @@ def read_data(dirs):
     # outputs
     try:
         mod.set_data(data_empty = False, max_record = data[2][0], compress_itv = data[2][1], 
-                    U = data[2][2], V = data[2][3], U_pi = data[2][4], V_pi = data[2][5])
+                    U = data[2][2], V = data[2][3], Upi = data[2][4], Vpi = data[2][5])
     except:
         raise ValueError('Invalid model results saved in data')
     

piegy/figures.py

@@ -14,13 +14,13 @@ Plots for population:
 
 
 Plots for payoff:
-- pi_heatmap:       Used for 2D space, plot distribution of U_pi & V_pi within a specified time interval.
+- pi_heatmap:       Used for 2D space, plot distribution of Upi & Vpiwithin a specified time interval.
                     Average payoff over that interval is taken.
 - pi_bar:           Used for 1D space, counterpart of pi_heatmap.
-                    Plot average distribution of U_pi & V_pi in a specified time interval in a bar plot.
-- pi_dyna:         Plot change of total U_pi, V_pi overtime.
-- pi_hist:          Make a histogram of U_pi, V_pi in a specified time interval.
-- pi_std:           Plot change of standard deviation of U_pi, V_pi over time.
+                    Plot average distribution of Upi & Vpiin a specified time interval in a bar plot.
+- pi_dyna:         Plot change of total Upi, Vpiovertime.
+- pi_hist:          Make a histogram of Upi, Vpiin a specified time interval.
+- pi_std:           Plot change of standard deviation of Upi, Vpiover time.
 
 
 Popu-payoff correlation:
@@ -329,15 +329,15 @@ def pi_heatmap(mod, ax_U = None, ax_V = None, U_color = 'BuPu', V_color = 'YlGn'
     start_index = int(mod.max_record * start)
     end_index = int(mod.max_record * end)
     
-    U_pi_ave = figure_t.ave_interval(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
     U_title = figure_t.gen_title('Payoff ' + r'$p_U$', start, end)
-    U_text = figure_t.gen_text(np.mean(U_pi_ave), np.std(U_pi_ave))
+    U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
     V_title = figure_t.gen_title('Payoff ' + r'$p_V$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
-    ax_U = figure_t.heatmap(U_pi_ave, ax_U, U_color, annot, fmt, U_title, U_text)
+    ax_U = figure_t.heatmap(Upi_ave, ax_U, U_color, annot, fmt, U_title, U_text)
     ax_V = figure_t.heatmap(V_pi_ave, ax_V, V_color, annot, fmt, V_title, V_text)
 
     return ax_U, ax_V
@@ -357,15 +357,15 @@ def pi_bar(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowg
     start_index = int(mod.max_record * start)
     end_index = int(mod.max_record * end)
     
-    U_pi_ave = figure_t.ave_interval_1D(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval_1D(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval_1D(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval_1D(mod.Vpi, start_index, end_index)
     
     U_title = figure_t.gen_title(r'$p_U$', start, end)
-    U_text = figure_t.gen_text(np.mean(U_pi_ave), np.std(U_pi_ave))
+    U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
     V_title = figure_t.gen_title(r'$p_V$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
-    ax_U = figure_t.bar(U_pi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_U$', U_title, U_text)
+    ax_U = figure_t.bar(Upi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_U$', U_title, U_text)
     ax_V = figure_t.bar(V_pi_ave, ax_V, V_color, 'Patches', 'Payoff ' + r'$p_V$', V_title, V_text)
 
     return ax_U, ax_V
@@ -389,8 +389,8 @@ def pi_dyna(mod, ax = None, interval = 20, grid = True):
     interval_num = int(mod.max_record / interval)
     
     for i in range(interval_num):
-        U_ave = figure_t.ave_interval(mod.U_pi, i * interval, (i + 1) * interval)
-        V_ave = figure_t.ave_interval(mod.V_pi, i * interval, (i + 1) * interval)
+        U_ave = figure_t.ave_interval(mod.Upi, i * interval, (i + 1) * interval)
+        V_ave = figure_t.ave_interval(mod.Vpi, i * interval, (i + 1) * interval)
     
         U_curve.append(np.sum(U_ave))
         V_curve.append(np.sum(V_ave))
@@ -427,8 +427,8 @@ def pi_hist(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellow
     start_index = int(start * mod.max_record)
     end_index = int(end * mod.max_record)
 
-    U_pi_ave = figure_t.ave_interval_1D(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval_1D(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval_1D(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval_1D(mod.Vpi, start_index, end_index)
     
     #### plot ####
     
@@ -436,7 +436,7 @@ def pi_hist(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellow
         _, ax_U = plt.subplots()
     ax_U.set_xlabel('Payoff ' + r'$p_U$')
     ax_U.set_ylabel('Density')
-    ax_U.hist(U_pi_ave, color = U_color, density = True)
+    ax_U.hist(Upi_ave, color = U_color, density = True)
     ax_U.set_title(figure_t.gen_title('Payoff ' + r'$p_U$' + ' Hist', start, end))
     
     if ax_V == None:
@@ -463,23 +463,23 @@ def pi_std(mod, ax = None, interval = 20, grid = True):
     interval = figure_t.scale_interval(interval, mod.compress_itv)
     interval_num = int(mod.max_record / interval)
     
-    U_pi_std = []
+    Upi_std = []
     V_pi_std = []
     
     for i in range(interval_num):
-        U_pi_ave = figure_t.ave_interval(mod.U_pi, i * interval, (i + 1) * interval)
-        V_pi_ave = figure_t.ave_interval(mod.V_pi, i * interval, (i + 1) * interval)
+        Upi_ave = figure_t.ave_interval(mod.Upi, i * interval, (i + 1) * interval)
+        V_pi_ave = figure_t.ave_interval(mod.Vpi, i * interval, (i + 1) * interval)
         
-        U_pi_std.append(np.std(U_pi_ave))
+        Upi_std.append(np.std(Upi_ave))
         V_pi_std.append(np.std(V_pi_ave))
     
     #### plot ####
-    xaxis = np.linspace(0, mod.maxtime, len(U_pi_std))
+    xaxis = np.linspace(0, mod.maxtime, len(Upi_std))
     
     if ax == None:
         _, ax = plt.subplots()
     ax.grid(grid)
-    ax.plot(xaxis, U_pi_std, CURVE_TYPE, label = r'$p_U$' + ' std')
+    ax.plot(xaxis, Upi_std, CURVE_TYPE, label = r'$p_U$' + ' std')
     ax.plot(xaxis, V_pi_std, CURVE_TYPE, label = r'$p_V$' + ' std')
     ax.legend()
     ax.set_xlabel('Time')
@@ -506,11 +506,11 @@ def UV_pi(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowgr
     U_ave = figure_t.ave_interval_1D(mod.U, start_index, end_index)
     V_ave = figure_t.ave_interval_1D(mod.V, start_index, end_index)
 
-    U_pi_ave = figure_t.ave_interval(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
     
-    ax_U = figure_t.scatter(U_ave, U_pi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_U$', title = 'U - ' + r'$p_U$')
+    ax_U = figure_t.scatter(U_ave, Upi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_U$', title = 'U - ' + r'$p_U$')
     ax_V = figure_t.scatter(V_ave, V_pi_ave, ax_V, V_color, alpha, xlabel = 'V', ylabel = 'Payoff ' + r'$p_V$', title = 'V - ' + r'$p_V$')
     
     return ax_U, ax_V

piegy/simulation.py

@@ -35,7 +35,7 @@ from timeit import default_timer as timer
 # data type used by model.U and model.V
 UV_DTYPE = 'float64'
 
-# data type used by model.U_pi and V_pi
+# data type used by model.Upi and V_pi
 PI_DTYPE = 'float64'
 
 # data type for storing rates in single_test an single_init
@@ -63,7 +63,7 @@ class patch:
             Set pointers to neighbors of this patch object.
 
         update_pi:
-            Update U_pi, V_pi and payoff rates (payoff rates are the first two numbers in self.pi_death_rates).
+            Update Upi, V_pi and payoff rates (payoff rates are the first two numbers in self.pi_death_rates).
         
         update_k:
             Update natural death rates (the last two numbers in self.pi_death_rates).
@@ -82,8 +82,8 @@ class patch:
 
         self.U = U                          # int, U population. Initialized upon creating object.
         self.V = V                          # int, V population
-        self.U_pi = 0                       # float, payoff
-        self.V_pi = 0
+        self.Upi = 0                       # float, payoff
+        self.Vpi = 0
 
         self.matrix = matrix                # np.array or list, len = 4, payoff matrix
         self.mu1 = patch_var[0]             # float, how much proportion of the population migrates (U) each time
@@ -105,7 +105,7 @@ class patch:
     def __str__(self):
         self_str = ''
         self_str += 'U, V = ' + str(self.U) + ', ' + str(self.V) + '\n'
-        self_str += 'pi = ' + str(self.U_pi) + ', ' + str(self.V_pi) + '\n'
+        self_str += 'pi = ' + str(self.Upi) + ', ' + str(self.Vpi) + '\n'
         self_str += 'matrix = ' + str(self.matrix) + '\n'
         self_str += 'mu1, mu2 = ' + str(self.mu1) + ', ' + str(self.mu2) + '\n'
         self_str += 'w1, w2 = ' + str(self.w1) + ', ' + str(self.w2) + '\n'
@@ -138,23 +138,23 @@ class patch:
             
             if U != 0:
                 # no payoff if U == 0
-                self.U_pi = (U - 1) / sum_minus_1 * self.matrix[0] + V / sum_minus_1 * self.matrix[1]
+                self.Upi = (U - 1) / sum_minus_1 * self.matrix[0] + V / sum_minus_1 * self.matrix[1]
             else:
-                self.U_pi = 0
+                self.Upi = 0
                 
             if V != 0:
-                self.V_pi = U / sum_minus_1 * self.matrix[2] + (V - 1) / sum_minus_1 * self.matrix[3]
+                self.Vpi = U / sum_minus_1 * self.matrix[2] + (V - 1) / sum_minus_1 * self.matrix[3]
             else:
-                self.V_pi = 0
+                self.Vpi = 0
                 
         else:
             # no interaction, hence no payoff, if only 1 individual
-            self.U_pi = 0
-            self.V_pi = 0
+            self.Upi = 0
+            self.Vpi = 0
 
         # update payoff rates
-        self.pi_death_rates[0] = abs(U * self.U_pi)
-        self.pi_death_rates[1] = abs(V * self.V_pi)
+        self.pi_death_rates[0] = abs(U * self.Upi)
+        self.pi_death_rates[1] = abs(V * self.Vpi)
 
         # update natural death rates
         self.pi_death_rates[2] = self.kappa1 * U * (sum_minus_1 + 1)
@@ -173,8 +173,8 @@ class patch:
 
         for i in range(4):
             if self.nb[i] != None:
-                U_weight[i] = 1 + pow(math.e, self.w1 * self.nb[i].U_pi)
-                V_weight[i] = 1 + pow(math.e, self.w2 * self.nb[i].V_pi)
+                U_weight[i] = 1 + pow(math.e, self.w1 * self.nb[i].Upi)
+                V_weight[i] = 1 + pow(math.e, self.w2 * self.nb[i].Vpi)
 
         mu1_U = self.mu1 * self.U
         mu2_V = self.mu2 * self.V
@@ -232,7 +232,7 @@ class patch:
                 self.U -= 1
         # s = 2 for natural birth / death, due to payoff
         elif s == 2:
-            if self.U_pi > 0:
+            if self.Upi > 0:
                 self.U += 1   # natural growth due to payoff
             elif self.U > 0:
                 self.U -= 1   # natural death due to payoff
@@ -244,7 +244,7 @@ class patch:
             if self.V > 0:
                 self.V -= 1
         else:
-            if self.V_pi > 0:
+            if self.Vpi > 0:
                 self.V += 1
             elif self.V > 0:
                 self.V -= 1
@@ -268,7 +268,7 @@ class model:
             Return a deep copy of self. Can choose whether to copy data as well. Default is to copy.
 
         clear_data:
-            clear all data stored, set U, V, U_pi, V_pi to zero arrays
+            clear all data stored, set U, V, Upi, V_pi to zero arrays
 
         change_maxtime:
             Changes maxtime of self. Update data storage as well.
@@ -314,8 +314,8 @@ class model:
                                                     # Default is 1, not to take average.
         self.U = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)      # N x M x max_record np.array, float32, stores population of U in every patch over tiem
         self.V = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
-        self.U_pi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)   # similar to U, but for U's payoff and float 64
-        self.V_pi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
+        self.Upi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)   # similar to U, but for U's payoff and float 64
+        self.Vpi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
 
 
     def check_valid_input(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct):
@@ -449,7 +449,7 @@ class model:
 
         if copy_data:
             # copy data as well
-            sim2.set_data(self.data_empty, self.max_record, self.compress_itv, self.U, self.V, self.U_pi, self.V_pi)
+            sim2.set_data(self.data_empty, self.max_record, self.compress_itv, self.U, self.V, self.Upi, self.Vpi)
 
         return sim2
 
@@ -462,8 +462,8 @@ class model:
                     for t in range(self.max_record):
                         self.U[i][j][t] /= self.sim_time
                         self.V[i][j][t] /= self.sim_time
-                        self.U_pi[i][j][t] /= self.sim_time
-                        self.V_pi[i][j][t] /= self.sim_time
+                        self.Upi[i][j][t] /= self.sim_time
+                        self.Vpi[i][j][t] /= self.sim_time
 
 
     def change_maxtime(self, maxtime):
@@ -486,7 +486,7 @@ class model:
         self.init_storage()
 
 
-    def set_data(self, data_empty, max_record, compress_itv, U, V, U_pi, V_pi):
+    def set_data(self, data_empty, max_record, compress_itv, U, V, Upi, V_pi):
         # set data to the given data values
         # copies are made
         self.check_valid_data(data_empty, max_record, compress_itv)
@@ -496,8 +496,8 @@ class model:
         self.compress_itv = compress_itv
         self.U = np.copy(U)
         self.V = np.copy(V)
-        self.U_pi = np.copy(U_pi)
-        self.V_pi = np.copy(V_pi)
+        self.Upi = np.copy(Upi)
+        self.Vpi = np.copy(V_pi)
 
 
     def compress_data(self, compress_itv = 5):
@@ -515,7 +515,7 @@ class model:
 
         U_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
         V_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
-        U_pi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
+        Upi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
         V_pi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
 
         for i in range(self.N):
@@ -525,13 +525,13 @@ class model:
                     upper = lower + compress_itv
                     U_reduced[i][j][k] = np.mean(self.U[i, j, lower : upper])
                     V_reduced[i][j][k] = np.mean(self.V[i, j, lower : upper])
-                    U_pi_reduced[i][j][k] = np.mean(self.U_pi[i, j, lower : upper])
-                    V_pi_reduced[i][j][k] = np.mean(self.V_pi[i, j, lower : upper])
+                    Upi_reduced[i][j][k] = np.mean(self.Upi[i, j, lower : upper])
+                    V_pi_reduced[i][j][k] = np.mean(self.Vpi[i, j, lower : upper])
         
         self.U = U_reduced
         self.V = V_reduced
-        self.U_pi = U_pi_reduced
-        self.V_pi = V_pi_reduced
+        self.Upi = Upi_reduced
+        self.Vpi = V_pi_reduced
 
 
 
@@ -895,8 +895,8 @@ def single_init(mod, rng):
                 for k in range(record_index):
                     mod.U[i][j][k] += world[i][j].U
                     mod.V[i][j][k] += world[i][j].V
-                    mod.U_pi[i][j][k] += world[i][j].U_pi
-                    mod.V_pi[i][j][k] += world[i][j].V_pi
+                    mod.Upi[i][j][k] += world[i][j].Upi
+                    mod.Vpi[i][j][k] += world[i][j].Vpi
                     # we simply add to that entry, and later divide by sim_time to get the average (division in run function)
     
     return time, world, nb_indices, patch_rates, sum_rates_by_row, sum_rates, signal
@@ -1037,8 +1037,8 @@ def single_test(mod, front_info, end_info, update_sum_frequency, rng):
                         for k in range(record_index, record_index + multi_records):
                             mod.U[i][j][k] += world[i][j].U
                             mod.V[i][j][k] += world[i][j].V
-                            mod.U_pi[i][j][k] += world[i][j].U_pi
-                            mod.V_pi[i][j][k] += world[i][j].V_pi
+                            mod.Upi[i][j][k] += world[i][j].Upi
+                            mod.Vpi[i][j][k] += world[i][j].Vpi
                 record_index += multi_records
         else:
             # if already exceeds maxtime
@@ -1047,8 +1047,8 @@ def single_test(mod, front_info, end_info, update_sum_frequency, rng):
                     for k in range(record_index, max_record):
                         mod.U[i][j][k] += world[i][j].U
                         mod.V[i][j][k] += world[i][j].V
-                        mod.U_pi[i][j][k] += world[i][j].U_pi
-                        mod.V_pi[i][j][k] += world[i][j].V_pi
+                        mod.Upi[i][j][k] += world[i][j].Upi
+                        mod.Vpi[i][j][k] += world[i][j].Vpi
 
     ### Large while loop ends ###
     

piegy/test_var.py

@@ -7,7 +7,7 @@ Test influence of one variable:
 - test_var1:    Test how a certain patch variable (mu, w, kappa) influences results.
                 Run simulations across different values of that variable and save data.
 - var_UV1:      Plot how U, V change across different values of a specified variable.
-- var_pi1:      Plot how U_pi, V_pi change across different values of a specified variable.
+- var_pi1:      Plot how Upi, V_pi change across different values of a specified variable.
                     
 
 Test influence of two variables:
@@ -15,7 +15,7 @@ Test influence of two variables:
                 Run simulations across different values of the two specified variables and save data.
 - var_UV2:      Plot how U, V change across the two variables.
                 x-axis is values of the variable 2, y-axis is U or V. Values of variable 1 are shown by multiple curves.
-- var_pi2:      Plot how U_pi & V_pi change across the two variables.
+- var_pi2:      Plot how Upi & V_pi change across the two variables.
 
 
 Additional tools (can be called directly):
@@ -305,7 +305,7 @@ def var_UV2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
 def var_pi1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end = 1.0, U_color = 'violet', V_color  = 'yellowgreen'):
     '''
     Plot function for test_var1. Plot influence of var on U, V's payoff.
-    Make U_pi, V_pi - var curves. y-axis is payoff, x-axis is values of var.
+    Make Upi, V_pi - var curves. y-axis is payoff, x-axis is values of var.
 
     Inputs:
     - var_dirs:   return value of test_var1. A 1D list of directories where all data are stored.
@@ -334,8 +334,8 @@ def var_pi1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end =
         end_index = int(simk.max_record * end)
         NM = int(simk.N * simk.M)
 
-        U_ave.append(np.sum(figure_t.ave_interval(simk.U_pi, start_index, end_index)) / NM)
-        V_ave.append(np.sum(figure_t.ave_interval(simk.V_pi, start_index, end_index)) / NM)
+        U_ave.append(np.sum(figure_t.ave_interval(simk.Upi, start_index, end_index)) / NM)
+        V_ave.append(np.sum(figure_t.ave_interval(simk.Vpi, start_index, end_index)) / NM)
 
         del simk
             
@@ -364,7 +364,7 @@ def var_pi1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end =
 def var_pi2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, var1_on_xaxis = True, start = 0.95, end = 1.0, U_color = 'viridis', V_color = 'viridis', rgb_alpha = 1):
     '''
     Plot function for test_var2. Plot how var1 and var2 influence payoff.
-    Make U_pi, V_pi - var2 curves. y-axis is payoff, x-axis is values of var2,
+    Make Upi, V_pi - var2 curves. y-axis is payoff, x-axis is values of var2,
     var1 is represented by different curves. One curve corresponds to one value of var1.
 
     Inputs:
@@ -398,8 +398,8 @@ def var_pi2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
             end_index = int(simk.max_record * end)
             NM = int(simk.N * simk.M)
 
-            U_ave[k1].append(np.sum(figure_t.ave_interval(simk.U_pi, start_index, end_index)) / NM)
-            V_ave[k1].append(np.sum(figure_t.ave_interval(simk.V_pi, start_index, end_index)) / NM)
+            U_ave[k1].append(np.sum(figure_t.ave_interval(simk.Upi, start_index, end_index)) / NM)
+            V_ave[k1].append(np.sum(figure_t.ave_interval(simk.Vpi, start_index, end_index)) / NM)
 
             del simk    # manually delete this large object
 

{piegy-1.1.4.dist-info → piegy-1.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: piegy
-Version: 1.1.4
+Version: 1.1.6
 Summary: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
 Author-email: Chenning Xu <cxu7@caltech.edu>
 License: BSD 3-Clause License
@@ -87,16 +87,16 @@ The *piegy* package also provides a wide range of analytic and supportive tools
 To get started, simply get our demo model and run simulation:
 
 ```python
-from piegy import model, figures
+from piegy import simulation, figures
 import matplotlib.pyplot as plt
 
-sim = model.demo_model()
-model.run(sim)
+mod = simulation.demo_model()
+simulation.run(mod)
 
 fig1, ax1 = plt.subplots()
-figures.UV_dyna(sim, ax1)
+figures.UV_dyna(mod, ax1)
 fig2, ax2 = plt.subplots(1, 2, figsize = (12.8, 4.8))
-U_hmap, V_hmap = figures.UV_heatmap(sim, ax2[0], ax2[1])
+U_hmap, V_hmap = figures.UV_heatmap(mod, ax2[0], ax2[1])
 ```
 
 The figures reveal population dynamics and steady state population distribution.

piegy-1.1.6.dist-info/RECORD

@@ -0,0 +1,16 @@
+piegy/__init__.py,sha256=plq8y9IE9ilaKtEFIblJ_QexipAvPBXoalXhXLbs71Q,3244
+piegy/__version__.py,sha256=Z8QjDLipX03j5ebaea7PhH2aJiiWo_JzOehTw_Gr8L0,1041
+piegy/analysis.py,sha256=2GBsBbi7LdstSEAM0-F2bfL2kHu3MElcrw8bxZ1x6LI,8719
+piegy/data_tools.py,sha256=9gCt5dPRQfMDm5HUJpzlLvCEGPtVgpa_vnCvxRfGTVM,3545
+piegy/figures.py,sha256=TP9AoNnKwGZxBNmJGbplpb_ewr9US3jziBzOh1arGeY,19014
+piegy/simulation.py,sha256=ezbXTm2Ri6aLM49FLD85NBGdf0eclgFyiCWvYJ-jjII,45130
+piegy/test_var.py,sha256=gMyonZbtLEAS5bH1QwcFnshpvwEsq7YWGb9My0PStts,23596
+piegy/videos.py,sha256=QfSpOdwfaDsrQYRoiHmZ6gowzRQHom3m8kx1P65_8sM,10218
+piegy/tools/__init__.py,sha256=eYOl_HJHDonYexfrmKh3koOlxvtSo46vH6jHvCEEB4k,300
+piegy/tools/figure_tools.py,sha256=54vJSJMReXidFnSPE_xFvedtgnJU3d55zQDPNBLGs98,6975
+piegy/tools/file_tools.py,sha256=ncxFWeHfIE-GYLQlOrahFlhBgqPyuY3R5_93fpQeCEs,630
+piegy-1.1.6.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
+piegy-1.1.6.dist-info/METADATA,sha256=TSeyMPsCS6VXvZy9BiLw09bjZT1T6tXwkW0wC70BHGo,5306
+piegy-1.1.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+piegy-1.1.6.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
+piegy-1.1.6.dist-info/RECORD,,

piegy-1.1.4.dist-info/RECORD

@@ -1,16 +0,0 @@
-piegy/__init__.py,sha256=plq8y9IE9ilaKtEFIblJ_QexipAvPBXoalXhXLbs71Q,3244
-piegy/__version__.py,sha256=p8vZzyuX_tcu2qlBukCqdCu3SozzbpVqCUOaVaEe8rE,856
-piegy/analysis.py,sha256=5X6cpEAgFlHiRoaVmqYALlUvkep_LmrqpJHLCtQrd9Q,8727
-piegy/data_tools.py,sha256=Rw1fzeCGbxAB8MqTxZNZnOkVn7FmoUGoRz21scTAvF0,3550
-piegy/figures.py,sha256=bMHS7gTYtWdixUMW_wokBD6NSj_WOjQtnWp0R8VXChw,19059
-piegy/simulation.py,sha256=ngyLGzXAePYlyrcRznxWA7FEvGl9Gad976Sh1gHT0hU,45178
-piegy/test_var.py,sha256=g6BS_G_sewLn-8urUdTnlaVd8LYt_5GDvQQr_4bmNDU,23604
-piegy/videos.py,sha256=QfSpOdwfaDsrQYRoiHmZ6gowzRQHom3m8kx1P65_8sM,10218
-piegy/tools/__init__.py,sha256=eYOl_HJHDonYexfrmKh3koOlxvtSo46vH6jHvCEEB4k,300
-piegy/tools/figure_tools.py,sha256=54vJSJMReXidFnSPE_xFvedtgnJU3d55zQDPNBLGs98,6975
-piegy/tools/file_tools.py,sha256=ncxFWeHfIE-GYLQlOrahFlhBgqPyuY3R5_93fpQeCEs,630
-piegy-1.1.4.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
-piegy-1.1.4.dist-info/METADATA,sha256=R3zSrrCR85dtpvtQBmfMTikrnuqSPSJveHjOtIcUr-E,5291
-piegy-1.1.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-piegy-1.1.4.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
-piegy-1.1.4.dist-info/RECORD,,