From 633425e73e86401fff96b67aacf96470d9b96e61 Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:20:47 -0400 Subject: [PATCH 01/13] Initial commit --- README.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..c9b75db --- /dev/null +++ b/README.md @@ -0,0 +1,2 @@ +# RP4-ABM-Hamster +RP4 Code for Agent Based Hamster Model From 3a00e3052c1118e07554b201037011e3c7a07292 Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:21:52 -0400 Subject: [PATCH 02/13] Add files via upload --- Netlogo analysis.py | 98 + RP4 Hamster Model final.html | 80653 ++++++++++++++++++++++++++++++++ RP4 Hamster Model final.nlogo | 702 + 3 files changed, 81453 insertions(+) create mode 100644 Netlogo analysis.py create mode 100644 RP4 Hamster Model final.html create mode 100644 RP4 Hamster Model final.nlogo diff --git a/Netlogo analysis.py b/Netlogo analysis.py new file mode 100644 index 0000000..6f2673d --- /dev/null +++ b/Netlogo analysis.py @@ -0,0 +1,98 @@ +# RP4 - Agent Based Model Analysis +# Ben Mazin +# 03/26/2024 +# School of Interdisciplinary Science, McMaster University + +# This script reads in the csv files from the Netlogo model and analyzes the data to determine if the chemo treatment is effective +# It then saves the results to a csv file + +import pandas as pd +from scipy import stats + +# Set the number of trials and initial hamsters +number_of_trials = 20000 +initial_hamsters = 100 + +# Create an empty DataFrame with 4 columns +all_data = [] + +# Function to read CSV with inconsistent rows +def read_inconsistent_csv(file_path, delimiter=','): + with open(file_path, 'r') as file: + lines = file.readlines() + + # Determine the maximum number of columns by checking all rows + max_columns = max(len(line.split(delimiter)) for line in lines) + + # Split each line into columns and pad with None if they are too short + data = [line.strip().split(delimiter) + [None] * (max_columns - len(line.split(delimiter))) for line in lines] + + # Convert the list of lists into a DataFrame + df = pd.DataFrame(data, columns=range(max_columns)) # Set index to match column numbers + return df + +# Run for number_of_trials +for i in range(1, number_of_trials + 1): + + # Read in the csv file + file_path = f'/Users/benmazin/Movies/netlogo output/world{i}.csv' + data = read_inconsistent_csv(file_path, delimiter=',') + + # Get the value of ChemoWork + chemowork = data.iat[6, 5] + if chemowork != '"true"' and chemowork != '"false"': + chemowork = data.iat[6, 3] + + # Clean up the data + data = data.iloc[18:] + data = data.reset_index(drop=True) + + # Get the total dead and max percent infected + total_dead = initial_hamsters - int(data.iloc[-1, 9].replace('"', '')) + max_percent_infect = int(data.iloc[2:, 1].str.replace('"', '').astype(int).max()) + + # Append the data to the proper list + if chemowork == '"true"': + all_data.append({ + 'Trial': i, + 'ChemoTotalDead': total_dead, + 'ChemoPercentInfect': max_percent_infect, + 'NoChemoTotalDead': None, + 'NoChemoPercentInfect': None + }) + + elif chemowork == '"false"': + all_data.append({ + 'Trial': i, + 'ChemoTotalDead': None, + 'ChemoPercentInfect': None, + 'NoChemoTotalDead': total_dead, + 'NoChemoPercentInfect': max_percent_infect + }) + + else: + print("Error: ChemoWork is not true or false") + print(i) + +#save dataframe to csv +results = pd.DataFrame(all_data) + +# get the mean for each data column +chemo_total_dead_mean = results['ChemoTotalDead'].mean() +chemo_percent_infect_mean = results['ChemoPercentInfect'].mean() +no_chemo_total_dead_mean = results['NoChemoTotalDead'].mean() +no_chemo_percent_infect_mean = results['NoChemoPercentInfect'].mean() + +# run a t-test to determine if the means are significantly different for total dead and percent infect +totalDeadTtest = stats.ttest_ind(results['ChemoTotalDead'], results['NoChemoTotalDead'] , nan_policy='omit') +percentInfectTtest = stats.ttest_ind(results['ChemoPercentInfect'], results['NoChemoPercentInfect'], nan_policy='omit') + +# create a new dataframe with the means and t-test results +resultSum = pd.DataFrame({ + 'Category': ['ChemoTotalDeadMean', 'ChemoPercentInfectMean', 'NoChemoTotalDeadMean', 'NoChemoPercentInfectMean', 'TotalDeadTtest', 'PercentInfectTtest'], + 'Value': [chemo_total_dead_mean, chemo_percent_infect_mean, no_chemo_total_dead_mean, no_chemo_percent_infect_mean, totalDeadTtest, percentInfectTtest] +}) + +# save the summary and results to csv +resultSum.to_csv('/Users/benmazin/Movies/netlogo results/summary.csv', index=False) +results.to_csv('/Users/benmazin/Movies/netlogo results/results.csv', index=False) \ No newline at end of file diff --git a/RP4 Hamster Model final.html b/RP4 Hamster Model final.html new file mode 100644 index 0000000..3b140bf --- /dev/null +++ b/RP4 Hamster Model final.html @@ -0,0 +1,80653 @@ + + + + + + + + + + + + + + + + +
+
+ + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/RP4 Hamster Model final.nlogo b/RP4 Hamster Model final.nlogo new file mode 100644 index 0000000..a1e09bb --- /dev/null +++ b/RP4 Hamster Model final.nlogo @@ -0,0 +1,702 @@ +turtles-own + [chemo? + tumor-size + tumor-days + tumor-prechemo + body-size +] + +globals + [ %infected + %on-chemo + mri-status +] + + +to setup + clear-all + setup-turtles + update-global-variables + update-display + reset-ticks + set mri-status 0 +end + +to setup-turtles + create-turtles inital-hamsters + [ setxy random-xcor random-ycor + set size 2.7 + get-healthy + set shape "hamster" + set body-size 1500000 + random 2000000 ;;min + random (max-min) + ] + ask n-of inital_cancer turtles + [ set tumor-size 1 + set tumor-days 5 ] +end + + +to get-healthy + set tumor-size 0 + set tumor-prechemo 0 + set chemo? false +end + +to move ;; turtle procedure + rt random 100 + lt random 100 + fd 1 +end + +to infect + let first-hamster-tumor-size tumor-size ;; so as to not get confused w other hamster + ask other turtles-here with [tumor-size < 1 and not chemo?] + [if random-float 100 < infectiousness + [ set tumor-size 1 ] ] +end + +to MRI + if chemo-work [ if tumor-size > 0 [ set chemo? true set tumor-prechemo tumor-size ]] + if chemo? [ + if tumor-size < 0.01 [get-healthy]] ;; get off chemo and assume healthy when tumor is super small +end + +to tumor-grow + ;; assuming shrinking rate includes growth rate in it! + if chemo? = false [ + if tumor-days > 4 [ + set tumor-size (0.4574 * (tumor-days - 4) ^ 3 - 4.9283 * (tumor-days - 4) ^ 2 + 22.188 * (tumor-days - 4))]] + ;; this equation found on excel through data approxtimations and line of best fit w R^2 value 0.9966 +end + +to tumor-shrink + set tumor-size tumor-size - tumor-prechemo * 0.05 + ;; 68% reduction in 14 days from article ~ 5% reduction rate every day + ;; set as function of original tumor size when chemo began +end + +to update-global-variables + if count turtles > 0 + [ set %infected (count turtles with [ tumor-size > 0 ] / count turtles) * 100 + set %on-chemo (count turtles with [ chemo? ] / count turtles) * 100 + ] +end + +to update-display + ask turtles + [ set color ifelse-value tumor-size > 0 [ ifelse-value chemo? [blue] [red] ] [ green ] ] +end + +to go + ask turtles [ + move + if mri-status = MRI-frequency [ + MRI + ] + if tumor-size > 0[ + infect + set tumor-days tumor-days + 1 + if (tumor-size / body-size) > death-threshold [die] + if tumor-days > 4 [tumor-grow] ;; latent period! + if chemo? [tumor-shrink] + ] + ] + update-global-variables + update-display + if mri-status = MRI-frequency [ + set mri-status 0 + ] + set mri-status mri-status + 1 + if %infected = 0 [ + export-plot "Populations" (word "/Users/benmazin/Movies/netlogo output/world" behaviorspace-run-number ".csv") + stop + ] + tick +end +@#$#@#$#@ +GRAPHICS-WINDOW +280 +10 +778 +509 +-1 +-1 +14.0 +1 +10 +1 +1 +1 +0 +1 +1 +1 +-17 +17 +-17 +17 +1 +1 +1 +ticks +30.0 + +SLIDER +5 +145 +140 +178 +infectiousness +infectiousness +0.0 +100 +60.0 +1.0 +1 +NIL +HORIZONTAL + +BUTTON +155 +275 +265 +350 +NIL +go +T +1 +T +OBSERVER +NIL +NIL +NIL +NIL +0 + +PLOT +15 +440 +267 +604 +Populations +days +hamsters +0.0 +60.0 +0.0 +100.0 +true +true +"" "" +PENS +"sick" 1.0 0 -2674135 true "" "plot count turtles with [ tumor-size > 0 ]" +"healthy" 1.0 0 -10899396 true "" "plot count turtles with [ tumor-size > 0 ]" +"total" 1.0 0 -1184463 true "" "plot count turtles" +"%on chemo" 1.0 0 -14070903 true "" "plot count turtles with [ chemo? ]" + +MONITOR +15 +395 +80 +440 +NIL +%infected +1 +1 +11 + +MONITOR +155 +395 +205 +440 +days +ticks +1 +1 +11 + +SLIDER +115 +40 +275 +73 +inital_cancer +inital_cancer +0 +inital-hamsters +25.0 +1 +1 +NIL +HORIZONTAL + +MONITOR +90 +395 +145 +440 +%chemo +%on-chemo +1 +1 +11 + +SLIDER +115 +75 +275 +108 +MRI-frequency +MRI-frequency +1 +30 +7.0 +1 +1 +days +HORIZONTAL + +SLIDER +5 +180 +182 +213 +death-threshold +death-threshold +0.001 +0.005 +0.004 +0.0001 +1 +% +HORIZONTAL + +BUTTON +15 +275 +140 +308 +NIL +setup +NIL +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +INPUTBOX +5 +40 +110 +100 +inital-hamsters +100.0 +1 +0 +Number + +TEXTBOX +90 +10 +240 +35 +Study Setup +15 +0.0 +1 + +TEXTBOX +90 +120 +240 +138 +Cancer Traits +15 +0.0 +1 + +TEXTBOX +115 +245 +265 +263 +Control +15 +0.0 +1 + +MONITOR +217 +395 +267 +440 +Dead +inital-hamsters - count turtles +0 +1 +11 + +TEXTBOX +120 +365 +270 +390 +Output +15 +0.0 +1 + +SWITCH +15 +315 +140 +348 +chemo-work +chemo-work +0 +1 +-1000 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false 144 174 42 +Circle -16777216 true false 24 174 42 +Circle -7500403 false true 24 174 42 +Circle -7500403 false true 144 174 42 +Circle -7500403 false true 234 174 42 + +turtle +true +0 +Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 +Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 +Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 +Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 +Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 +Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99 + +wheel +false +0 +Circle -7500403 true true 3 3 294 +Circle -16777216 true false 30 30 240 +Line -7500403 true 150 285 150 15 +Line -7500403 true 15 150 285 150 +Circle -7500403 true true 120 120 60 +Line -7500403 true 216 40 79 269 +Line -7500403 true 40 84 269 221 +Line -7500403 true 40 216 269 79 +Line -7500403 true 84 40 221 269 + +x +false +0 +Polygon -7500403 true true 270 75 225 30 30 225 75 270 +Polygon -7500403 true true 30 75 75 30 270 225 225 270 +@#$#@#$#@ +NetLogo 6.4.0 +@#$#@#$#@ +@#$#@#$#@ +@#$#@#$#@ + + + setup + go + + + + + + + + + + + + + + + + + + + + + +@#$#@#$#@ +@#$#@#$#@ +default +0.0 +-0.2 0 0.0 1.0 +0.0 1 1.0 0.0 +0.2 0 0.0 1.0 +link direction +true +0 +Line -7500403 true 150 150 90 180 +Line -7500403 true 150 150 210 180 +@#$#@#$#@ +1 +@#$#@#$#@ From d2ae2cecb87222e40143cdcf446f737664a73b90 Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:26:56 -0400 Subject: [PATCH 03/13] Create index.html --- index.html | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 index.html diff --git a/index.html b/index.html new file mode 100644 index 0000000..712804a --- /dev/null +++ b/index.html @@ -0,0 +1,58 @@ + + + + + My GitHub Repository + + + +
+

Welcome to My GitHub Repository

+

This is a collection of my projects and files. Feel free to explore the files listed below:

+ +
+ + From 4dd41c267adbad9e8bee25c5cafc16670536badd Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:32:52 -0400 Subject: [PATCH 04/13] Update index.html --- index.html | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/index.html b/index.html index 712804a..bbbfed5 100644 --- a/index.html +++ b/index.html @@ -2,7 +2,7 @@ - My GitHub Repository + RP4 ABM Hamster

Welcome to the GitHub Repository for the Hamster Agent Based Model Group

-

This is a collection our model and anlysis code. Feel free to explore the files listed below:

+

This is a collection of our model and analysis code. Feel free to explore the files listed below:

From 9e503859122992724df6b03c7c96befac5f78bb6 Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:52:28 -0400 Subject: [PATCH 08/13] Update index.html --- index.html | 77 ++++++++++++++++++++++++++++++++---------------------- 1 file changed, 46 insertions(+), 31 deletions(-) diff --git a/index.html b/index.html index cad6d85..dd2170c 100644 --- a/index.html +++ b/index.html @@ -2,76 +2,91 @@ - RP4 ABM Hamster + RP4 ABM Hamster Project +
-

Welcome to the GitHub Repository for the Hamster Agent Based Model Group

-

This is a collection of our model and analysis code. Feel free to explore the files listed below:

+

Hamster Agent Based Model (ABM) Project

+

Welcome to the official repository of the RP4 Hamster Agent Based Model (ABM) Group. Here you will find our interactive model and analysis code used in this iSci Project. Dive into the links below to explore our work.

+

Group Members

+
From 6cf043349a2e93af91578fdfa02f5a859483f7dd Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:55:32 -0400 Subject: [PATCH 09/13] Update index.html --- index.html | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/index.html b/index.html index dd2170c..855c8f2 100644 --- a/index.html +++ b/index.html @@ -66,8 +66,17 @@ background-color: #d6eaf8; } + .member-list { + display: flex; + flex-wrap: wrap; + justify-content: start; + gap: 10px; + margin-bottom: 24px; + } + .member-list li { background-color: #f0f4f7; + border-radius: 8px; } @@ -75,11 +84,6 @@

Hamster Agent Based Model (ABM) Project

Welcome to the official repository of the RP4 Hamster Agent Based Model (ABM) Group. Here you will find our interactive model and analysis code used in this iSci Project. Dive into the links below to explore our work.

-

Group Members

+
From 56abb0c0a7a9ce256f32556580943e48fd02fdc9 Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 22:59:48 -0400 Subject: [PATCH 10/13] Update README.md --- README.md | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c9b75db..12709e7 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,27 @@ -# RP4-ABM-Hamster -RP4 Code for Agent Based Hamster Model +# Hamster Agent Based Model (ABM) Project + +Welcome to the official repository of the RP4 Hamster Agent Based Model (ABM) Group. Here you will find our interactive model and analysis code used in this iSci Project. Dive into the links below to explore our work. + +## Group Members + +- Ben Mazin +- Kyla Lewis +- Siya Sood +- Sarah Winter +- Jasleen Dhillon + +## Project Files + +- [Interactive NetLogo Model (Browser Version)](RP4%20Hamster%20Model%20final.html) +- [NetLogo Model File (Downloadable)](RP4%20Hamster%20Model%20final.nlogo) +- [Python Analysis Script (Downloadable)](Netlogo%20analysis.py) + +## About the Project + +The Hamster ABM project aims to simulate the behaviors and interactions of hamsters in various environments to study their social structures, movement patterns, and overall ecosystem impact. This model is implemented using NetLogo, allowing for interactive exploration and analysis. + +We encourage you to download our models and scripts to see the detailed workings and to contribute by providing feedback or enhancements to our project. + +--- + +Feel free to check out our work and contribute to our research in understanding hamster behaviors through agent-based modeling! From f6e60018e504aaddb1870e8c9711c7374b0488af Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 23:01:49 -0400 Subject: [PATCH 11/13] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 12709e7..9a86a7f 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Welcome to the official repository of the RP4 Hamster Agent Based Model (ABM) Gr ## Project Files -- [Interactive NetLogo Model (Browser Version)](RP4%20Hamster%20Model%20final.html) +- [Interactive NetLogo Model (Browser Version)]([RP4%20Hamster%20Model%20final.html](https://benmazin1.github.io/RP4-ABM-Hamster/RP4%20Hamster%20Model%20final.html)) - [NetLogo Model File (Downloadable)](RP4%20Hamster%20Model%20final.nlogo) - [Python Analysis Script (Downloadable)](Netlogo%20analysis.py) From da0a4d3844a1fda7993a9b932a882092eb2a063b Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Tue, 26 Mar 2024 23:02:57 -0400 Subject: [PATCH 12/13] Update README.md --- README.md | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/README.md b/README.md index 9a86a7f..3c5bcac 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,7 @@ Welcome to the official repository of the RP4 Hamster Agent Based Model (ABM) Gr ## Project Files -- [Interactive NetLogo Model (Browser Version)]([RP4%20Hamster%20Model%20final.html](https://benmazin1.github.io/RP4-ABM-Hamster/RP4%20Hamster%20Model%20final.html)) +- [Interactive NetLogo Model (Browser Version)](https://benmazin1.github.io/RP4-ABM-Hamster/RP4%20Hamster%20Model%20final.html) - [NetLogo Model File (Downloadable)](RP4%20Hamster%20Model%20final.nlogo) - [Python Analysis Script (Downloadable)](Netlogo%20analysis.py) -## About the Project - -The Hamster ABM project aims to simulate the behaviors and interactions of hamsters in various environments to study their social structures, movement patterns, and overall ecosystem impact. This model is implemented using NetLogo, allowing for interactive exploration and analysis. - -We encourage you to download our models and scripts to see the detailed workings and to contribute by providing feedback or enhancements to our project. - ---- - -Feel free to check out our work and contribute to our research in understanding hamster behaviors through agent-based modeling! From a3fd5b9de7d036ae46f9ba49e9a09ae656c12d2d Mon Sep 17 00:00:00 2001 From: BenMazin <92589195+BenMazin1@users.noreply.github.com> Date: Wed, 27 Mar 2024 01:17:06 -0400 Subject: [PATCH 13/13] Add files via upload --- Netlogo analysis.py | 36 ++++++++++++++++++++++++++++++++---- 1 file changed, 32 insertions(+), 4 deletions(-) diff --git a/Netlogo analysis.py b/Netlogo analysis.py index 6f2673d..63da5f0 100644 --- a/Netlogo analysis.py +++ b/Netlogo analysis.py @@ -8,11 +8,15 @@ import pandas as pd from scipy import stats +import matplotlib.pyplot as plt # Set the number of trials and initial hamsters -number_of_trials = 20000 +number_of_trials = 200000 initial_hamsters = 100 +# save path for the results +save_path = '/Users/benmazin/Movies/' + # Create an empty DataFrame with 4 columns all_data = [] @@ -35,7 +39,7 @@ def read_inconsistent_csv(file_path, delimiter=','): for i in range(1, number_of_trials + 1): # Read in the csv file - file_path = f'/Users/benmazin/Movies/netlogo output/world{i}.csv' + file_path = f'{save_path}netlogo output/world{i}.csv' data = read_inconsistent_csv(file_path, delimiter=',') # Get the value of ChemoWork @@ -93,6 +97,30 @@ def read_inconsistent_csv(file_path, delimiter=','): 'Value': [chemo_total_dead_mean, chemo_percent_infect_mean, no_chemo_total_dead_mean, no_chemo_percent_infect_mean, totalDeadTtest, percentInfectTtest] }) +# Plot an individual distribution for each category and save to a png in the same directory +save_path = save_path + 'netlogo results/' + +results['ChemoTotalDead'].plot.kde() +plt.xlabel('Chemo Total Dead') +plt.savefig(save_path + 'ChemoTotalDeadDist.png') +plt.close() + +results['ChemoPercentInfect'].plot.kde() +plt.xlabel('Chemo Percent Infect') +plt.savefig(save_path + 'ChemoPercentInfectDist.png') +plt.close() + +results['NoChemoTotalDead'].plot.kde() +plt.xlabel('No Chemo Total Dead') +plt.savefig(save_path + 'NoChemoTotalDeadDist.png') +plt.close() + +results['NoChemoPercentInfect'].plot.kde() +plt.xlabel('No Chemo Percent Infect') +plt.savefig(save_path + 'NoChemoPercentInfectDist.png') +plt.close() + + # save the summary and results to csv -resultSum.to_csv('/Users/benmazin/Movies/netlogo results/summary.csv', index=False) -results.to_csv('/Users/benmazin/Movies/netlogo results/results.csv', index=False) \ No newline at end of file +resultSum.to_csv(save_path + 'summary.csv', index=False) +results.to_csv(save_path + 'results.csv', index=False) \ No newline at end of file