add citation

Author: obonhamcarter

README.md

@@ -263,11 +263,8 @@ for x in `ls *.tar.gz`
 
 ## Citations
 
-- Accepted at FLAIRS-38 (The Florida Artificial Intelligence Research Society).
-- Formal reference to follow when available.
+  - Bonham-Carter, O. (2025). An Efficient Text Analysis Tool for Streamlining Literature Reviews: Text Analysis To Streamline Literature Reviews. The International FLAIRS Conference Proceedings, 38(1). https://doi.org/10.32473/flairs.38.1.138991
 
-  - Bonham-Carter, Oliver. "An Efficient Text Analysis Tool for Streamlining Literature Reviews", Proceedings of FLAIRS-38
-  
 ## Developer Notes
 
 - Added dependency:

execution_log.md

@@ -0,0 +1,221 @@
+
+---
+**Command:** `cargo run --bin 1_beagleTA_parser`
+
+**Success:** true
+
+**Output:**
+```
+
+    _█ █ █ █ █________________________________________ █ █________________ █ █ █ █ █ █______ █ █_____
+    _█ █____ █ █____ █ █ █____ █ █ █________ █ █ █ █__ █ █______ █ █ █________ █ █________ █ █ █ █___
+    _█ █ █ █ █____ █ █ █ █ █______ █ █____ █ █__ █ █__ █ █____ █ █ █ █ █______ █ █______ █ █____ █ █_
+    _█ █____ █ █__ █ █________ █ █ █ █______ █ █ █ █__ █ █____ █ █____________ █ █______ █ █ █ █ █ █_
+    _█ █ █ █ █______ █ █ █ █__ █ █ █ █ █________ █ █__ █ █ █____ █ █ █ █______ █ █______ █ █____ █ █_
+    _______________________________________ █ █ █ █___________________________________________________
+    
+	 Package name: 'BeagleTA'.
+	 Package version: '1.5.11'.
+	 Package edition: '2021'.
+
+	 Usage: cargo run <keyword_file.txt> <corpus_dir>
+	 🐕  Enter the path to the keyword text file: 	 🐕  Enter the path to the data directory: 	 Keyword path cannot be empty!
+	 Directory path cannot be empty!
+
+[stderr]:    Compiling proc-macro2 v1.0.94
+   Compiling unicode-ident v1.0.18
+   Compiling libc v0.2.171
+   Compiling crossbeam-utils v0.8.21
+   Compiling serde v1.0.219
+   Compiling memchr v2.7.4
+   Compiling zerocopy v0.8.23
+   Compiling rayon-core v1.12.1
+   Compiling utf8parse v0.2.2
+   Compiling cfg-if v1.0.0
+   Compiling anstyle-parse v0.2.6
+   Compiling is_terminal_polyfill v1.70.1
+   Compiling anstyle v1.0.10
+   Compiling colorchoice v1.0.3
+   Compiling hashbrown v0.15.2
+   Compiling equivalent v1.0.2
+   Compiling anstyle-query v1.1.2
+   Compiling anstream v0.6.18
+   Compiling aho-corasick v1.1.3
+   Compiling strsim v0.11.1
+   Compiling clap_lex v0.7.4
+   Compiling indexmap v2.8.0
+   Compiling ryu v1.0.20
+   Compiling itoa v1.0.15
+   Compiling futures v0.1.31
+   Compiling crossbeam-epoch v0.9.18
+   Compiling quote v1.0.40
+   Compiling crossbeam-deque v0.8.6
+   Compiling getrandom v0.2.15
+   Compiling rand_core v0.6.4
+   Compiling syn v2.0.100
+   Compiling iovec v0.1.4
+   Compiling num_cpus v1.16.0
+   Compiling crossbeam-channel v0.5.15
+   Compiling crossbeam-queue v0.3.12
+   Compiling byteorder v1.5.0
+   Compiling regex-syntax v0.8.5
+   Compiling either v1.15.0
+   Compiling winnow v0.7.4
+   Compiling serde_json v1.0.140
+   Compiling rayon v1.10.0
+   Compiling crossbeam v0.8.4
+   Compiling futures-cpupool v0.1.8
+   Compiling bytes v0.4.12
+   Compiling ppv-lite86 v0.2.21
+   Compiling clap_builder v4.5.35
+   Compiling rand_chacha v0.3.1
+   Compiling csv-core v0.1.12
+   Compiling fs v0.0.5
+   Compiling rand v0.8.5
+   Compiling colored v3.0.0
+   Compiling regex-automata v0.4.9
+   Compiling serde_derive v1.0.219
+   Compiling jwalk v0.8.1
+   Compiling clap v4.5.35
+   Compiling regex v1.11.1
+   Compiling serde_spanned v0.6.8
+   Compiling toml_datetime v0.6.8
+   Compiling csv v1.3.1
+   Compiling toml_edit v0.22.24
+   Compiling toml v0.8.20
+   Compiling BeagleTA v1.5.11 (/Users/obonhamcarter/Desktop/mini_research_TA/BeagleTA)
+    Finished `dev` profile [unoptimized + debuginfo] target(s) in 7.00s
+     Running `target/debug/1_beagleTA_parser`
+```
+
+**Time:** 7.2878 seconds
+
+---
+**Command:** `cargo run --bin 2_csv_cleaner_filter/`
+
+**Success:** false
+
+**Output:**
+```
+[stderr]: error: no bin target named `2_csv_cleaner_filter/`
+
+	Did you mean `2_csv_cleaner_filter`?
+```
+
+**Time:** 0.0611 seconds
+
+---
+**Command:** `cargo run --bin 2_csv_cleaner_filter`
+
+**Success:** false
+
+**Output:**
+```
+
+
+    ___█ █ █ █ █ __█ █ _______________________________________________________________
+    _█ █ __________█ █ ______█ █ █ ____█ █ █ ______█ █ █ █ ______█ █ █ ____█ █ __█ █ _
+    _█ █ __________█ █ ____█ █ █ █ █ ______█ █ ____█ █ __█ █ __█ █ █ █ █ __█ █ █ █ ___
+    _█ █ __________█ █ ____█ █ ________█ █ █ █ ____█ █ __█ █ __█ █ ________█ █ _______
+    ___█ █ █ █ █ __█ █ █ ____█ █ █ █ __█ █ █ █ █ __█ █ __█ █ ____█ █ █ █ __█ █ _______
+    __________________________________________________________________________________
+    
+        
+
+[stderr]:    Compiling BeagleTA v1.5.11 (/Users/obonhamcarter/Desktop/mini_research_TA/BeagleTA)
+    Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.22s
+     Running `target/debug/2_csv_cleaner_filter`
+error: the following required arguments were not provided:
+  --input <input>
+  --output <output>
+  --column <column>
+
+Usage: 2_csv_cleaner_filter --input <input> --output <output> --column <column>
+
+For more information, try '--help'.
+```
+
+**Time:** 0.4488 seconds
+
+---
+**Command:** `cargo run examples/kws.txt examples/corpus_short/`
+
+**Success:** false
+
+**Output:**
+```
+[stderr]: error: `cargo run` could not determine which binary to run. Use the `--bin` option to specify a binary, or the `default-run` manifest key.
+available binaries: 1_beagleTA_parser, 2_csv_cleaner_filter, 3_csv_random_sampler
+```
+
+**Time:** 0.0413 seconds
+
+---
+**Command:** `cargo run --bin -- 1_beagleTA_parser examples/kws.txt examples/corpus_short/`
+
+**Success:** false
+
+**Output:**
+```
+[stderr]: error: "--bin" takes one argument.
+Available binaries:
+    1_beagleTA_parser
+    2_csv_cleaner_filter
+    3_csv_random_sampler
+```
+
+**Time:** 0.0379 seconds
+
+---
+**Command:** `cargo run -- --bin 1_beagleTA_parser examples/kws.txt examples/corpus_short/`
+
+**Success:** false
+
+**Output:**
+```
+[stderr]: error: `cargo run` could not determine which binary to run. Use the `--bin` option to specify a binary, or the `default-run` manifest key.
+available binaries: 1_beagleTA_parser, 2_csv_cleaner_filter, 3_csv_random_sampler
+```
+
+**Time:** 0.0331 seconds
+
+---
+**Command:** `cargo run --bin 1_beagleTA_parser examples/kws.txt examples/corpus_short/`
+
+**Success:** true
+
+**Output:**
+```
+
+    _█ █ █ █ █________________________________________ █ █________________ █ █ █ █ █ █______ █ █_____
+    _█ █____ █ █____ █ █ █____ █ █ █________ █ █ █ █__ █ █______ █ █ █________ █ █________ █ █ █ █___
+    _█ █ █ █ █____ █ █ █ █ █______ █ █____ █ █__ █ █__ █ █____ █ █ █ █ █______ █ █______ █ █____ █ █_
+    _█ █____ █ █__ █ █________ █ █ █ █______ █ █ █ █__ █ █____ █ █____________ █ █______ █ █ █ █ █ █_
+    _█ █ █ █ █______ █ █ █ █__ █ █ █ █ █________ █ █__ █ █ █____ █ █ █ █______ █ █______ █ █____ █ █_
+    _______________________________________ █ █ █ █___________________________________________________
+    
+	 Package name: 'BeagleTA'.
+	 Package version: '1.5.11'.
+	 Package edition: '2021'.
+
+	 Usage: cargo run <keyword_file.txt> <corpus_dir>
+	 Found 63 files in the directory 'examples/corpus_short/'.
+	 Key words : ["2024", "ethic", "bio", "machine", "mitochondria"]
+ 	 * PMC314466.txt -> 1 of 63 	 * PMC314300.txt -> 2 of 63 	 * PMC314472.txt -> 3 of 63 	 * PMC193604.txt -> 4 of 63 	 * PMC193605.txt -> 5 of 63 	 * PMC314473.txt -> 6 of 63 	 * PMC314467.txt -> 7 of 63 	 * PMC314301.txt -> 8 of 63 	 * PMC314471.txt -> 9 of 63 	 * PMC314465.txt -> 10 of 63 	 * PMC193607.txt -> 11 of 63 	 * PMC193606.txt -> 12 of 63 	 * PMC314464.txt -> 13 of 63 	 * PMC314470.txt -> 14 of 63 	 * PMC314474.txt -> 15 of 63 	 * PMC314475.txt -> 16 of 63 	 * PMC314463.txt -> 17 of 63 	 * PMC314477.txt -> 18 of 63 	 * PMC314476.txt -> 19 of 63 	 * PMC314462.txt -> 20 of 63 	 * PMC212706.txt -> 21 of 63 	 * PMC300882.txt -> 22 of 63 	 * PMC212699.txt -> 23 of 63 	 * PMC212698.txt -> 24 of 63 	 * PMC300883.txt -> 25 of 63 	 * PMC212705.txt -> 26 of 63 	 * PMC300881.txt -> 27 of 63 	 * PMC212704.txt -> 28 of 63 	 * PMC176548.txt -> 29 of 63 	 * PMC212700.txt -> 30 of 63 	 * PMC300884.txt -> 31 of 63 	 * PMC300700.txt -> 32 of 63 	 * PMC300885.txt -> 33 of 63 	 * PMC300675.txt -> 34 of 63 	 * PMC212701.txt -> 35 of 63 	 * PMC212703.txt -> 36 of 63 	 * PMC212688.txt -> 37 of 63 	 * PMC212689.txt -> 38 of 63 	 * PMC300886.txt -> 39 of 63 	 * PMC212702.txt -> 40 of 63 	 * PMC212690.txt -> 41 of 63 	 * PMC212691.txt -> 42 of 63 	 * PMC261870.txt -> 43 of 63 	 * PMC212687.txt -> 44 of 63 	 * PMC212693.txt -> 45 of 63 	 * PMC212692.txt -> 46 of 63 	 * PMC176545.txt -> 47 of 63 	 * PMC212319.txt -> 48 of 63 	 * PMC212696.txt -> 49 of 63 	 * PMC212697.txt -> 50 of 63 	 * PMC176546.txt -> 51 of 63 	 * PMC212695.txt -> 52 of 63 	 * PMC212694.txt -> 53 of 63 	 * PMC176547.txt -> 54 of 63 	 * PMC314478.txt -> 55 of 63 	 * PMC314479.txt -> 56 of 63 	 * PMC314469.txt -> 57 of 63 	 * PMC314482.txt -> 58 of 63 	 * PMC314468.txt -> 59 of 63 	 * PMC314481.txt -> 60 of 63 	 * PMC314480.txt -> 61 of 63
+	 ✨ Run commands to create virtual environment with Python for the following commands ...
+	 python3 -m venv ~/Desktop/venv
+	 source ~/Desktop/venv/bin/activate
+	 pip install plotly matplotlib numpy pandas networkx seaborn scikit-learn pyvis
+
+	 ✨ Run commands to create keyword analysis and other visualizations ...
+	 cd 0_out && python3 visualizations.py && cd ..
+	 cd 0_out && python3 interactive_network_1.py --datafile output.csv --threshold 6 && cd .. 
+	 cd 0_out && python3 interactive_network_2.py --datafile output.csv && cd .. 
+	 cd 0_out && python3 complete_network.py -f output.csv -t 6 -nc blue -ec green  && cd .. 
+
+
+[stderr]:     Finished `dev` profile [unoptimized + debuginfo] target(s) in 0.03s
+     Running `target/debug/1_beagleTA_parser examples/kws.txt examples/corpus_short/`
+```
+
+**Time:** 0.5581 seconds