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Complete Assignment 2: Arthritis drug efficacy analysis #2

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Complete Assignment 2: Arthritis drug efficacy analysis #2

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117 changes: 105 additions & 12 deletions 02_activities/assignments/assignment_2.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -72,11 +72,23 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {
"id": "n0m48JsS-nMC"
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Line 1: 0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0\n",
"Line 2: 0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1\n",
"Line 3: 0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1\n",
"Line 4: 0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1\n",
"Line 5: 0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1\n"
]
}
],
"source": [
"all_paths = [\n",
" \"../../05_src/data/assignment_2_data/inflammation_01.csv\",\n",
Expand All @@ -95,10 +107,23 @@
"\n",
"with open(all_paths[0], 'r') as f:\n",
" # YOUR CODE HERE: Use the readline() or readlines() method to read the .csv file into a variable\n",
" \n",
" # YOUR CODE HERE: Iterate through the variable using a for loop and print each row for inspection"
" \n",
" lines = f.readlines()\n",
"\n",
" # YOUR CODE HERE: Iterate through the variable using a for loop and print each row for inspection\n",
"\n",
" for i, line in enumerate(lines[:5], start=1): \n",
" print(f\"Line {i}: {line.strip()}\")\n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {
Expand Down Expand Up @@ -130,7 +155,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"metadata": {
"id": "82-bk4CBB1w4"
},
Expand All @@ -145,13 +170,20 @@
" # Implement the specific operation based on the 'operation' argument\n",
" if operation == 'mean':\n",
" # YOUR CODE HERE: Calculate the mean (average) number of flare-ups for each patient\n",
" \n",
" summary_values = np.mean(data, axis=ax)\n",
"\n",
" elif operation == 'max':\n",
" # YOUR CODE HERE: Calculate the maximum number of flare-ups experienced by each patient\n",
"\n",
" summary_values = np.max(data, axis=ax)\n",
"\n",
"\n",
" elif operation == 'min':\n",
" # YOUR CODE HERE: Calculate the minimum number of flare-ups experienced by each patient\n",
"\n",
" summary_values = np.min(data, axis=ax)\n",
"\n",
" else:\n",
" # If the operation is not one of the expected values, raise an error\n",
" raise ValueError(\"Invalid operation. Please choose 'mean', 'max', or 'min'.\")\n",
Expand All @@ -161,11 +193,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {
"id": "3TYo0-1SDLrd"
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"60\n"
]
}
],
"source": [
"# Test it out on the data file we read in and make sure the size is what we expect i.e., 60\n",
"# Your output for the first file should be 60\n",
Expand Down Expand Up @@ -251,7 +291,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 14,
"metadata": {
"id": "LEYPM5v4JT0i"
},
Expand All @@ -262,20 +302,72 @@
"def detect_problems(file_path):\n",
" #YOUR CODE HERE: Use patient_summary() to get the means and check_zeros() to check for zeros in the means\n",
"\n",
" return"
" means = patient_summary(file_path, 'mean')\n",
" result = check_zeros(means)\n",
"\n",
" return result"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"def check_zeros(x):\n",
" '''\n",
" Given an array, x, check whether any values in x equal 0.\n",
" Return True if any values found, else returns False.\n",
" '''\n",
" flag = np.where(x == 0)[0]\n",
" return len(flag) > 0\n"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"False\n"
]
}
],
"source": [
"# Test out your code here\n",
"# Your output for the first file should be False\n",
"print(detect_problems(all_paths[0]))"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"False\n",
"False\n"
]
}
],
"source": [
"print(detect_problems(all_paths[0])) # should be False\n",
"print(detect_problems(all_paths[1])) # may be True or False\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {
Expand Down Expand Up @@ -314,7 +406,8 @@
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "venv",
"language": "python",
"name": "python3"
},
"language_info": {
Expand All @@ -327,7 +420,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.8"
"version": "3.12.7"
}
},
"nbformat": 4,
Expand Down
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