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are 12 animals in each group.": [[17, "q2-calculate-the-smallest-effect-size-if-there-are-12-animals-in-each-group"]], "Q2: Consider how pro-inflamatory markers are related to neurological impairment.": [[6, "q2-consider-how-pro-inflamatory-markers-are-related-to-neurological-impairment"]], "Q2: Create a regression for the processing domain that accounts for demographic covariates.": [[14, "q2-create-a-regression-for-the-processing-domain-that-accounts-for-demographic-covariates"]], "Q2: Describe the graph": [[11, "q2-describe-the-graph"]], "Q2: Determine the predomininant phylum across regions.": [[4, "q2-determine-the-predomininant-phylum-across-regions"]], "Q2: Do cocaine users or non-users have a higher average level of mcp1?": [[8, "q2-do-cocaine-users-or-non-users-have-a-higher-average-level-of-mcp1"]], "Q2: Is Visuospatial impairment linked with ART therapy?": [[12, "q2-is-visuospatial-impairment-linked-with-art-therapy"]], "Q2: Is race and education correlated in this 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Create a new DataFrame that includes only the treated individuals.": [[2, "q3-create-a-new-dataframe-that-includes-only-the-treated-individuals"]], "Q3: Describing the reaction yield": [[1, "q3-describing-the-reaction-yield"]], "Q3: Does Sex impact the effect of cocaine use on the average level of mcp1 expression?": [[8, "q3-does-sex-impact-the-effect-of-cocaine-use-on-the-average-level-of-mcp1-expression"]], "Q3: Hypothesis generation": [[6, "q3-hypothesis-generation"]], "Q3: Is Visuospatial score linked with ART therapy?": [[12, "q3-is-visuospatial-score-linked-with-art-therapy"]], "Q3: Is covariate controlled EDZ still correlated with PDZ?": [[14, "q3-is-covariate-controlled-edz-still-correlated-with-pdz"]], "Q3: Use the appropriate non-parametric method.": [[13, "q3-use-the-appropriate-non-parametric-method"]], "Q3: What is the molarity of each Paragon sample?": [[0, "q3-what-is-the-molarity-of-each-paragon-sample"]], "Q3: Which body site has the largest increase in Actinobacteria 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"inflamatori": 6, "inform": [0, 4, 5, 19], "initi": 2, "initial_viral_load": 3, "inspect": 15, "interfac": [9, 28], "introduct": [0, 2, 3, 4, 5, 6, 12, 13, 19, 38], "jupyt": 20, "lab": [0, 2, 4, 6, 8, 10, 12, 14, 16], "largest": 4, "learn": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "length": [2, 8], "level": [8, 9], "limit": 19, "linear": [9, 32], "link": 12, "lint": 1, "lmplot": 9, "load": 2, "log": 35, "long": [2, 24], "low": 2, "m": 9, "make": 2, "mani": [11, 12], "map": 10, "markdown": 19, "marker": 6, "matplotlib": 7, "mcp1": 8, "me": 19, "measur": [9, 11, 13], "melt": [5, 9], "merg": [4, 5, 10], "method": 13, "minimum": 16, "miss": 16, "model": 9, "modul": [18, 21, 23, 25, 26, 27, 29, 31, 32, 33], "molar": [0, 1, 22], "molecular": 0, "more": [15, 24], "most": 15, "multi": 13, "multipl": [9, 15], "neurolog": [6, 7], "new": [2, 16], "non": [8, 13, 24], "normal": [15, 24], "notebook": 20, "number": 13, "numer": 7, "numpi": 3, "object": [0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "onli": [2, 17], "organ": 24, "other": 17, "otter": 19, "outcom": 4, "over": 15, "pacbio": 0, "panda": [3, 26], "paragon": 0, "parametr": 13, "particip": [2, 6, 12, 13], "patient": 5, "pd": 9, "pdz": 14, "perform": 15, "persist": 4, "phagocytosi": 11, "phylum": [4, 5], "pingouin": 13, "pivot": 5, "plate": 10, "plot": [7, 9, 26], "popul": 3, "posit": 4, "potenti": 12, "power": [17, 33], "predict": 4, "predominin": 4, "pro": 6, "problem": 1, "process": 14, "programmat": 1, "protocol": 0, "python": [1, 19], "q1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19], "q2": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 19], "q3": [0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15], "q4": [0, 1, 2, 3, 4, 5, 6, 8, 12, 14, 15, 16], "q5": [0, 2, 4, 8, 16], "q6": [2, 4, 16], "q7": 4, "quantifi": 9, "quantit": 34, "queri": 3, "question": [2, 16, 36], "quick": 19, "race": 13, "rate": 19, "reaction": 1, "reason": 34, "refer": [2, 3], "region": [4, 5], "regress": [9, 14, 15, 32], "relat": [6, 9], "relev": 0, "relplot": 9, "replic": 29, "reserv": 19, "residu": 15, "resourc": [22, 39], "restart": 20, "risk": [16, 17], "rodent": 16, "row": [2, 3], "run": 20, "same": 2, "sampl": [0, 1, 2, 4, 11, 29], "score": [12, 14, 15], "seaborn": 28, "session": 20, "sever": 4, "severe_diseas": 5, "sex": [8, 13], "shape": 24, "short": 2, "simpl": 21, "singl": 5, "site": [4, 5], "size": [16, 17], "sk609": 16, "smallest": 17, "spread": 9, "spreadsheet": 24, "standard": 15, "statist": 2, "statu": 7, "step": [16, 17], "still": 14, "string": 1, "stripplot": 9, "subject": 19, "submiss": [4, 8, 10, 12, 14, 16, 19], "success": [16, 17], "suffer": 12, "sumar": 11, "summar": [5, 16, 17], "summari": 16, "swabbabl": 4, "t": 20, "tabl": [2, 4], "target": 19, "templat": [0, 1], "test": [13, 17, 31], "text": 0, "therapi": 12, "thi": [13, 37], "through": 1, "tissu": 4, "toler": [16, 17], "treat": [2, 3], "try": 19, "two": [2, 13, 17], "typic": 4, "uncertainti": 9, "unnorm": 24, "untreat": 3, "upper": 19, "us": [8, 13, 17, 19], "usabl": 0, "user": 8, "valu": 4, "variabl": [7, 15], "vegf": 7, "vehicl": 16, "viral": 2, "visual": [9, 10, 27], "visuospati": 12, "walkthrough": [1, 3, 5, 7, 9, 11, 13, 15, 17, 19], "week": 3, "weeks_to_failur": [2, 3], "weight": [0, 1], "well": 11, "well_level_data": 10, "what": [0, 1, 16], "when": 4, "which": [0, 1, 4, 15], "whole": 3, "why": 19, "wide": 24, "work": 40, "world": 18, "write": 1, "yield": [0, 1], "your": [16, 17], "z": 15, "zone": 19}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"A Power Analysis in 6 steps": [[17, "a-power-analysis-in-6-steps"]], "ANCOVA": [[15, "ancova"]], "About this book": [[37, "about-this-book"]], "Acting on Columns": [[3, "acting-on-columns"]], "Acting on Rows": [[3, "acting-on-rows"]], "Basic Plotting": [[7, "basic-plotting"]], "Basic regression": [[15, "basic-regression"]], "Boolean Indexing": [[3, "boolean-indexing"]], "Box Plots": [[7, "box-plots"]], "Calculate a aerobic target heart rate?": [[19, "calculate-a-aerobic-target-heart-rate"]], "Calculating Concentration": [[22, "calculating-concentration"]], "Calulating Molarity": [[22, "calulating-molarity"]], "Categorical Comparisons": [[9, "categorical-comparisons"]], "Categorical comparisons": [[13, "categorical-comparisons"]], "Categorical with catplot": [[9, "categorical-with-catplot"]], "Cells": [[20, "cells"]], "Change Log": [[35, "change-log"]], "Coding expectations": [[19, "coding-expectations"]], "Common Biological Distributions": [[30, "common-biological-distributions"]], "Comparing Distributions": [[9, "comparing-distributions"]], "Comparison of Variables": [[7, "comparison-of-variables"]], "Conclusion": [[0, "conclusion"], [1, "conclusion"], [3, "conclusion"]], "Continious comparisons": [[13, "continious-comparisons"]], "Counting with countplot": [[9, "counting-with-countplot"]], "Data": [[7, "data"]], "Data Form": [[24, "data-form"]], "Data Shape": [[24, "data-shape"]], "Dataset Reference": [[2, "dataset-reference"], [3, "dataset-reference"]], "Decoding samples": [[11, "decoding-samples"]], "Documentation": [[9, "documentation"]], "Don\u2019t be afraid to Restart & Run all": [[20, null]], "Even more forms": [[24, "even-more-forms"]], "Even more regression": [[15, "even-more-regression"]], "Exploration": [[15, "exploration"]], "Explore the effect of cocaine use on mcp1": [[8, "explore-the-effect-of-cocaine-use-on-mcp1"]], "Exploring a single patient": [[5, "exploring-a-single-patient"]], "Extra Resources": [[22, "extra-resources"]], "Figure Level Interface": [[9, "figure-level-interface"]], "First Normal Form (1NF)": [[24, "first-normal-form-1nf"]], "Frequently Asked Questions": [[36, "frequently-asked-questions"]], "Functions": [[1, "functions"]], "Goal": [[24, null]], "Grammar of Graphics": [[28, "grammar-of-graphics"]], "Haphazard Form": [[24, "haphazard-form"]], "Histograms": [[7, "histograms"]], "How full is each cell?": [[10, "how-full-is-each-cell"]], "Hypothesis Testing": [[13, "hypothesis-testing"], [13, "id1"]], "Imports": [[3, "imports"]], "Indexing": [[3, "indexing"]], "Introduction": [[0, "introduction"], [2, "introduction"], [3, "introduction"], [4, "introduction"], [5, "introduction"], [6, "introduction"], [12, "introduction"], [13, "introduction"], [19, "introduction"]], "I\u2019m pd.melting": [[9, "i-m-pd-melting"]], "Jupyter Notebooks": [[20, "jupyter-notebooks"]], "Lab": [[0, "lab"], [2, "lab"], [4, "lab"], [6, "lab"], [8, "lab"], [10, "lab"], [12, "lab"], [14, "lab"], [16, "lab"]], "Learning Objectives": [[0, "learning-objectives"], [1, "learning-objectives"], [2, "learning-objectives"], [3, "learning-objectives"], [5, "learning-objectives"], [6, "learning-objectives"], [7, "learning-objectives"], [8, "learning-objectives"], [9, "learning-objectives"], [10, "learning-objectives"], [11, "learning-objectives"], [12, "learning-objectives"], [13, "learning-objectives"], [14, "learning-objectives"], [15, "learning-objectives"], [16, "learning-objectives"], [17, "learning-objectives"]], "Linear model regression plots with lmplot": [[9, "linear-model-regression-plots-with-lmplot"]], "Linting through color": [[1, "linting-through-color"]], "Long Format": [[24, "long-format"]], "Markdown": [[19, "markdown"]], "Matplotlib": [[7, "matplotlib"]], "Matplotlib Gotchas": [[7, "matplotlib-gotchas"]], "Measuring Correlation": [[9, "measuring-correlation"]], "Measuring Spread": [[9, "measuring-spread"]], "Measuring Uncertainty": [[9, "measuring-uncertainty"]], "Measuring phagocytosis": [[11, "measuring-phagocytosis"]], "Melting": [[5, "melting"]], "Merging data": [[5, "merging-data"]], "Module 10: Power Analysis": [[33, "module-10-power-analysis"]], "Module 1: Hello World": [[18, "module-1-hello-world"]], "Module 2: Simple calculations": [[21, "module-2-simple-calculations"]], "Module 3: DataFrames": [[23, "module-3-dataframes"]], "Module 4: Analysis by groups": [[25, "module-4-analysis-by-groups"]], "Module 5: Plotting with Pandas": [[26, "module-5-plotting-with-pandas"]], "Module 6: Visualizing with Confidence": [[27, "module-6-visualizing-with-confidence"]], "Module 7: Samples and Replicates": [[29, "module-7-samples-and-replicates"]], "Module 8: Hypothesis Testing": [[31, "module-8-hypothesis-testing"]], "Module 9: Linear Regression": [[32, "module-9-linear-regression"]], "Molarity Calculations": [[22, "molarity-calculations"]], "Multi-group measurement": [[13, "multi-group-measurement"]], "Multiple Regression": [[15, "multiple-regression"]], "Non-Normalized (Unnormalized Form)": [[24, "non-normalized-unnormalized-form"]], "Non-parametric comparisons": [[13, "non-parametric-comparisons"]], "Notebook basics": [[20, "notebook-basics"]], "Numeric Variables": [[7, "numeric-variables"]], "Numpy": [[3, "numpy"]], "Otter Grader": [[19, "otter-grader"]], "Over fitting": [[15, "over-fitting"]], "Pandas": [[3, "pandas"]], "Pingouin": [[13, "pingouin"]], "Pivoting": [[5, "pivoting"]], "Pivoting & Melting Dataframes": [[5, "pivoting-melting-dataframes"]], "Plot Handles": [[7, "plot-handles"]], "Plotting Multiple Columns": [[9, "plotting-multiple-columns"]], "Programmatic Arithmetic in Python": [[1, "programmatic-arithmetic-in-python"]], "Protocol Evaluation": [[0, "protocol-evaluation"]], "Q1: Are Processing domain and Executive domain scores correlated?": [[14, "q1-are-processing-domain-and-executive-domain-scores-correlated"]], "Q1: By inspection, which variable is most correlated?": [[15, "q1-by-inspection-which-variable-is-most-correlated"]], "Q1: Calculate the molarity of the sample": [[1, "q1-calculate-the-molarity-of-the-sample"]], "Q1: Calculate the power if there are only two animals in each group.": [[17, "q1-calculate-the-power-if-there-are-only-two-animals-in-each-group"]], "Q1: Count the number of participants of each sex and race.": [[13, "q1-count-the-number-of-participants-of-each-sex-and-race"]], "Q1: Create an fraction_area_covered column": [[10, "q1-create-an-fraction-area-covered-column"]], "Q1: Do cocaine users have a higher level of expression of mcp1?": [[8, "q1-do-cocaine-users-have-a-higher-level-of-expression-of-mcp1"]], "Q1: Explore the cocaine_use and cannabinoid_use columns.": [[7, "q1-explore-the-cocaine-use-and-cannabinoid-use-columns"]], "Q1: Explore the neurological function of the participants in the dataset.": [[6, "q1-explore-the-neurological-function-of-the-participants-in-the-dataset"]], "Q1: Extract the information for patient 3116": [[5, "q1-extract-the-information-for-patient-3116"]], "Q1: Extract the initial_viral_load column ?": [[3, "q1-extract-the-initial-viral-load-column"]], "Q1: Extract the relevant information from the text above": [[0, "q1-extract-the-relevant-information-from-the-text-above"]], "Q1: How many cells are in each well?": [[11, "q1-how-many-cells-are-in-each-well"]], "Q1: How many participants are suffering from impairment?": [[12, "q1-how-many-participants-are-suffering-from-impairment"]], "Q1: Load in the data from the CSV file.": [[2, "q1-load-in-the-data-from-the-csv-file"]], "Q1: Merge the biome_data table with the sample information": [[4, "q1-merge-the-biome-data-table-with-the-sample-information"]], "Q1: Using the information above, calculate the subject\u2019s heart rate reserve.": [[19, "q1-using-the-information-above-calculate-the-subject-s-heart-rate-reserve"]], "Q1: What is the average difference in misses between vehicle control and SK609 rodents?": [[16, "q1-what-is-the-average-difference-in-misses-between-vehicle-control-and-sk609-rodents"]], "Q2: By inspection, which variable has the most between class difference?": [[15, "q2-by-inspection-which-variable-has-the-most-between-class-difference"]], "Q2: Calculate the amount of sample to add.": [[1, "q2-calculate-the-amount-of-sample-to-add"]], "Q2: Calculate the average count across regions for each phylum for patient 3116.": [[5, "q2-calculate-the-average-count-across-regions-for-each-phylum-for-patient-3116"]], "Q2: Calculate the average weeks_to_failure for the whole population?": [[3, "q2-calculate-the-average-weeks-to-failure-for-the-whole-population"]], "Q2: Calculate the effect size.": [[16, "q2-calculate-the-effect-size"]], "Q2: Calculate the length of for each row.": [[2, "q2-calculate-the-length-of-for-each-row"]], "Q2: Calculate the molecular weight of each template": [[0, "q2-calculate-the-molecular-weight-of-each-template"]], "Q2: Calculate the smallest effect size if there are 12 animals in each group.": [[17, "q2-calculate-the-smallest-effect-size-if-there-are-12-animals-in-each-group"]], "Q2: Consider how pro-inflamatory markers are related to neurological impairment.": [[6, "q2-consider-how-pro-inflamatory-markers-are-related-to-neurological-impairment"]], "Q2: Create a regression for the processing domain that accounts for demographic covariates.": [[14, "q2-create-a-regression-for-the-processing-domain-that-accounts-for-demographic-covariates"]], "Q2: Describe the graph": [[11, "q2-describe-the-graph"]], "Q2: Determine the predomininant phylum across regions.": [[4, "q2-determine-the-predomininant-phylum-across-regions"]], "Q2: Do cocaine users or non-users have a higher average level of mcp1?": [[8, "q2-do-cocaine-users-or-non-users-have-a-higher-average-level-of-mcp1"]], "Q2: Is Visuospatial impairment linked with ART therapy?": [[12, "q2-is-visuospatial-impairment-linked-with-art-therapy"]], "Q2: Is race and education correlated in this dataset?": [[13, "q2-is-race-and-education-correlated-in-this-dataset"]], "Q2: Is the expression of infalpha or vegf different across neurological impairment status?": [[7, "q2-is-the-expression-of-infalpha-or-vegf-different-across-neurological-impairment-status"]], "Q2: Merge well_level_data with plate-map and visualize": [[10, "q2-merge-well-level-data-with-plate-map-and-visualize"]], "Q2: Using the information above, calculate the upper limit of the subject\u2019s target heart rate zone.": [[19, "q2-using-the-information-above-calculate-the-upper-limit-of-the-subject-s-target-heart-rate-zone"]], "Q3: Are the residuals normally distributed?": [[15, "q3-are-the-residuals-normally-distributed"]], "Q3: Calculate the average counts of each phylum by body site.": [[5, "q3-calculate-the-average-counts-of-each-phylum-by-body-site"]], "Q3: Calculate the average weeks to failure for the treated population?": [[3, "q3-calculate-the-average-weeks-to-failure-for-the-treated-population"]], "Q3: Create a new DataFrame that includes only the treated individuals.": [[2, "q3-create-a-new-dataframe-that-includes-only-the-treated-individuals"]], "Q3: Describing the reaction yield": [[1, "q3-describing-the-reaction-yield"]], "Q3: Does Sex impact the effect of cocaine use on the average level of mcp1 expression?": [[8, "q3-does-sex-impact-the-effect-of-cocaine-use-on-the-average-level-of-mcp1-expression"]], "Q3: Hypothesis generation": [[6, "q3-hypothesis-generation"]], "Q3: Is Visuospatial score linked with ART therapy?": [[12, "q3-is-visuospatial-score-linked-with-art-therapy"]], "Q3: Is covariate controlled EDZ still correlated with PDZ?": [[14, "q3-is-covariate-controlled-edz-still-correlated-with-pdz"]], "Q3: Use the appropriate non-parametric method.": [[13, "q3-use-the-appropriate-non-parametric-method"]], "Q3: What is the molarity of each Paragon sample?": [[0, "q3-what-is-the-molarity-of-each-paragon-sample"]], "Q3: Which body site has the largest increase in Actinobacteria when comparing typical and severe disease outcomes?": [[4, "q3-which-body-site-has-the-largest-increase-in-actinobacteria-when-comparing-typical-and-severe-disease-outcomes"]], "Q4: Are EDZ and PDZ correlated after controlling for covariates?": [[14, "q4-are-edz-and-pdz-correlated-after-controlling-for-covariates"]], "Q4: Calculate the average counts of each phylum by severe_disease.": [[5, "q4-calculate-the-average-counts-of-each-phylum-by-severe-disease"]], "Q4: Calculate the average weeks_to_failure for the treated population?": [[3, "q4-calculate-the-average-weeks-to-failure-for-the-treated-population"]], "Q4: Calculate the average weeks_to_failure for the untreated population?": [[3, "q4-calculate-the-average-weeks-to-failure-for-the-untreated-population"]], "Q4: Calculate the minimum change detectable with 16 animals.": [[16, "q4-calculate-the-minimum-change-detectable-with-16-animals"]], "Q4: Evaluate a potential covariate": [[12, "q4-evaluate-a-potential-covariate"]], "Q4: Exploration": [[6, "q4-exploration"]], "Q4: Is there a correlation between infection length and mcp1 expression?": [[8, "q4-is-there-a-correlation-between-infection-length-and-mcp1-expression"]], "Q4: Make two new tables that contain high and low initial viral load samples of the treated individuals.": [[2, "q4-make-two-new-tables-that-contain-high-and-low-initial-viral-load-samples-of-the-treated-individuals"]], "Q4: Perform an ANOVA between ART on the Executive Domain Z-score.": [[15, "q4-perform-an-anova-between-art-on-the-executive-domain-z-score"]], "Q4: What is the yield of each PacBio sample?": [[0, "q4-what-is-the-yield-of-each-pacbio-sample"]], "Q4: Which tissues are \u201cswabbable\u201d?": [[4, "q4-which-tissues-are-swabbable"]], "Q4: Write a function which calculates the reaction yield": [[1, "q4-write-a-function-which-calculates-the-reaction-yield"]], "Q5: Calculate descriptive statistics on the weeks_to_failure column to compare the high and low viral load participants.": [[2, "q5-calculate-descriptive-statistics-on-the-weeks-to-failure-column-to-compare-the-high-and-low-viral-load-participants"]], "Q5: Calculate new effect sizes for these conditions.": [[16, "q5-calculate-new-effect-sizes-for-these-conditions"]], "Q5: Does cocaine use impact the correlation between infection length and mcp1 expression?": [[8, "q5-does-cocaine-use-impact-the-correlation-between-infection-length-and-mcp1-expression"]], "Q5: Which samples are high?": [[4, "q5-which-samples-are-high"]], "Q5: Which samples are usable?": [[0, "q5-which-samples-are-usable"]], "Q6 Summary Questions": [[16, "q6-summary-questions"]], "Q6: Calculate the same descriptive statistics on the weeks_to_failure column to compare the treated participants with short and long infection lengths.": [[2, "q6-calculate-the-same-descriptive-statistics-on-the-weeks-to-failure-column-to-compare-the-treated-participants-with-short-and-long-infection-lengths"]], "Q6: Which swabbable region has the highest positive 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