{"id":5587,"date":"2022-09-27T14:56:31","date_gmt":"2022-09-27T14:56:31","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/?post_type=chapter&#038;p=5587"},"modified":"2022-10-18T08:02:46","modified_gmt":"2022-10-18T08:02:46","slug":"18d-inclass","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/chapter\/18d-inclass\/","title":{"raw":"18D InClass","rendered":"18D InClass"},"content":{"raw":"<div id=\"bp-page-1\" class=\"page\" data-page-number=\"1\" data-loaded=\"true\">\r\n<div class=\"textLayer\">During the COVID-19 pandemic, clinical trials were conducted to determine which factors may help reduce COVID-19 risk. One vitamin in particular, vitamin D, looked promising for reducing this risk. News headlines such as \u201cVitamin D Can Help Reduce COVID-19 Risks: Here\u2019s How\u201d[footnote]Curley, B. (2020, September 13). Vitamin D can help reduce COVID-19 risks: Here\u2019s how. Healthline.https:\/\/www.healthline.com\/health-news\/vitamin-d-can-help-reduce-covid19-risks2Castillo, M.E., Costa, L. M.E., Barrios, J. M.V., D\u00edaz, J. F.A., Miranda, J.L., Bouillon, R., &amp; Gomez, J. M.Q.(2020, October). Effect of calcifediol treatment and best available therapy versus best available therapy on intensive care unit admission and mortality among patients hospitalized for COVID-19: A pilot randomized clinical study. Journal of Steroid Biochemistry and Molecular Biology, 203. https:\/\/doi.org\/10.1016\/j.jsbmb.2020.105751Credit:iStock\/tungphoto[\/footnote] started appearing in Fall 2020. But were these headlines valid? In this in-class activity, we will examine data from one study designed to determine if vitamin D may reduce the severity of illness if one does test positive for COVID-19.2<\/div>\r\n<div><img class=\"alignnone wp-image-2212\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/5738\/2022\/01\/27024552\/Picture144-300x200.jpg\" alt=\"A pile of clear yellow pills.\" width=\"920\" height=\"613\" \/><\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 1<\/h3>\r\n1) How would you design a study to determine if vitamin D reducesthe risk of intensive care unit (ICU) admission due toCOVID-19?\r\n\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">In a small, randomized clinical trialconducted in Spain, 76 patients hospitalized with COVID-19 were randomized to either receive a calcifediol (vitamin D) treatment or not. All the patients were treated with the standard intervention for COVID-19, which at the time was a combination of hydroxychloroquine and azithromycin. Researchers recorded whether each patient was admitted to the ICU or not.<\/div>\r\n<\/div>\r\n<div id=\"bp-page-2\" class=\"page\" data-page-number=\"2\" data-loaded=\"true\">\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 2<\/h3>\r\n<div class=\"textLayer\">2) What variable distinguishesthe two groups comparedin this study?a)Whether the patient was hospitalized with COVID-19 or notb)Whether the patient received the calcifedioltreatment or notc)Whether the patient was admitted to the ICU or notd)Whether the patient was treated with the standard intervention or not<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 3<\/h3>\r\n<div class=\"textLayer\">3) What is the variable of interestin this study?<\/div>\r\n<div class=\"textLayer\">a) Whether the patient was hospitalized with COVID-19 or not<\/div>\r\n<div class=\"textLayer\">b) Whether the patient received the calcifedioltreatment or not<\/div>\r\n<div class=\"textLayer\">c) Whether the patient was admitted to the ICU or not<\/div>\r\n<div class=\"textLayer\">d) Whether the patient was treated with the standard intervention or not<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 4<\/h3>\r\n<div class=\"textLayer\">4) Is this study a randomized experiment or an observational study?<\/div>\r\n<div class=\"textLayer\">a) Randomized experiment, since patients were randomly assigned to receive calcifediolor not<\/div>\r\n<div class=\"textLayer\">b) Randomized experiment, since there were two different treatments<\/div>\r\n<div class=\"textLayer\">c) Observational study, since whether the patient was admitted to the ICU was not randomly assigned<\/div>\r\n<div class=\"textLayer\">d) Observational study, since patients were not randomly selected from the population of all COVID-19 infected individuals<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 5<\/h3>\r\n<div class=\"textLayer\">5) Before the data are collected, you should state the research hypothesis.What were the researchers hoping to show in this study?<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 6<\/h3>\r\n6) Let \ud835\udc5d\ud835\udc36\ud835\udc4e\ud835\udc59\ud835\udc50be the probability of admission to the ICU for COVID-19 patients on the calcifedioltreatment and \ud835\udc5d\ud835\udc48\ud835\udc5b\ud835\udc61\ud835\udc5fbe the probability of admission to the ICU for COVID-19 patients not treated with calcifediol. State the null and alternative hypotheses in terms of these parameters.\r\n\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 7<\/h3>\r\n7) Of the 50 patients randomly assigned to the calcifedioltreatment, only one was admitted totheICU, whereas 13 of the 26 patients who did not receive the calcifedioltreatment were admitted to the ICU.Organize these results into thefollowing2\u00d72 table.\r\n<table>\r\n<tbody>\r\n<tr>\r\n<td><\/td>\r\n<td>Treated with calcifediol<\/td>\r\n<td>Untreated with calcifediol<\/td>\r\n<td>Total<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Admitted to ICU<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Not admitted to ICU<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Total<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 8<\/h3>\r\n8) What proportion of the 76 patients in the study were admitted to the ICU?\r\n\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 9<\/h3>\r\n9) What proportion of the patients on the calcifedioltreatment were admitted to the ICU? What proportion of the untreated patients were admitted to the ICU? What isthe appropriate statistical notation for each of these values?\r\n\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 10<\/h3>\r\n<div class=\"textLayer\">10) Calculate the difference in proportionsof ICU admissions between the two groups (use calcifediol-treated \u2013calcifediol-untreatedas the order of subtraction).<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div>\r\n<div class=\"textLayer\">The following is a segmented bar graph of the data.<\/div>\r\n<div><img class=\"alignnone wp-image-3086\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/5738\/2022\/01\/11200738\/Picture1461-300x273.png\" alt=\"A vertical stacked bar chart. On the x-axis, it is labeled \u201cTreatment\u201d and on the y-axis, it is labeled \u201cProportion.\u201d To the right of the graph is a legend labeled \u201cICU\u201d showing that pink indicates \u201cno\u201d and blue indicates \u201cyes.\u201d For \u201cCalcifediol,\u201d the blue portion of the bar goes to approximately 0.05 and the pink portion goes the rest of the way to 1. For \u201cUntreated,\u201d the blue portion of the bar goes to approximately 0.5 and the pink portion goes the rest of the way to 1.\" width=\"902\" height=\"821\" \/><\/div>\r\n<\/div>\r\n<div id=\"bp-page-2\" class=\"page\" data-page-number=\"2\" data-loaded=\"true\">\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 11<\/h3>\r\n11) If the calcifedioltreatment had no effect on the severity of COVID-19 symptoms, how would you expect this graph to appear?Explain.\r\n\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">If the calcifediol treatment had no effect on the severity of COVID-19 symptoms, each patient would have either been admitted to the ICU or not regardless of the treatment to which they were assigned. In other words, the 13 patients admitted to the ICU who were in the group that did not receive calcifediol would have ended up being admitted to the ICU even if they had received calcifediol. While it is possible that calcifediol does not help lower the risk of admission to the ICU for COVID-19 patients and the researchers were unlucky and just happened to \u201cdraw\u201d more of the subjects who were going to be admitted to the ICU into the untreated group, we would like to determine whether this outcome is probable. If 14 out of the 76 patients were going to be admitted to the ICU no matter what, we would have expected around the same proportion of those patients to end up in each group. The key question is how unlikely the observed difference in proportions of patients admitted to the ICU is by the random assignment process alone.We will answer this question by replicating the random assignment process all over again, under the assumption that calcifediol does not decrease the risk of ICU admission. We\u2019ll start with 14 ICU admissions and 62 ICU non-admissions and then randomly assign 50 of these 76 subjects to the calcifediol-treated group and the other 26 to the calcifediol-untreated group.<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 12<\/h3>\r\n<div class=\"textLayer\">12) Go to the DCMP Association Between Two Categorical Variables tool at https:\/\/dcmathpathways.shinyapps.io\/Association_Categorical\/.\u2022Under \u201cData Entry &amp; Descriptive Statistics:\u201doSelect \u201cContingency Table\u201d under \u201cEnter Data.\u201doType \u201cICU\u201d for the row variable, with \u201cAdmitted\u201d and \u201cNot admitted\u201d for the category labels.oType \u201cGroup\u201d for the columnvariable, with \u201cTreated\u201d and \u201cUntreated\u201d as the category labels.oEnter the contingency table completed in Question 7.\u2022Now select \u201cPermutation Distribution\u201d in the top right.You should see the contingency table you entered as the \u201cObserved Contingency Table.\u201d Check \u201cICU\u201d under \u201cPermutate Labels of\u201dandthen generate a single permutation of the data.<\/div>\r\n<div class=\"textLayer\">Part A:The shuffled counts in each group are shown under \u201cDataset from last permutation\u201don the right. Copy these resultsinto thefollowing2\u00d72 table.<\/div>\r\n<div>\r\n<table>\r\n<tbody>\r\n<tr>\r\n<td><\/td>\r\n<td>Treated with calcifediol<\/td>\r\n<td>Untreated with calcifediol<\/td>\r\n<td>Total<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Admitted to ICU<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Not admitted to ICU<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Total<\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<\/div>\r\n<div class=\"textLayer\">Part B:Calculate theshuffled difference in proportionsof ICU admissions between the two groups (use calcifediol-treated \u2013calcifediol-untreatedas the order of subtraction) in your simulated table from Part A.Hint: This should match the difference in proportions shown in the toolunder \u201cDataset from last permutation.\u201d<\/div>\r\n<div class=\"textLayer\">Part C:Is the result of this simulated random assignment as \u201cextreme\u201d as the actual results that the researchers obtained? That is, did one or fewer of the ICU admissions end up in the calcifediol-treated group?<\/div>\r\n<div class=\"textLayer\">Part D:Combine your results with those from your classmates, producing a well-labeled dotplot. In what proportion of the simulated-random assignments were one or fewer of the ICU admissions assigned to the calcifediol-treated group?<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>\r\n<div id=\"bp-page-6\" class=\"page\" data-page-number=\"6\" data-loaded=\"true\">\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 13<\/h3>\r\n<div class=\"textLayer\">13) We can use the tool to simulate 1,000s of random assignments. Click \u201cReset,\u201d select \u201c1,000\u201dfor \u201cNumber of permutations of the original data,\u201d and then click \u201cGenerate Permutation(s).\u201d<\/div>\r\n<div class=\"textLayer\">Part A: Examine the histogram of shuffled differences in proportions. Where is this plot centered? Explain.<\/div>\r\n<div class=\"textLayer\">Part B: Based on the histogram of shuffled differences in proportions, does it seem like the actual experimental result (only oneICU admission in the calcifediol-treated group) would besurprising to arise solely from the random assignment process under the assumption that calcifediolhas no effect on the severity of COVID-19 symptoms? Explain.<\/div>\r\n<div class=\"textLayer\">Part C: Select \u201cShow statistical summary of permutation distribution\u201d under \u201cOptions.\u201d The tool will display the number and percentageof shuffled differences in proportions that are equal to or less than the one observed in the actual data at the bottom of the page. What percentageof the simulated randomizations resulted in a difference in proportions less than or equal to the one observed in the actual data?<\/div>\r\n<\/div>\r\n<\/div>\r\n<div class=\"textLayer\">You have just conducted what is called a randomization test (also sometimes called a permutation test)of the hypotheses you stated in Question 6, and your answer toQuestion 13, Part Cis an approximate P-value for this test. A P-value is the probability of obtaining the actual results or something more extreme, under the assumption of the null hypothesis. This can be approximated by simulating many, many randomizations under the null hypothesis and calculating the proportion of randomizations that produce results like ours\u2014or something more extreme.<\/div>\r\n<div class=\"textLayer\">\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Question 14<\/h3>\r\n<div class=\"textLayer\">14) Consider your approximate P-value from Question 13, Part C.<\/div>\r\n<div class=\"textLayer\">Part A:Is this P-value small enough so that you would consider the actualoutcomesurprising(or more extreme) under the null model that calcifediolhas no effect on the severity of COVID-19 symptoms? Explain.<\/div>\r\n<div class=\"textLayer\">Part B:Would you say that the researchers obtained strong evidence that the risk of ICU admission decreases when treated with calcifediol? Explain your reasoning based on your simulation results, including a discussion of the purpose of the simulation process and what information it revealed to help you answer this research question.<\/div>\r\n<div class=\"textLayer\">Part C:Are you willing to draw a cause-and-effect conclusion about calcifediol-treatment and ICU admissionbased on these results? Justify your answer based on the design of the study.<\/div>\r\n<div class=\"textLayer\">Part D:Are you willing to generalize these conclusions to all COVID-19 patients? Justify your answer based on the design of the study.<\/div>\r\n<\/div>\r\n<\/div>\r\n<\/div>","rendered":"<div id=\"bp-page-1\" class=\"page\" data-page-number=\"1\" data-loaded=\"true\">\n<div class=\"textLayer\">During the COVID-19 pandemic, clinical trials were conducted to determine which factors may help reduce COVID-19 risk. One vitamin in particular, vitamin D, looked promising for reducing this risk. News headlines such as \u201cVitamin D Can Help Reduce COVID-19 Risks: Here\u2019s How\u201d<a class=\"footnote\" title=\"Curley, B. (2020, September 13). Vitamin D can help reduce COVID-19 risks: Here\u2019s how. Healthline.https:\/\/www.healthline.com\/health-news\/vitamin-d-can-help-reduce-covid19-risks2Castillo, M.E., Costa, L. M.E., Barrios, J. M.V., D\u00edaz, J. F.A., Miranda, J.L., Bouillon, R., &amp; Gomez, J. M.Q.(2020, October). Effect of calcifediol treatment and best available therapy versus best available therapy on intensive care unit admission and mortality among patients hospitalized for COVID-19: A pilot randomized clinical study. Journal of Steroid Biochemistry and Molecular Biology, 203. https:\/\/doi.org\/10.1016\/j.jsbmb.2020.105751Credit:iStock\/tungphoto\" id=\"return-footnote-5587-1\" href=\"#footnote-5587-1\" aria-label=\"Footnote 1\"><sup class=\"footnote\">[1]<\/sup><\/a> started appearing in Fall 2020. But were these headlines valid? In this in-class activity, we will examine data from one study designed to determine if vitamin D may reduce the severity of illness if one does test positive for COVID-19.2<\/div>\n<div><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-2212\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/5738\/2022\/01\/27024552\/Picture144-300x200.jpg\" alt=\"A pile of clear yellow pills.\" width=\"920\" height=\"613\" \/><\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 1<\/h3>\n<p>1) How would you design a study to determine if vitamin D reducesthe risk of intensive care unit (ICU) admission due toCOVID-19?<\/p>\n<\/div>\n<\/div>\n<div class=\"textLayer\">In a small, randomized clinical trialconducted in Spain, 76 patients hospitalized with COVID-19 were randomized to either receive a calcifediol (vitamin D) treatment or not. All the patients were treated with the standard intervention for COVID-19, which at the time was a combination of hydroxychloroquine and azithromycin. Researchers recorded whether each patient was admitted to the ICU or not.<\/div>\n<\/div>\n<div id=\"bp-page-2\" class=\"page\" data-page-number=\"2\" data-loaded=\"true\">\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 2<\/h3>\n<div class=\"textLayer\">2) What variable distinguishesthe two groups comparedin this study?a)Whether the patient was hospitalized with COVID-19 or notb)Whether the patient received the calcifedioltreatment or notc)Whether the patient was admitted to the ICU or notd)Whether the patient was treated with the standard intervention or not<\/div>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 3<\/h3>\n<div class=\"textLayer\">3) What is the variable of interestin this study?<\/div>\n<div class=\"textLayer\">a) Whether the patient was hospitalized with COVID-19 or not<\/div>\n<div class=\"textLayer\">b) Whether the patient received the calcifedioltreatment or not<\/div>\n<div class=\"textLayer\">c) Whether the patient was admitted to the ICU or not<\/div>\n<div class=\"textLayer\">d) Whether the patient was treated with the standard intervention or not<\/div>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 4<\/h3>\n<div class=\"textLayer\">4) Is this study a randomized experiment or an observational study?<\/div>\n<div class=\"textLayer\">a) Randomized experiment, since patients were randomly assigned to receive calcifediolor not<\/div>\n<div class=\"textLayer\">b) Randomized experiment, since there were two different treatments<\/div>\n<div class=\"textLayer\">c) Observational study, since whether the patient was admitted to the ICU was not randomly assigned<\/div>\n<div class=\"textLayer\">d) Observational study, since patients were not randomly selected from the population of all COVID-19 infected individuals<\/div>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 5<\/h3>\n<div class=\"textLayer\">5) Before the data are collected, you should state the research hypothesis.What were the researchers hoping to show in this study?<\/div>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 6<\/h3>\n<p>6) Let \ud835\udc5d\ud835\udc36\ud835\udc4e\ud835\udc59\ud835\udc50be the probability of admission to the ICU for COVID-19 patients on the calcifedioltreatment and \ud835\udc5d\ud835\udc48\ud835\udc5b\ud835\udc61\ud835\udc5fbe the probability of admission to the ICU for COVID-19 patients not treated with calcifediol. State the null and alternative hypotheses in terms of these parameters.<\/p>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 7<\/h3>\n<p>7) Of the 50 patients randomly assigned to the calcifedioltreatment, only one was admitted totheICU, whereas 13 of the 26 patients who did not receive the calcifedioltreatment were admitted to the ICU.Organize these results into thefollowing2\u00d72 table.<\/p>\n<table>\n<tbody>\n<tr>\n<td><\/td>\n<td>Treated with calcifediol<\/td>\n<td>Untreated with calcifediol<\/td>\n<td>Total<\/td>\n<\/tr>\n<tr>\n<td>Admitted to ICU<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>Not admitted to ICU<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>Total<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 8<\/h3>\n<p>8) What proportion of the 76 patients in the study were admitted to the ICU?<\/p>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 9<\/h3>\n<p>9) What proportion of the patients on the calcifedioltreatment were admitted to the ICU? What proportion of the untreated patients were admitted to the ICU? What isthe appropriate statistical notation for each of these values?<\/p>\n<\/div>\n<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 10<\/h3>\n<div class=\"textLayer\">10) Calculate the difference in proportionsof ICU admissions between the two groups (use calcifediol-treated \u2013calcifediol-untreatedas the order of subtraction).<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div>\n<div class=\"textLayer\">The following is a segmented bar graph of the data.<\/div>\n<div><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3086\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/5738\/2022\/01\/11200738\/Picture1461-300x273.png\" alt=\"A vertical stacked bar chart. On the x-axis, it is labeled \u201cTreatment\u201d and on the y-axis, it is labeled \u201cProportion.\u201d To the right of the graph is a legend labeled \u201cICU\u201d showing that pink indicates \u201cno\u201d and blue indicates \u201cyes.\u201d For \u201cCalcifediol,\u201d the blue portion of the bar goes to approximately 0.05 and the pink portion goes the rest of the way to 1. For \u201cUntreated,\u201d the blue portion of the bar goes to approximately 0.5 and the pink portion goes the rest of the way to 1.\" width=\"902\" height=\"821\" \/><\/div>\n<\/div>\n<div id=\"bp-page-2\" class=\"page\" data-page-number=\"2\" data-loaded=\"true\">\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 11<\/h3>\n<p>11) If the calcifedioltreatment had no effect on the severity of COVID-19 symptoms, how would you expect this graph to appear?Explain.<\/p>\n<\/div>\n<\/div>\n<div class=\"textLayer\">If the calcifediol treatment had no effect on the severity of COVID-19 symptoms, each patient would have either been admitted to the ICU or not regardless of the treatment to which they were assigned. In other words, the 13 patients admitted to the ICU who were in the group that did not receive calcifediol would have ended up being admitted to the ICU even if they had received calcifediol. While it is possible that calcifediol does not help lower the risk of admission to the ICU for COVID-19 patients and the researchers were unlucky and just happened to \u201cdraw\u201d more of the subjects who were going to be admitted to the ICU into the untreated group, we would like to determine whether this outcome is probable. If 14 out of the 76 patients were going to be admitted to the ICU no matter what, we would have expected around the same proportion of those patients to end up in each group. The key question is how unlikely the observed difference in proportions of patients admitted to the ICU is by the random assignment process alone.We will answer this question by replicating the random assignment process all over again, under the assumption that calcifediol does not decrease the risk of ICU admission. We\u2019ll start with 14 ICU admissions and 62 ICU non-admissions and then randomly assign 50 of these 76 subjects to the calcifediol-treated group and the other 26 to the calcifediol-untreated group.<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 12<\/h3>\n<div class=\"textLayer\">12) Go to the DCMP Association Between Two Categorical Variables tool at https:\/\/dcmathpathways.shinyapps.io\/Association_Categorical\/.\u2022Under \u201cData Entry &amp; Descriptive Statistics:\u201doSelect \u201cContingency Table\u201d under \u201cEnter Data.\u201doType \u201cICU\u201d for the row variable, with \u201cAdmitted\u201d and \u201cNot admitted\u201d for the category labels.oType \u201cGroup\u201d for the columnvariable, with \u201cTreated\u201d and \u201cUntreated\u201d as the category labels.oEnter the contingency table completed in Question 7.\u2022Now select \u201cPermutation Distribution\u201d in the top right.You should see the contingency table you entered as the \u201cObserved Contingency Table.\u201d Check \u201cICU\u201d under \u201cPermutate Labels of\u201dandthen generate a single permutation of the data.<\/div>\n<div class=\"textLayer\">Part A:The shuffled counts in each group are shown under \u201cDataset from last permutation\u201don the right. Copy these resultsinto thefollowing2\u00d72 table.<\/div>\n<div>\n<table>\n<tbody>\n<tr>\n<td><\/td>\n<td>Treated with calcifediol<\/td>\n<td>Untreated with calcifediol<\/td>\n<td>Total<\/td>\n<\/tr>\n<tr>\n<td>Admitted to ICU<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>Not admitted to ICU<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>Total<\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<div class=\"textLayer\">Part B:Calculate theshuffled difference in proportionsof ICU admissions between the two groups (use calcifediol-treated \u2013calcifediol-untreatedas the order of subtraction) in your simulated table from Part A.Hint: This should match the difference in proportions shown in the toolunder \u201cDataset from last permutation.\u201d<\/div>\n<div class=\"textLayer\">Part C:Is the result of this simulated random assignment as \u201cextreme\u201d as the actual results that the researchers obtained? That is, did one or fewer of the ICU admissions end up in the calcifediol-treated group?<\/div>\n<div class=\"textLayer\">Part D:Combine your results with those from your classmates, producing a well-labeled dotplot. In what proportion of the simulated-random assignments were one or fewer of the ICU admissions assigned to the calcifediol-treated group?<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"bp-page-6\" class=\"page\" data-page-number=\"6\" data-loaded=\"true\">\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 13<\/h3>\n<div class=\"textLayer\">13) We can use the tool to simulate 1,000s of random assignments. Click \u201cReset,\u201d select \u201c1,000\u201dfor \u201cNumber of permutations of the original data,\u201d and then click \u201cGenerate Permutation(s).\u201d<\/div>\n<div class=\"textLayer\">Part A: Examine the histogram of shuffled differences in proportions. Where is this plot centered? Explain.<\/div>\n<div class=\"textLayer\">Part B: Based on the histogram of shuffled differences in proportions, does it seem like the actual experimental result (only oneICU admission in the calcifediol-treated group) would besurprising to arise solely from the random assignment process under the assumption that calcifediolhas no effect on the severity of COVID-19 symptoms? Explain.<\/div>\n<div class=\"textLayer\">Part C: Select \u201cShow statistical summary of permutation distribution\u201d under \u201cOptions.\u201d The tool will display the number and percentageof shuffled differences in proportions that are equal to or less than the one observed in the actual data at the bottom of the page. What percentageof the simulated randomizations resulted in a difference in proportions less than or equal to the one observed in the actual data?<\/div>\n<\/div>\n<\/div>\n<div class=\"textLayer\">You have just conducted what is called a randomization test (also sometimes called a permutation test)of the hypotheses you stated in Question 6, and your answer toQuestion 13, Part Cis an approximate P-value for this test. A P-value is the probability of obtaining the actual results or something more extreme, under the assumption of the null hypothesis. This can be approximated by simulating many, many randomizations under the null hypothesis and calculating the proportion of randomizations that produce results like ours\u2014or something more extreme.<\/div>\n<div class=\"textLayer\">\n<div class=\"textbox key-takeaways\">\n<h3>Question 14<\/h3>\n<div class=\"textLayer\">14) Consider your approximate P-value from Question 13, Part C.<\/div>\n<div class=\"textLayer\">Part A:Is this P-value small enough so that you would consider the actualoutcomesurprising(or more extreme) under the null model that calcifediolhas no effect on the severity of COVID-19 symptoms? Explain.<\/div>\n<div class=\"textLayer\">Part B:Would you say that the researchers obtained strong evidence that the risk of ICU admission decreases when treated with calcifediol? Explain your reasoning based on your simulation results, including a discussion of the purpose of the simulation process and what information it revealed to help you answer this research question.<\/div>\n<div class=\"textLayer\">Part C:Are you willing to draw a cause-and-effect conclusion about calcifediol-treatment and ICU admissionbased on these results? Justify your answer based on the design of the study.<\/div>\n<div class=\"textLayer\">Part D:Are you willing to generalize these conclusions to all COVID-19 patients? Justify your answer based on the design of the study.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<hr class=\"before-footnotes clear\" \/><div class=\"footnotes\"><ol><li id=\"footnote-5587-1\">Curley, B. (2020, September 13). Vitamin D can help reduce COVID-19 risks: Here\u2019s how. Healthline.https:\/\/www.healthline.com\/health-news\/vitamin-d-can-help-reduce-covid19-risks2Castillo, M.E., Costa, L. M.E., Barrios, J. M.V., D\u00edaz, J. F.A., Miranda, J.L., Bouillon, R., &amp; Gomez, J. M.Q.(2020, October). Effect of calcifediol treatment and best available therapy versus best available therapy on intensive care unit admission and mortality among patients hospitalized for COVID-19: A pilot randomized clinical study. Journal of Steroid Biochemistry and Molecular Biology, 203. https:\/\/doi.org\/10.1016\/j.jsbmb.2020.105751Credit:iStock\/tungphoto <a href=\"#return-footnote-5587-1\" class=\"return-footnote\" aria-label=\"Return to footnote 1\">&crarr;<\/a><\/li><\/ol><\/div>","protected":false},"author":23592,"menu_order":68,"template":"","meta":{"_candela_citation":"[]","CANDELA_OUTCOMES_GUID":"","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-5587","chapter","type-chapter","status-publish","hentry"],"part":5563,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapters\/5587","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/wp\/v2\/users\/23592"}],"version-history":[{"count":3,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapters\/5587\/revisions"}],"predecessor-version":[{"id":5678,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapters\/5587\/revisions\/5678"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/parts\/5563"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapters\/5587\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/wp\/v2\/media?parent=5587"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/pressbooks\/v2\/chapter-type?post=5587"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/wp\/v2\/contributor?post=5587"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/lumen-danacenter-statsmockup\/wp-json\/wp\/v2\/license?post=5587"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}