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Meta analysis Conducting Meta-Analyses in R
Whatis meta-analysis? Science is a cumulative process . Therefore, it is not surprising that one can often find dozens and sometimes hundreds of studies addressing the same basic question.  Researches trying to aggregate and synthesize the literature on a particular topic are increasinglyconducting meta-analyses
Why do we need meta-analyses? Literature expansion in research Allows researchers the ability to statistically combine countless studies to increase power Allows us to measure “how much” of a relationship exists, rather than just whether a relationship exists Allows us to account for the variation in results between similar studies based on procedural characteristics of individual studies
What is meta-analysis? A standardized secondary analysis of primary data results from different studies that share same hypothesis A quantitative aggregation of findings during a research synthesis Calculating a standardized effect size for multiple studies
Effect Size in MA Effect size makes meta-analysis possible it is the “dependent variable” it standardizes findings across studies such that they can be directly compared Any standardized index can be an “effect size” (e.g., standardized mean difference, correlation coefficient, odds-ratio) as long as: It is comparable across studies  It represents the magnitude and direction of the relationship of interest It is independent of sample size Different meta-analyses may use different effect size indices
Examples of Different Types of Effect Sizes: Standardized Mean Difference (continuous outcome) group contrast research treatment groups naturally occurring groups Odds-Ratio (dichotomous outcome) group contrast research treatment groups naturally occurring groups Correlation Coefficient association between variables research
Statistical significance Turns out a lot of researchers do not know what precisely p < .05 actually means Cohen (1994) Article: The earth is round (p<.05) What it means: "Given that H0 is true, what is the probability of these (or more extreme) data?” Trouble is most people want to know "Given these data, what is the probability that H0 is true?"
Always a difference With most analyses we commonly define the null hypothesis as ‘no relationship’ between our predictor and outcome (i.e. the ‘nil’ hypothesis) With sample data, differences between groups always exist (at some level of precision), correlations are always non-zero. Obtaining statistical significance can be seen as just a matter of sample size Furthermore, the importance and magnitude of an effect are not accurately reflected  because of the role of sample size in probability value attained
What should we be doing? We want to make sure we have looked hard enough for the difference – power analysis Figure out how big the thing we are looking for is – effect size Effect size refers to the magnitude of the impact of some variable on another
Examples of Different Types of Effect Sizes: Standardized Mean Difference (continuous outcome) group contrast research treatment groups naturally occurring groups Odds-Ratio (dichotomous outcome) group contrast research treatment groups naturally occurring groups Correlation Coefficient association between variables research
The Standardized Mean Difference Represents a standardized group comparison on a continuous outcome measure.  Uses the pooled standard deviation (some situations use control group standard deviation).  Commonly called “Cohen’s d” or occasionally “Hedges’ g”.
The Correlation Coefficient Represents the strength of association between two continuous measures. Generally reported directly as “r” (the Pearson product moment coefficient).
Odds-Ratios The Odds-Ratio is based on a 2 by 2 contingency table, such as the one below.  The Odds-Ratio is the odds of success in the treatment group relative to the odds of success in the control group.
Converting results into a common metric Can convert p-values t, F, etc. into the standardized effect size metric being used in the meta-analysis (e.g., d, r)
Interpreting Effect Size Results Cohen’s “Rules-of-Thumb” standardized mean difference effect size small = 0.20 medium = 0.50 large = 0.80 correlation coefficient small = 0.10 medium = 0.25 large = 0.40
Cohen’s d (Hedge’s g) Defined d for the one-sample case
Cohen’s d Now compare to the one-sample t-statistic So This shows how the test statistic (and its observed p-value) is in part determined by the effect size, but is confounded with sample size This means small effects may be statistically significant in many studies (esp. social sciences)
Example Average number of times MGEC students curse in the presence of others out of total frustration over the course of a day Currently taking R course vs. not Data:
Example Find the pooled variance and sd Equal groups so just average the two variances such that  and sp2 = 6.25
Odds ratios Especially good for 2X2 tables Take a ratio of two outcomes Although neither gets the majority, we could say which they were more likely to vote for respectively Odds Clinton among Dems= 564/636 = .887 Odds McCain among Reps= 450/550 = .818 .887/.818 (the odds ratio) means they’d be 1.08 times as likely to vote Clinton among democrats than McCain among republicans However, the 95% CI for the odds ratio is: .92 to 1.28
Voting Method Voting method was commonly employed for aggregation of studies before the conception of meta-analysis   Procedure:  Studies with a dependent variable and a specific independent variable  are examined Studies are dichotomized as either statistically significant or not statistically significant Classification with higher tally is considered to be the “true” relationship between variables
Voting Method Researcher A is conducting a study on the effects of RtI on a group of 1st graders’ fluency rate. In A’s study, which has a sample size of n=180, 110 children are given RtI and 70 children are given traditional instruction.  After 12 weeks of instruction, children are dichotomized as either “pass” or “fail” on a reading measure.  The improvement rate for the RtI group is .45 vs. .43 for the control group.
Voting Method Researcher B conducts the same study at a different site In B’s study, which has a sample size of n=230, 90 children receive RtI and 140 receive traditional instruction  Again the improvement rate for the RtI group is .67 vs. .64 for the control group.  That’s 2-0 for the experimental group!
Aggregation of Raw Data Suppose another researcher aggregates the data from the same studies by summing the raw data instead of employing the voting method  Add the number of subjects in both studies that received treatment and control: n=200 received RtI and n=210 received traditional instruction When dichotomized into “pass” or “fail”, the improvement rate for the treatment group is now .55 vs. 0.57 for the control group!  This is known as Simpson’s Paradox
Voting Method Flaws: Bias in favor of large-sample studies  Why is this a problem?  No weighting of sample size Tells us nothing about strength of relationship Does not control for variation between studies
Methodological Considerations Determine the statistic of interest to calculate individual study effect sizes: ,[object Object]
What do the preponderance of your studies report as an effect size, if any?
Based on this information you will choose one standardized effect size: r, d, or odds-ratio in your meta-analysis,[object Object]
Calculating Effect Sizes d-index formula: , where:
Calculating Effect Sizes So, if you were to calculate the standardized mean difference in the fluency rate of the following two groups in an RtI study, what would you get as the effect size? Group 1 (experimental): M1 = 80, SD1 =10, n1= 250 Group 2 (control): M2 = 65, SD2 = 20, n2=230 Effect size = ? What if you had three groups?
Calculating Effect Sizes What if the means and SDs aren’t reported and you only have a t-value? What if you have the  F-value for two means? Formula for d-index when the F-value of two means is reported: dferror = (n1+n2-2)
Calculating Effect Sizes r-index The correlation coefficient tells you about the strength of the relationship between two variables Most appropriate metric for expressing an effect size when interested in the relationship strength of two continuous variables Most common in correlational studies Usually reported when appropriate EX: relationship between years of schooling and yearly salary
Calculating Effect Sizes What if you only have a t-value? Formula for r-index when only t-value is reported:
Calculating Effect Sizes Think back to the previous RtI study on slide 16. The effect size was d = 0.96. The difference between the control/experimental group. Suppose you want to convert this d-index into an r-index: , where  ,[object Object]
r = ?
What could this correlation represent?Or vice-versa:
Calculating Effect Sizes Odds-Ratio (OR) Applicable when both variables are dichotomous The relationship between two sets of odds EX: Suppose a study measures the effects of RtI on whether students in two groups (e.g., experimental/control ) “pass” or “fail” a math test.
Calculating Effect Sizes Of n=80 in RtI, the ratio of passing is 15 to 1. Of n =65 in control, the ratio of passing is 1.6 to 1. Calculate the odds ratio: 				OR = ad/bc= ?
Combining Effect Sizes Once individual study effect sizes have been calculated, the next step involves combining them to provide an average effect size. You must weight the individual effect sizes. What do you base this weight on?
Combining Effect Sizes Suppose you have 7 d-indexes and group ns that compares the effect of homework vs. no homework on a measure of academic achievement:
Combining Effect Sizes Step One: Weighting Formula: EX: Study 1 	wi = 2(259+ 265) 259* 265/2(259+ 265)2+ 259*    265* .022= 130.98
Combining Effect Sizes Calculations:
Combining Effect Sizes Step Two: Multiply each weighted effect size and original d-index Formula:  diwi EX: What is the answer for Study 1?
Combining Effect Sizes Calculations:
Combining Effect Sizes Step Three: Divide the sum of these products by the sum of the weights. Formula: EX: d. = 62.56/544.27 = +.115 (average ES)
Combining Effect Sizes Step Four: Computing Confidence Intervals Formula: EX:  Thus, we expect 95% of estimates of this effect to fall between .031 and .199. Do we reject the null?
Combining Effect Sizes Suppose that you have 6 r-indexes and ns that show the relationship between the amount students spend on homework and their score on an achievement test. Step One: Transform the r-indexes into a z-scores because as r gets larger the distribution gets more skewed. Formula:
Combining Effect Sizes Step Two: Weighting Formula: ni - 3 EX: Study 1 	3,505-3 = 3,502
Combining Effect Sizes Calculations:
Combining Effect Sizes Step Three: multiply the weight and the effect size (i.e., z-score) Formula: (ni – 3) zi EX: Study 1 		(3,502).06 = 210.12
Combining Effect Sizes Calculations:
Combining Effect Sizes  Step Four: Divide the sum of these products by the sum of the weights. Formula: EX: z. = 5462.97/26,372 = +.207 (average ES)
Combining Effect Sizes Step Five: Computing Confidence Intervals Formula: EX: CIz95% = .207 ± 1.96/ √26,372 			 = .207 ± .012 ,[object Object],[object Object]
Funnel Plots Funnel plots are a device for checking for publication bias. ,[object Object]
As sample size increases, the width of the confidence interval should decrease.
Result should be located in a symmetric, triangular area centered on the overall effect for all studies.,[object Object]
The unopposed positive studies will shift the apparent treatment effect (blue line) towards a larger effect size than it really is.,[object Object]
If most studies are similar to each other and show a similar result (low heterogeneity), this increases confidence that the effect being measured is real.
If results from different studies are vastly different from each other, this suggests that each study is measuring something slightly different from the other studies.
High heterogeneity can be due to:
Random chance
Differences in patient populations between studies
Differences in treatment
Differences in assessing outcomes
Other differences in study methodology,[object Object]
Forestplots
Reading Forest Plots  ,[object Object]
The size of the square is proportional to the number of subjects in the group.
The horizontal lines show the 95% confidence interval.
The black diamonds represent the combined results for each subgroup.
Note that this analysis used a fixed effects model.,[object Object]

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Meta analysis with R

  • 1. Meta analysis Conducting Meta-Analyses in R
  • 2. Whatis meta-analysis? Science is a cumulative process . Therefore, it is not surprising that one can often find dozens and sometimes hundreds of studies addressing the same basic question. Researches trying to aggregate and synthesize the literature on a particular topic are increasinglyconducting meta-analyses
  • 3. Why do we need meta-analyses? Literature expansion in research Allows researchers the ability to statistically combine countless studies to increase power Allows us to measure “how much” of a relationship exists, rather than just whether a relationship exists Allows us to account for the variation in results between similar studies based on procedural characteristics of individual studies
  • 4. What is meta-analysis? A standardized secondary analysis of primary data results from different studies that share same hypothesis A quantitative aggregation of findings during a research synthesis Calculating a standardized effect size for multiple studies
  • 5. Effect Size in MA Effect size makes meta-analysis possible it is the “dependent variable” it standardizes findings across studies such that they can be directly compared Any standardized index can be an “effect size” (e.g., standardized mean difference, correlation coefficient, odds-ratio) as long as: It is comparable across studies It represents the magnitude and direction of the relationship of interest It is independent of sample size Different meta-analyses may use different effect size indices
  • 6. Examples of Different Types of Effect Sizes: Standardized Mean Difference (continuous outcome) group contrast research treatment groups naturally occurring groups Odds-Ratio (dichotomous outcome) group contrast research treatment groups naturally occurring groups Correlation Coefficient association between variables research
  • 7. Statistical significance Turns out a lot of researchers do not know what precisely p < .05 actually means Cohen (1994) Article: The earth is round (p<.05) What it means: "Given that H0 is true, what is the probability of these (or more extreme) data?” Trouble is most people want to know "Given these data, what is the probability that H0 is true?"
  • 8. Always a difference With most analyses we commonly define the null hypothesis as ‘no relationship’ between our predictor and outcome (i.e. the ‘nil’ hypothesis) With sample data, differences between groups always exist (at some level of precision), correlations are always non-zero. Obtaining statistical significance can be seen as just a matter of sample size Furthermore, the importance and magnitude of an effect are not accurately reflected because of the role of sample size in probability value attained
  • 9. What should we be doing? We want to make sure we have looked hard enough for the difference – power analysis Figure out how big the thing we are looking for is – effect size Effect size refers to the magnitude of the impact of some variable on another
  • 10. Examples of Different Types of Effect Sizes: Standardized Mean Difference (continuous outcome) group contrast research treatment groups naturally occurring groups Odds-Ratio (dichotomous outcome) group contrast research treatment groups naturally occurring groups Correlation Coefficient association between variables research
  • 11. The Standardized Mean Difference Represents a standardized group comparison on a continuous outcome measure. Uses the pooled standard deviation (some situations use control group standard deviation). Commonly called “Cohen’s d” or occasionally “Hedges’ g”.
  • 12. The Correlation Coefficient Represents the strength of association between two continuous measures. Generally reported directly as “r” (the Pearson product moment coefficient).
  • 13. Odds-Ratios The Odds-Ratio is based on a 2 by 2 contingency table, such as the one below. The Odds-Ratio is the odds of success in the treatment group relative to the odds of success in the control group.
  • 14. Converting results into a common metric Can convert p-values t, F, etc. into the standardized effect size metric being used in the meta-analysis (e.g., d, r)
  • 15. Interpreting Effect Size Results Cohen’s “Rules-of-Thumb” standardized mean difference effect size small = 0.20 medium = 0.50 large = 0.80 correlation coefficient small = 0.10 medium = 0.25 large = 0.40
  • 16. Cohen’s d (Hedge’s g) Defined d for the one-sample case
  • 17. Cohen’s d Now compare to the one-sample t-statistic So This shows how the test statistic (and its observed p-value) is in part determined by the effect size, but is confounded with sample size This means small effects may be statistically significant in many studies (esp. social sciences)
  • 18. Example Average number of times MGEC students curse in the presence of others out of total frustration over the course of a day Currently taking R course vs. not Data:
  • 19. Example Find the pooled variance and sd Equal groups so just average the two variances such that and sp2 = 6.25
  • 20. Odds ratios Especially good for 2X2 tables Take a ratio of two outcomes Although neither gets the majority, we could say which they were more likely to vote for respectively Odds Clinton among Dems= 564/636 = .887 Odds McCain among Reps= 450/550 = .818 .887/.818 (the odds ratio) means they’d be 1.08 times as likely to vote Clinton among democrats than McCain among republicans However, the 95% CI for the odds ratio is: .92 to 1.28
  • 21. Voting Method Voting method was commonly employed for aggregation of studies before the conception of meta-analysis Procedure: Studies with a dependent variable and a specific independent variable are examined Studies are dichotomized as either statistically significant or not statistically significant Classification with higher tally is considered to be the “true” relationship between variables
  • 22. Voting Method Researcher A is conducting a study on the effects of RtI on a group of 1st graders’ fluency rate. In A’s study, which has a sample size of n=180, 110 children are given RtI and 70 children are given traditional instruction. After 12 weeks of instruction, children are dichotomized as either “pass” or “fail” on a reading measure. The improvement rate for the RtI group is .45 vs. .43 for the control group.
  • 23. Voting Method Researcher B conducts the same study at a different site In B’s study, which has a sample size of n=230, 90 children receive RtI and 140 receive traditional instruction Again the improvement rate for the RtI group is .67 vs. .64 for the control group. That’s 2-0 for the experimental group!
  • 24. Aggregation of Raw Data Suppose another researcher aggregates the data from the same studies by summing the raw data instead of employing the voting method Add the number of subjects in both studies that received treatment and control: n=200 received RtI and n=210 received traditional instruction When dichotomized into “pass” or “fail”, the improvement rate for the treatment group is now .55 vs. 0.57 for the control group! This is known as Simpson’s Paradox
  • 25. Voting Method Flaws: Bias in favor of large-sample studies Why is this a problem? No weighting of sample size Tells us nothing about strength of relationship Does not control for variation between studies
  • 26.
  • 27. What do the preponderance of your studies report as an effect size, if any?
  • 28.
  • 29. Calculating Effect Sizes d-index formula: , where:
  • 30. Calculating Effect Sizes So, if you were to calculate the standardized mean difference in the fluency rate of the following two groups in an RtI study, what would you get as the effect size? Group 1 (experimental): M1 = 80, SD1 =10, n1= 250 Group 2 (control): M2 = 65, SD2 = 20, n2=230 Effect size = ? What if you had three groups?
  • 31. Calculating Effect Sizes What if the means and SDs aren’t reported and you only have a t-value? What if you have the F-value for two means? Formula for d-index when the F-value of two means is reported: dferror = (n1+n2-2)
  • 32. Calculating Effect Sizes r-index The correlation coefficient tells you about the strength of the relationship between two variables Most appropriate metric for expressing an effect size when interested in the relationship strength of two continuous variables Most common in correlational studies Usually reported when appropriate EX: relationship between years of schooling and yearly salary
  • 33. Calculating Effect Sizes What if you only have a t-value? Formula for r-index when only t-value is reported:
  • 34.
  • 35. r = ?
  • 36. What could this correlation represent?Or vice-versa:
  • 37. Calculating Effect Sizes Odds-Ratio (OR) Applicable when both variables are dichotomous The relationship between two sets of odds EX: Suppose a study measures the effects of RtI on whether students in two groups (e.g., experimental/control ) “pass” or “fail” a math test.
  • 38. Calculating Effect Sizes Of n=80 in RtI, the ratio of passing is 15 to 1. Of n =65 in control, the ratio of passing is 1.6 to 1. Calculate the odds ratio: OR = ad/bc= ?
  • 39. Combining Effect Sizes Once individual study effect sizes have been calculated, the next step involves combining them to provide an average effect size. You must weight the individual effect sizes. What do you base this weight on?
  • 40. Combining Effect Sizes Suppose you have 7 d-indexes and group ns that compares the effect of homework vs. no homework on a measure of academic achievement:
  • 41. Combining Effect Sizes Step One: Weighting Formula: EX: Study 1 wi = 2(259+ 265) 259* 265/2(259+ 265)2+ 259* 265* .022= 130.98
  • 42. Combining Effect Sizes Calculations:
  • 43. Combining Effect Sizes Step Two: Multiply each weighted effect size and original d-index Formula: diwi EX: What is the answer for Study 1?
  • 44. Combining Effect Sizes Calculations:
  • 45. Combining Effect Sizes Step Three: Divide the sum of these products by the sum of the weights. Formula: EX: d. = 62.56/544.27 = +.115 (average ES)
  • 46. Combining Effect Sizes Step Four: Computing Confidence Intervals Formula: EX: Thus, we expect 95% of estimates of this effect to fall between .031 and .199. Do we reject the null?
  • 47. Combining Effect Sizes Suppose that you have 6 r-indexes and ns that show the relationship between the amount students spend on homework and their score on an achievement test. Step One: Transform the r-indexes into a z-scores because as r gets larger the distribution gets more skewed. Formula:
  • 48. Combining Effect Sizes Step Two: Weighting Formula: ni - 3 EX: Study 1 3,505-3 = 3,502
  • 49. Combining Effect Sizes Calculations:
  • 50. Combining Effect Sizes Step Three: multiply the weight and the effect size (i.e., z-score) Formula: (ni – 3) zi EX: Study 1 (3,502).06 = 210.12
  • 51. Combining Effect Sizes Calculations:
  • 52. Combining Effect Sizes Step Four: Divide the sum of these products by the sum of the weights. Formula: EX: z. = 5462.97/26,372 = +.207 (average ES)
  • 53.
  • 54.
  • 55. As sample size increases, the width of the confidence interval should decrease.
  • 56.
  • 57.
  • 58. If most studies are similar to each other and show a similar result (low heterogeneity), this increases confidence that the effect being measured is real.
  • 59. If results from different studies are vastly different from each other, this suggests that each study is measuring something slightly different from the other studies.
  • 62. Differences in patient populations between studies
  • 65.
  • 67.
  • 68. The size of the square is proportional to the number of subjects in the group.
  • 69. The horizontal lines show the 95% confidence interval.
  • 70. The black diamonds represent the combined results for each subgroup.
  • 71.
  • 72. Conducting Meta-Analyses in R meta, rmeta and metaforpackages for conducting meta-analysesin R.
  • 73. Tuberculosis The data set taken from van Houwelingen, Arends, and Stijnen (2002) consists of randomized controlled trials of a vaccine, Bacillus Calmette-Guerin (BCG), for the preventionof tuberculosis (TB). The data presented consist of the sample size and the number of cases of tuberculosis. Furthermore some covariates are available that might explain the heterogeneity among studies: geographic latitude of the place where the study was done, year of publication, and method of treatment allocation (random, alternate, orsystematic).
  • 77. Dentifrices The data set is taken from Abrams and Sanso (1998) and concerns a previously published meta-analysis which was conducted of all randomized controlled trials comparing sodiummonofluorophosphate (SMFP) tosodiumfluoride (NaF) dentifrices(toothpastes) in the prevention of caries; see Johnson (1993). The outcome in each trial was the change from baseline in the decayed missing (due to caries) filled surface (DMFS) dental index at three years follow-up.
  • 80.
  • 81. Validity Thestudies were usually conducted in multisection courses in which the sections had different instructors but all sections used a common final examination. The index of validity was a correlation coefficient (a partial correlation coefficient, controlling for a measure of student ability) between the section mean instructor ratings and the sectionmean examination score.