# Multilevel Propensity Score Analysis

## Introduction

Given the large amount of data to be summarized, the use of graphics are an integral component of representing the results. Pruzek and Helmreich (2009) introduced a class of graphics for visualizing dependent sample tests (see also Pruzek & Helmreich, 2010; Danielak, Pruzek, Doane, Helmreich, & Bryer, 2011). This framework was then extended for propensity score methods using stratification (Helmreich & Pruzek, 2009). In particular, the representation of confidence intervals relative to the unit line (i.e. the line y=x) provided a new way of determining whether there is a statistically significant diﬀerence between two groups. The `multilevelPSA` package provides a number of graphing functions that extend these frameworks for multilevel PSA. The figure below represents a multilevel PSA assessment plot with annotations. This graphic represents the results of comparing private and public schools in North America using the Programme of International Student Assessment (PISA; Organisation for Economic Co-Operation and Development, 2009). The PISA data to create this graphic are included in the `multilevelPSA` package and a more detailed description of how to create this graphic are discussed in the next section. Additionally, the use of PISA makes more visible certain features of the graphics used. As discussed in chapters four and five, the diﬀerences between charter and traditional public schools is minimal and therefore some features of the figures are less apparent. The following section focuses on the features of this graphic.

In the figure below, the x-axis corresponds to math scores for private schools and the y-axis corresponds to public school maths cores. Each colored circle (a) is a country with its size corresponding to the number of students sampled within each country. Each country is projected to the lower left, parallel to the unit line, such that a tick mark is placed on the line with slope -1 (b). These tick marks represent the distribution of diﬀerences between private and public schools across countries. Diﬀerences are aggregated (and weighted by size) across countries. For math, the overall adjusted mean for private schools is 487, and the overall adjusted mean for public schools is 459 and represented by the horizontal (c) and vertical (d) blue lines, respectively. The dashed blue line parallel to the unit line (e) corresponds to the overall adjusted mean diﬀerence and likewise, the dashed green lines (f) correspond to the confidence interval. Lastly, rug plots along the right and top edges of the graphic (g) correspond to the distribution of each country’s overall mean private and public school math scores, respectively.

The figure represents a large amount of data and provides insight into the data and results. The figure provides overall results that would be present in a traditional table, for instance the fact that the green dashed lines do not span the unit line (i.e. y = x) indicates that there is a statistically significant diﬀerence between the two groups. However additional information is diﬃcult to convey in tabular format. For example, the rug plots indicate that the spread in the performance of both private and public schools across countries is large. Also observe that Canada, which has the largest PISA scores for both groups, also has the largest diﬀerence (in favor of private schools) as represented by the larger distance from the unit line.

Annotated multilevel PSA assessment plot. This plot compares private schools (x- axis) against public schools (y-axis) for North America from the Programme of International Student Assessment.

## Working Example

The `multilevelPSA` package includes North American data from the Programme of International Student Assessment (PISA; Organisation for Economic Co-Operation and Development, 2009). This data is made freely available for research and is utilized here so that the R code is reproducible9. This example compares the performance of private and public schools clustered by country. Note that PISA provide five plausible values for the academic scores since students complete a subset of the total assessment. For simplicity, the math score used for analysis is the average of these five plausible scores.

    library(multilevelPSA)
    library(party)

    data(pisana)
    data(pisa.psa.cols)
    pisana$MathScore <- apply(pisana[,paste0('PV', 1:5, 'MATH')], 1, sum) / 5

The `mlpsa.ctree` function performs phase I of the propensity score analysis using classification trees, specifically using the `ctree` function in the party package. The getStrata function returns a data frame with a number of rows equivalent to the original data frame indicating the stratum for each student.

    mlpsa <- mlpsa.ctree(pisana[,c('CNT', 'PUBPRIV', pisa.psa.cols)],
                         formula = PUBPRIV ~ .,
                         level2 = 'CNT')
    mlpsa.df <- getStrata(mlpsa, pisana, level2 = 'CNT')

Similarly, the `mlpsa.logistic` estimates propensity scores using logistic regression. The `getPropensityScores` function returns a data frame with a number of rows equivalent to the original data frame.

    mlpsa.lr <- mlpsa.logistic(pisana[,c('CNT', 'PUBPRIV', pisa.psa.cols)],
                               formula = PUBPRIV ~ .,
                               level2 = 'CNT')
    mlpsa.lr.df <- getPropensityScores(mlpsa.lr, nStrata = 5)

    head(mlpsa.lr.df)
    #>   level2   ps strata
    #> 1    CAN 0.92      2
    #> 2    CAN 0.94      3
    #> 3    CAN 0.97      4
    #> 4    CAN 0.93      2
    #> 5    CAN 0.84      1
    #> 6    CAN 0.97      4

The `covariate.balance` function calculates balance statistics for each covariate by estimating the eﬀect of each covariate before and after adjustment. The results can be converted to a data frame to view numeric results or the `plot` function provides a balance plot. This figure depicts the eﬀect size of each covariate before (blue triangle) and after (red circle) propensity score adjustment. As shown here, the eﬀect size for nearly all covariates is smaller than the unadjusted eﬀect size. The few exceptions are for covariates where the unadjusted eﬀect size was already small. There is no established threshold for what is considered a suﬃciently small eﬀect size. In general, I recommend adjusted eﬀect sizes less than 0.1 which reflect less than 1% of variance explained.

    cv.bal <- covariate.balance(covariates = pisana[,pisa.psa.cols],
                                treatment = pisana$PUBPRIV,
                                level2 = pisana$CNT,
                                strata = mlpsa.df$strata)
    head(as.data.frame(cv.bal))
    #>                        covariate es.adj es.adj.wtd es.unadj
    #> 1                    (Intercept)  0.000    0.0e+00      NaN
    #> 2 ST05Q01Yes, more than one year  0.097    2.3e-04    0.287
    #> 3   ST05Q01Yes, one year or less  0.051    6.6e-05    0.220
    #> 4               ST07Q01Yes, once  0.103   -1.1e-03    0.235
    #> 5      ST07Q01Yes, twice or more  0.044   -3.7e-04    0.087
    #> 6         ST10Q01<ISCED level 2>  0.030   -1.7e-04    0.171
    plot(cv.bal)

Multilevel PSA balance plot for PISA. The eﬀect sizes (standardized mean diﬀerences) for each covariate are provided before PSA adjustment (blue triangles) and after PSA adjustment (red circles).

The `mlpsa` function performs phase II of propensity score analysis and requires four parameters: the response variable, treatment indicator, stratum, and clustering indicator. The `minN` parameter (which defaults to five) indicates what the minimum stratum size is to be included in the analysis. For this example, 463, or less than one percent of students were removed because the stratum (or leaf node for classification trees) did not contain at least five students from both the treatment and control groups.

    results.psa.math <- mlpsa(response = mlpsa.df$MathScore,
                              treatment = mlpsa.df$PUBPRIV,
                              strata = mlpsa.df$strata,
                              level2 = mlpsa.df$CNT)
    #> Removed 463 (0.696%) rows due to stratum size being less than 5

The `summary` function provides the overall treatment estimates as well as level one and two summaries.

    summary(results.psa.math)
    #> Multilevel PSA Model of 85 strata for 3 levels.
    #> Approx t: -10.8
    #> Confidence Interval: -31.3, -24.75
    #>    level2  strata Treat Treat.n Control Control.n ci.min ci.max
    #> 1     CAN Overall   579    1625     513     21093    -72  -59.6
    #> 2    <NA>       1   580      28     492      1128     NA     NA
    #> 3    <NA>       2   600       9     476      1326     NA     NA
    #> 4    <NA>       3   585      11     513       630     NA     NA
    #> 5    <NA>       4   571     140     508      2240     NA     NA
    #> 6    <NA>       5   578       8     470       179     NA     NA
    #> 7    <NA>       6   500      19     447       310     NA     NA
    #> 8    <NA>       7   584      83     503      3276     NA     NA
    #> 9    <NA>       8   471       5     464       120     NA     NA
    #> 10   <NA>       9   560      41     526       190     NA     NA
    #> 11   <NA>      10   502      20     463        91     NA     NA
    #> 12   <NA>      11   557      44     517       750     NA     NA
    #> 13   <NA>      12   559      34     521       292     NA     NA
    #> 14   <NA>      13   562       8     489       475     NA     NA
    #> 15   <NA>      14   534      21     463       151     NA     NA
    #> 16   <NA>      15   585     126     520      2134     NA     NA
    #> 17   <NA>      16   566      25     533       245     NA     NA
    #> 18   <NA>      17   613      49     576       137     NA     NA
    #> 19   <NA>      18   563      57     527       659     NA     NA
    #> 20   <NA>      19   598     113     542       318     NA     NA
    #> 21   <NA>      20   629      15     562       143     NA     NA
    #> 22   <NA>      21   589      46     523       398     NA     NA
    #> 23   <NA>      22   594      99     548       194     NA     NA
    #> 24   <NA>      23   580      40     542       183     NA     NA
    #> 25   <NA>      24   581      52     539       342     NA     NA
    #> 26   <NA>      25   582     103     526      1219     NA     NA
    #> 27   <NA>      26   626      11     525       113     NA     NA
    #> 28   <NA>      27   589      35     516       804     NA     NA
    #> 29   <NA>      28   524       5     482        15     NA     NA
    #> 30   <NA>      29   551      12     527       348     NA     NA
    #> 31   <NA>      30   588     145     526      1195     NA     NA
    #> 32   <NA>      31   603     147     545       822     NA     NA
    #> 33   <NA>      32   528      27     528         7     NA     NA
    #> 34   <NA>      33   552      47     510       659     NA     NA
    #> 35    MEX Overall   430    4044     423     34090    -10   -3.1
    #> 36   <NA>       1   516      83     485        13     NA     NA
    #> 37   <NA>       2   491     145     448        89     NA     NA
    #> 38   <NA>       3   494     151     475       178     NA     NA
    #> 39   <NA>       4   418      14     416       154     NA     NA
    #> 40   <NA>       5   454     127     438       484     NA     NA
    #> 41   <NA>       6   453      58     431       635     NA     NA
    #> 42   <NA>       7   496     247     487       293     NA     NA
    #> 43   <NA>       8   483     431     461       871     NA     NA
    #> 44   <NA>       9   472       6     467       110     NA     NA
    #> 45   <NA>      10   461      16     450       121     NA     NA
    #> 46   <NA>      11   481     285     470       696     NA     NA
    #> 47   <NA>      12   474      16     443       112     NA     NA
    #> 48   <NA>      13   405      33     413       943     NA     NA
    #> 49   <NA>      14   432     138     429      1484     NA     NA
    #> 50   <NA>      15   472      99     460       619     NA     NA
    #> 51   <NA>      16   445      78     438       898     NA     NA
    #> 52   <NA>      17   460      34     461       262     NA     NA
    #> 53   <NA>      18   460     113     455       367     NA     NA
    #> 54   <NA>      19   434      53     445       454     NA     NA
    #> 55   <NA>      20   458      69     446       367     NA     NA
    #> 56   <NA>      21   462      76     457       217     NA     NA
    #> 57   <NA>      22   477      93     452       150     NA     NA
    #> 58   <NA>      23   476     186     460       547     NA     NA
    #> 59   <NA>      24   477      10     437       130     NA     NA
    #> 60   <NA>      25   476      80     442       159     NA     NA
    #> 61   <NA>      26   437     167     428      1040     NA     NA
    #> 62   <NA>      27   436     146     435      1175     NA     NA
    #> 63   <NA>      28   442      45     429       406     NA     NA
    #> 64   <NA>      29   424      80     428      1963     NA     NA
    #> 65   <NA>      30   436      61     427       787     NA     NA
    #> 66   <NA>      31   426      48     428       645     NA     NA
    #> 67   <NA>      32   401     231     409      4314     NA     NA
    #> 68   <NA>      33   442      28     438       279     NA     NA
    #> 69   <NA>      34   424      34     426      1013     NA     NA
    #> 70   <NA>      35   420      63     427      2364     NA     NA
    #> 71   <NA>      36   408      18     400       234     NA     NA
    #> 72   <NA>      37   406     107     397      3632     NA     NA
    #> 73   <NA>      38   425      25     412      2434     NA     NA
    #> 74   <NA>      39   449      15     432       342     NA     NA
    #> 75   <NA>      40   362       7     348      1959     NA     NA
    #> 76   <NA>      41   381      15     346      1004     NA     NA
    #> 77   <NA>      42   510     313     488       146     NA     NA
    #> 78    USA Overall   505     345     485      4888    -32   -8.8
    #> 79   <NA>       1   479      50     475      1219     NA     NA
    #> 80   <NA>       2   490      16     448      1323     NA     NA
    #> 81   <NA>       3   502      34     488       462     NA     NA
    #> 82   <NA>       4   528      42     507       263     NA     NA
    #> 83   <NA>       5   512      42     503       335     NA     NA
    #> 84   <NA>       6   520      21     477       526     NA     NA
    #> 85   <NA>       7   565      80     559       278     NA     NA
    #> 86   <NA>       8   560      41     541       207     NA     NA
    #> 87   <NA>       9   511      14     529       259     NA     NA
    #> 88   <NA>      10   522       5     461        16     NA     NA

The `plot` function creates the multilevel assessment plot. Here it is depicted with side panels showing the distribution of math scores for all strata for public school students to the left and private school students below. These panels can be plotted separately using the `mlpsa.circ.plot` and mlpsa.distribution.plot functions.

    plot(results.psa.math)
    #> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
    #> ℹ Please use tidy evaluation idioms with `aes()`.
    #> ℹ See also `vignette("ggplot2-in-packages")` for more information.
    #> ℹ The deprecated feature was likely used in the multilevelPSA package.
    #>   Please report the issue at <https://github.com/jbryer/multilevelPSA/issues/>.
    #> This warning is displayed once every 8 hours.
    #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    #> generated.
    #> Warning: The `margin` argument should be constructed using the `margin()`
    #> function.
    #> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
    #> ℹ Please use `linewidth` instead.
    #> ℹ The deprecated feature was likely used in the multilevelPSA package.
    #>   Please report the issue at <https://github.com/jbryer/multilevelPSA/issues/>.
    #> This warning is displayed once every 8 hours.
    #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    #> generated.

Multilevel PSA assessment plot for PISA. The main panel provides the adjusted mean for private (x-axis) and public (y-axis) for each country. The left and lower panels provide the mean for each stratum for the public and private students, respectively. The overall adjusted mean diﬀerence is represented by the dashed blue line and the 95% confidence interval by the dashed green lines. There is a statistically significant diﬀerence between private and public school student performance as evidenced by the confidence interval not spanning zero (i.e. not crossing the unit line y=x.

Lastly, the `mlpsa.difference.plot` function plots the overall diﬀerences. The `sd` parameter is optional, but if specified, the x-axis can be interpreted as standardized eﬀect sizes.

    mlpsa.difference.plot(results.psa.math,
                          sd = mean(mlpsa.df$MathScore, na.rm=TRUE))
    #> Warning: The `margin` argument should be constructed using the `margin()`
    #> function.

Multilevel PSA diﬀerence plot for PISA. Each blue dot corresponds to the eﬀect size (standardized mean diﬀerence) for each country. The vertical blue line corresponds to the overall eﬀect size for all countries. The green lines correspond to the 95% confidence intervals. The dashed green lines Bonferroni-Sidak (c.f. Abdi, 2007) adjusted confidence intervals. The size of each dot is proportional to the sample size within each country.