# 8 Models

## 8.1 Regression Analysis With lm.sdf

After the data are read in with the EdSurvey package, a linear model can be fit to fully account for the complex sample design used for NCES data by using lm.sdf.

The lm.sdf function allows jackknife methods (i.e., JK1, JK2, or BRR) or the Taylor series method for variance estimation. By default, the standard error of coefficient is estimated with the jackknife replication method, but users can switch to the Taylor series when appropriate by setting the varMethod argument to varMethod="Taylor". When an explicit weight variable is not set, the lm.sdf function uses a default weight for the full sample in the analysis. For instance, origwt is the default weight in NAEP.

The data are read in and analyzed by the lm.sdf function—in this case, dsex, b017451, the five plausible values for composite, and the full sample weight origwt. By default, variance is estimated using the jackknife method, so the following call reads in the jackknife replicate weights:

lm1 <- lm.sdf(formula = composite ~ dsex + b017451, data = sdf)
summary(lm1)
#>
#> Formula: composite ~ dsex + b017451
#>
#> Weight variable: 'origwt'
#> Variance method: jackknife
#> JK replicates: 62
#> Plausible values: 5
#> jrrIMax: 1
#> full data n: 17606
#> n used: 16331
#>
#> Coefficients:
#>                                  coef        se        t
#> (Intercept)                 270.41112   1.02443 263.9615
#> dsexFemale                   -2.95858   0.60423  -4.8965
#> b017451Once every few weeks   4.23341   1.18327   3.5777
#> b017451About once a week     11.22612   1.25854   8.9200
#> b0174512 or 3 times a week   14.94591   1.18665  12.5951
#> b017451Every day              7.52998   1.30846   5.7549
#>                                dof  Pr(>|t|)
#> (Intercept)                 54.670 < 2.2e-16 ***
#> dsexFemale                  54.991 8.947e-06 ***
#> b017451Once every few weeks 57.316 0.0007131 ***
#> b017451About once a week    54.683 2.983e-12 ***
#> b0174512 or 3 times a week  72.582 < 2.2e-16 ***
#> b017451Every day            48.470 5.755e-07 ***
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Multiple R-squared: 0.0224

After the regression is run, the data are automatically removed from memory.

EdSurvey drops level 1 by default from the discrete predictor and treats it as the reference group. The reference level can be changed through the argument relevels. For example, in the previous model, the default reference group is males. In the following example, the reference group is changed to “Female” for the variable dsex:

lm1f <- lm.sdf(formula = composite ~ dsex + b017451, data = sdf,
relevels = list(dsex = "Female"))
summary(lm1f)
#>
#> Formula: composite ~ dsex + b017451
#>
#> Weight variable: 'origwt'
#> Variance method: jackknife
#> JK replicates: 62
#> Plausible values: 5
#> jrrIMax: 1
#> full data n: 17606
#> n used: 16331
#>
#> Coefficients:
#>                                  coef        se        t
#> (Intercept)                 267.45254   1.13187 236.2919
#> dsexMale                      2.95858   0.60423   4.8965
#> b017451Once every few weeks   4.23341   1.18327   3.5777
#> b017451About once a week     11.22612   1.25854   8.9200
#> b0174512 or 3 times a week   14.94591   1.18665  12.5951
#> b017451Every day              7.52998   1.30846   5.7549
#>                                dof  Pr(>|t|)
#> (Intercept)                 76.454 < 2.2e-16 ***
#> dsexMale                    54.991 8.947e-06 ***
#> b017451Once every few weeks 57.316 0.0007131 ***
#> b017451About once a week    54.683 2.983e-12 ***
#> b0174512 or 3 times a week  72.582 < 2.2e-16 ***
#> b017451Every day            48.470 5.755e-07 ***
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Multiple R-squared: 0.0224

The coefficient on dsex changed from negative in the previous run to positive of the exact same magnitude, whereas none of the other coefficients (aside from the intercept) changed; this is the expected result.

The standardized regression coefficient also can be returned by adding src=TRUE into the summary call for your regression model object:

summary(lm1f, src=TRUE)
#>
#> Formula: composite ~ dsex + b017451
#>
#> Weight variable: 'origwt'
#> Variance method: jackknife
#> JK replicates: 62
#> Plausible values: 5
#> jrrIMax: 1
#> full data n: 17606
#> n used: 16331
#>
#> Coefficients:
#>                                   coef         se        t
#> (Intercept)                 2.6745e+02 1.1319e+00 236.2919
#> dsexMale                    2.9586e+00 6.0423e-01   4.8965
#> b017451Once every few weeks 4.2334e+00 1.1833e+00   3.5777
#> b017451About once a week    1.1226e+01 1.2585e+00   8.9200
#> b0174512 or 3 times a week  1.4946e+01 1.1866e+00  12.5951
#> b017451Every day            7.5300e+00 1.3085e+00   5.7549
#>                                dof   Pr(>|t|) stdCoef
#> (Intercept)                 76.454 0.0000e+00      NA
#> dsexMale                    54.991 8.9474e-06  0.0407
#> b017451Once every few weeks 57.316 7.1311e-04  0.0458
#> b017451About once a week    54.683 2.9834e-12  0.1175
#> b0174512 or 3 times a week  72.582 0.0000e+00  0.1659
#> b017451Every day            48.470 5.7550e-07  0.0817
#>                                stdSE
#> (Intercept)                       NA
#> dsexMale                    0.008313 **
#> b017451Once every few weeks 0.012791 *
#> b017451About once a week    0.013175 *
#> b0174512 or 3 times a week  0.013175 *
#> b017451Every day            0.014200 *
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Multiple R-squared: 0.0224

By default, the standardized coefficients are calculated using standard deviations of the variables themselves, including averaging the standard deviation across any plausible values. When standardizeWithSamplingVar is set to TRUE, the variance of the standardized coefficient is calculated similar to a regression coefficient and therefore includes the sampling variance in the variance estimate of the outcome variable.

### 8.1.1 Calculating Multiple Comparisons in lm.sdf

A linear model is analyzed by the lm.sdf function—in this case, dsex, b017451, the five plausible values for composite, and the full sample weight origwt.

lm1 <- lm.sdf(formula = composite ~ dsex + b003501 + b003601, data = sdf)
summary(lm1)$coefmat Table 8.1. Coefficients coef se t dof Pr(>|t|) (Intercept) 262.52409 1.32295 198.43843 43.30064 0.00000 dsexFemale -1.51812 0.91367 -1.66156 68.46417 0.10117 b003501Graduated H.S. 4.08166 1.57890 2.58513 41.10442 0.01338 b003501Some ed after H.S. 15.03018 1.40534 10.69502 45.41276 0.00000 b003501I Don’t Know -1.59176 1.79932 -0.88465 34.72285 0.38243 b003601Graduated H.S. 2.89789 1.65445 1.75157 44.98221 0.08666 b003601Some ed after H.S. 9.15489 1.85547 4.93399 25.78984 0.00004 b003601I Don’t Know -4.12084 1.52672 -2.69914 37.56060 0.01036 The p-values for variables run in lm1 can be corrected for multiple testing. Notice that the only p-values adjusted in this example are in rows 6, 7, and 8 of the coefficients in lm1, and that column’s name is Pr(>|t|) so we can extract them with this command # p-values without adjustment summary(lm1)$coefmat[6:8, "Pr(>|t|)"]
#>  8.666330e-02 4.083289e-05 1.035995e-02

Here the Benjamini and Hochberg (1995) FDR adjustment is used in the argument method = "BH". The output below displays the adjusted p-values with the FDR adjustment:

# Benjamini and Hochberg adjusted p-values
p.adjust(p = lm1$coefmat[6:8, "Pr(>|t|)"], method = "BH") #>  0.0866633006 0.0001224987 0.0155399244 The next example adjusts the same p-values using the Bonferroni adjustment with method="bonferroni". Below shows the adjusted p-values: # Bonferroni adjusted p-values p.adjust(p = lm1$coefmat[6:8, "Pr(>|t|)"], method = "bonferroni")
#>  0.2599899019 0.0001224987 0.0310798488

We can compare all the values in a single table in

Table 8.2. Various p-values adjustments for b003501
raw BH Bonferroni
b003601Some ed after H.S. 0.000041 0.000122 0.000122
b003601I Don’t Know 0.010360 0.015540 0.031080

The coefficients matrix also can be overwritten by selecting the same vector in the lm1 linear regression object, updated here the Bonferroni p-values:

lm1$coefmat[6:8, "Pr(>|t|)"] <- p.adjust(lm1$coefmat[6:8, "Pr(>|t|)"], method = "bonferroni")
summary(lm1)$coefmat[6:8, ] Table 8.3. Coefficients table after using Bonferroni adjustment to the b003501 variable coef se t dof Pr(>|t|) b003601Graduated H.S. 2.89789 1.65445 1.75157 44.98221 0.25999 b003601Some ed after H.S. 9.15489 1.85547 4.93399 25.78984 0.00012 b003601I Don’t Know -4.12084 1.52672 -2.69914 37.56060 0.03108 ### 8.1.2 Adjusting p-Values From Multiple Sources Sometimes several values must be adjusted at once. In these cases, the p.adjust function must be called with all the p-values the researcher wishes to adjust together. For example, if one wishes to adjust values from two regressions and an additional value from another test, all these p-values must be put into a single vector and adjusted as a set. Therefore, p-value adjustments called on smaller portions of regressions/tests independently may return incorrect adjusted p-values and could result in an incorrect inference. In this example, the coefficients from b003501 and b003601—each from independent regressions—as well as another p-value of 0.02 are adjusted. lm2a <- lm.sdf(formula = composite ~ dsex + b003501, data = sdf) lm2b <- lm.sdf(formula = composite ~ dsex + b003601, data = sdf) # pvalues data.frame with missing values # values of coef that are not in this initial call but will be added pvalues <- data.frame(source=c(rep("lm2a",3), rep("lm2b",3), "otherp"), coef=rep("",7), p=rep(NA,7), stringsAsFactors=FALSE) This code is careful to note where the values came from to help avoid transcription errors. The pvalues object is then populated using p-values and coefficients from the lm2a and lm2b linear regression objects, rows 1–3 and 4–6 for each, respectively. # load in values from lm2a lm2aCoef <- summary(lm2a)$coefmat
pvalues$p[1:3] <- lm2aCoef[3:5,5] pvalues$coef[1:3] <- row.names(lm2aCoef)[3:5]
# load in values from lm2b
lm2bCoef <- summary(lm2b)$coefmat pvalues$p[4:6] <- lm2bCoef[3:5,5]
pvalues$coef[4:6] <- row.names(lm2aCoef)[3:5] The additional p-value due for adjustment is included in row 7: # load in other p-value pvalues$p <- 0.02
colnames(pvalues) <- "Pr(>|t|)"
# check matrix
pvalues
source coef Pr(>|t|)
lm2a b003501Some ed after H.S. 0.0000000
lm2a b003501I Don’t Know 0.0295389
lm2b b003501Some ed after H.S. 0.0000000
lm2b b003501I Don’t Know 0.0013006
otherp 0.0200000

Now that the aforementioned p-values are included in the same vector, they are adjusted via p.adjust using the Benjamini and Hochberg method:

pvalues[,"Adjusted Pr(>|t|)"] <- p.adjust(p = pvalues[,"Pr(>|t|)"], method = "BH")
pvalues
lm2a b003501Some ed after H.S. 0.0000000 0.0000000
lm2a b003501I Don’t Know 0.0295389 0.0295389
lm2b b003501Some ed after H.S. 0.0000000 0.0000000
lm2b b003501I Don’t Know 0.0013006 0.0018208
otherp 0.0200000 0.0233333

NOTE: The EdSurvey package produces p-values based on the assumption that tests are independent and unassociated with each other; yet this assumption is not always valid. Several possible methods have been developed for dealing with the multiple hypothesis testing problem.

## 8.2 Multivariate Regression With mvrlm.sdf

A multivariate regression model can be fit to fully account for the complex sample design used for NCES data by using mvrlm.sdf. This function implements an estimator that correctly handles multiple dependent variables that are continuous (such as plausible values), which allows for variance estimation using the jackknife replication method.

The vertical line symbol | separates dependent variables on the left-hand side of formula. In the following example, a multivariate regression is fit with two subject scales as the outcome variables (algebra and geometry) by two predictor variables signifying gender and a survey item concerning the ability to identify the best unit of area (dsex and m072801):

mvrlm1 <- mvrlm.sdf(algebra | geometry ~ dsex + m072801, data = sdf)
summary(mvrlm1)
#>
#> Formula: algebra | geometry ~ dsex + m072801
#>
#> jrrIMax:
#> Weight variable: 'origwt'
#> Variance method:
#> JK replicates: 62
#> full data n: 17606
#> n used: 3287
#>
#> Coefficients:
#>
#> algebra
#>                         coef        se         t    dof
#> (Intercept)        258.32980   2.38447 108.33839 42.729
#> dsexFemale           6.94298   1.51265   4.58995 49.897
#> m072801B *          24.78260   2.23171  11.10475 67.935
#> m072801C            11.75561   2.97489   3.95162 64.737
#> m072801D           -12.88466   6.55887  -1.96446 12.131
#> m072801E             1.96793   5.38314   0.36557 21.275
#> m072801Not Reached -33.52297  17.46008  -1.91998 10.968
#>                     Pr(>|t|)
#> (Intercept)        < 2.2e-16 ***
#> dsexFemale         3.021e-05 ***
#> m072801B *         < 2.2e-16 ***
#> m072801C           0.0001945 ***
#> m072801D           0.0728026 .
#> m072801E           0.7182938
#> m072801Not Reached 0.0812328 .
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> geometry
#>                          coef         se          t     dof
#> (Intercept)        255.351767   2.368025 107.833211 33.7224
#> dsexFemale           5.407780   1.584977   3.411898 35.8676
#> m072801B *          22.369806   2.212790  10.109321 57.1693
#> m072801C             8.850143   3.647400   2.426425 51.3747
#> m072801D            -9.260011   5.873402  -1.576601 12.8849
#> m072801E            -0.185649   5.919666  -0.031361 23.9251
#> m072801Not Reached -31.782791  23.915420  -1.328966  5.1159
#>                     Pr(>|t|)
#> (Intercept)        < 2.2e-16 ***
#> dsexFemale          0.001613 **
#> m072801B *         2.442e-14 ***
#> m072801C            0.018796 *
#> m072801D            0.139113
#> m072801E            0.975242
#> m072801Not Reached  0.240046
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Residual correlation matrix:
#>
#>          algebra geometry
#> algebra     1.00     0.85
#> geometry    0.85     1.00
#>
#> Multiple R-squared by dependent variable:
#>
#>  algebra geometry
#>   0.0926   0.0858

The mvrlm.sdf documentation provides examples to compare the regression outputs. See ?mvrlm.sdf for an overview of additional details that can be accessed through components of the returned object. In addition, the vignette titled Statistical Methods Used in EdSurvey goes into further detail by describing estimation of the reported statistics.

## 8.3 Logistic Regression Analysis With glm.sdf, logit.sdf, and probit.sdf

A logistic regression model can be fit to fully account for the complex sample design used for NCES data by using glm.sdf, logit.sdf, and probit.sdf. These functions predict binary outcomes from a set of predictor variables factoring in appropriate weights and variance estimates. glm.sdf is an umbrella function that currently fits logit and probit models. Alternatively, users can choose logit.sdf or probit.sdf functions for binomial outcomes.

The following example demonstrates how to use logit.sdf to predict the number of books at home with student gender. The example arguments are generalizable to glm.sdf and probit.sdf. For more information about how to use the latter two functions, check their help files by calling ?glm.sdf and ?probit.sdf, respectively.

In logit.sdf, although some variables might already be binary, the function I() will dichotomize a nonbinary variable and specify the desired outcome level. A logistic regression can be run exploring the association of gender (dsex) to the outcome variable: number of books at home (b013801), which is dichotomized with the level matching “more than 100 books at home” (">100") as the outcome level:

logit1 <- logit.sdf(I(b013801 %in% ">100") ~ dsex,
weightVar = 'origwt', data = sdf)
summary(logit1)
#>
#> Formula: b013801 ~ dsex
#> Family: binomial (logit)
#>
#> Weight variable: 'origwt'
#> Variance method: jackknife
#> JK replicates: 62
#> full data n: 17606
#> n used: 16359
#>
#> Coefficients:
#>                   coef         se          t    dof
#> (Intercept)  -0.920421   0.046355 -19.855835 60.636
#> dsexFemale    0.178274   0.050129   3.556331 54.578
#>              Pr(>|t|)
#> (Intercept) < 2.2e-16 ***
#> dsexFemale  0.0007863 ***
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

The log odds of having more than 100 books at home (versus less than or equal to 100 books) increases by 0.178274 for female students compared with male students.

Logistic regression results can be further interpreted with the assistance of the oddsRatio and waldTest functions.

### 8.3.1 Recovering Odds Ratios

The oddsRatio helper function converts coefficients from an EdSurvey logit regression model to odds ratios. Odds ratios are useful for understanding the real likelihood of an event occurring based on a transformation to the log odds returned in a logistic model.

In EdSurvey, odds ratios can be returned by specifying the logistic model object (logit1).

oddsRatio(logit1)
#>                    OR      2.5%     97.5%
#> (Intercept) 0.3983511 0.3630823 0.4370459
#> dsexFemale  1.1951531 1.0809029 1.3214796

The odds of having more than 100 books at home (versus less than or equal to 100 books) increases by 1.1951531 for female students compared with male students.

### 8.3.2 Wald Tests

The waldTest function allows the user to test composite hypotheses—those with multiple coefficients involved—even when the data include plausible values. Because there is no likelihood test for plausible values or residuals of large-scale assessment data analysis, the Wald test fills the role of the likelihood ratio test, analysis of variance, and the F-test.

Wald tests can be run by specifying the model and coefficients. The second coefficient in our logit1 model object (Female) is tested in the following example:

waldTest(model = logit1, coefficients = 2)
#> Wald test:
#> ----------
#> H0:
#> dsexFemale = 0
#>
#> Chi-square test:
#> X2 = 12.6, df = 1, P(> X2) = 0.00038
#>
#> F test:
#> W = 12.6, df1 = 1, df2 = 62, P(> W) = 0.00073

To learn more about conducting Wald tests, consult the vignette titled Methods and Overview of Using EdSurvey for Running Wald Tests.

## 8.4 Quantile Regression Analysis with rq.sdf

The rq.sdf function computes an estimate on the tau-th conditional quantile function of the response, given the covariates, as specified by the formula argument. Similar to lm.sdf, the function presumes a linear specification for the quantile regression model (i.e., the formula defines a model that is linear in parameter). Jackknife is the only applicable variance estimation method used by the function.

To conduct quantile regression at a given tau value (by default, tau is set as 0.5), specify using the tau argument (in this example tau = 0.8); all other arguments are otherwise consistent with lm.sdf, except for returnVarEstInputs, returnNumberOfPSU, and standardizeWithSamplingVar, which are not available.

rq1 <- rq.sdf(composite ~ dsex + b017451, data=sdf, tau = 0.8)
summary(rq1)
#>
#> Formula: composite ~ dsex + b017451
#>
#> tau: 0.8
#> jrrIMax: 1
#> Weight variable: 'origwt'
#> Variance method: jackknife
#> JK replicates: 62
#> full data n: 17606
#> n used: 16331
#>
#> Coefficients:
#>                                 coef       se        t
#> (Intercept)                 299.7680   1.8103 165.5883
#> dsexFemale                   -4.6280   1.2908  -3.5852
#> b017451Once every few weeks   6.5880   1.9086   3.4518
#> b017451About once a week     12.4800   2.2959   5.4359
#> b0174512 or 3 times a week   16.5420   2.4616   6.7201
#> b017451Every day             12.7420   1.6932   7.5253
#>                                dof  Pr(>|t|)
#> (Intercept)                 29.389 < 2.2e-16 ***
#> dsexFemale                  58.617 0.0006868 ***
#> b017451Once every few weeks 46.045 0.0012041 **
#> b017451About once a week    67.782 8.032e-07 ***
#> b0174512 or 3 times a week  29.867 1.943e-07 ***
#> b017451Every day            50.343 8.717e-10 ***
#> ---
#> Signif. codes:
#> 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

For further details on quantile regression models and how they are implemented in R, see the vignette from the quantreg package (accessible by the vignette("rq", package="quantreg")), on which the rq.sdf function is built.

## 8.5 Mixed Models With mixed.sdf

EdSurvey features the functionality of estimating mixed-effects models accounting for plausible values and survey weights. EdSurvey fits a weighted mixed model, also known as a weighted multilevel or hierarchical linear model using the WeMix package.

This example illustrates how the user might implement student-level weighting when using a survey (NAEP in this example) that does not have a weighting scheme previously implemented.

# Subset data to a sample of interest
sdf2 <- subset(sdf, scrpsu < 500)

# Extract variables of interest to a light.edsurvey.data.frame
lsdf <- getData(sdf2, c("composite","dsex","b017451","scrpsu","origwt","smsrswt"),

# Transform weights using your method (Note that this method is not recommended for NAEP)
lsdf$pwt1 <- lsdf$origwt/lsdf$smsrswt lsdf$pwt2 <- lsdf\$smsrswt

m1 <- mixed.sdf(composite ~ dsex + b017451 + (1|scrpsu), data=lsdf,
weightVar = c('pwt1', 'pwt2'))
summary(m1)
#> Call:
#> mixed.sdf(formula = composite ~ dsex + b017451 + (1 | scrpsu),
#>     data = lsdf, weightVars = c("pwt1", "pwt2"))
#>
#> Formula: composite ~ dsex + b017451 + (1 | scrpsu)
#>
#> Plausible Values: 5
#> Number of Groups:
#>  Level  Group n size mean wgt sum wgt
#>      2 scrpsu     22    1.281   28.19
#>      1    Obs    492    1.598  786.25
#>
#> Variance terms:
#>  Level    Group        Name Variance Std. Error Std.Dev.
#>      2   scrpsu (Intercept)    558.6     204.64    23.63
#>      1 Residual                876.8      74.69    29.61
#>
#> Fixed Effects:
#>                             Estimate Std. Error t value
#> (Intercept)                  266.795      8.200  32.537
#> dsexFemale                    -1.179      2.998  -0.393
#> b017451Once every few weeks    2.173      6.954   0.312
#> b017451About once a week       9.809      4.472   2.193
#> b0174512 or 3 times a week    10.863      6.098   1.781
#> b017451Every day               6.792      7.365   0.922
#>
#> Intraclass Correlation= 0.389

The following two examples illustrate how to model the random intercept of mathematics achievement at the school level with students’ gender as a covariate, using TIMSS 2015 datasets.


#Use all plausible values
#> Found cached data for country code "usa".
mix1 <- mixed.sdf(mmat ~ itsex + (1|idschool), data = TIMSS15USA,
weightVar=c("totwgt","schwgt"), weightTransformation=FALSE)
summary(mix1)
#> Call:
#> mixed.sdf(formula = mmat ~ itsex + (1 | idschool), data = TIMSS15USA,
#>     weightVars = c("totwgt", "schwgt"), weightTransformation = FALSE)
#>
#> Formula: mmat ~ itsex + (1 | idschool)
#>
#> Plausible Values: 5
#> Number of Groups:
#>  Level    Group n size mean wgt sum wgt
#>      2 idschool    250    255.9   63971
#>      1      Obs  10029    374.6 3757302
#>
#> Variance terms:
#>  Level    Group        Name Variance Std. Error Std.Dev.
#>      2 idschool (Intercept)     1758      173.7    41.93
#>      1 Residual                 4672      105.3    68.35
#>
#> Fixed Effects:
#>             Estimate Std. Error t value
#> (Intercept)  536.042      3.767 142.288
#> itsexMALE      6.091      1.500   4.061
#>
#> Intraclass Correlation= 0.273
# uses only one plausible value
mix2 <- mixed.sdf(asmmat01 ~ itsex + (1|idschool), data = TIMSS15USA,
weightVar=c("totwgt","schwgt"), weightTransformation=FALSE)
summary(mix2)
#> Call:
#> mixed.sdf(formula = asmmat01 ~ itsex + (1 | idschool), data = TIMSS15USA,
#>     weightVars = c("totwgt", "schwgt"), weightTransformation = FALSE)
#>
#> Formula: asmmat01 ~ itsex + (1 | idschool)
#> Number of Groups:
#>  Level    Group n size mean wgt sum wgt
#>      2 idschool    250    255.9   63971
#>      1      Obs  10029    374.6 3757302
#>
#> Variance terms:
#>  Level    Group        Name Variance Std. Error Std.Dev.
#>      2 idschool (Intercept)     1713      173.7    41.39
#>      1 Residual                 4658      105.3    68.25
#>
#> Fixed Effects:
#>             Estimate Std. Error t value
#> (Intercept)  536.847      3.668 146.349
#> itsexMALE      5.726      1.442   3.972
#>
#> lnl=-21290221.51
#> Intraclass Correlation= 0.269

For further guidance and use cases for mixed-effects models in EdSurvey, see the vignette titled Methods Used for Estimating Mixed-Effects Models in EdSurvey. For examples of how NCES recommends using weighted mixed-effects models, as well as their summary of the mathematical background and the description of the insufficiency of hierarchical linear models in this case, see Appendix D in the NCES working paper on analysis of TIMSS data at Using TIMSS to Analyze Correlates of Performance Variation in Mathematics.