Data Set and Model
This data set will be used for illustration:
library(manymome)
dat <- data_med
head(dat)
#> x m y c1 c2
#> 1 9.931992 17.89644 20.73893 1.426513 6.103290
#> 2 8.331493 17.92150 22.91594 2.940388 3.832698
#> 3 10.327471 17.83178 22.14201 3.012678 5.770532
#> 4 11.196969 20.01750 25.05038 3.120056 4.654931
#> 5 11.887811 22.08645 28.47312 4.440018 3.959033
#> 6 8.198297 16.95198 20.73549 2.495083 3.763712
It has one predictors (x), one mediator (m), one outcome variable (y), and two control variables (c1 and c2).
This simple mediation model with two control variables (c1 and c2) will be fitted:
Models Fitted by lavaan::sem()
We first fit the model by lavaan::sem():
mod <-
"
m ~ x + c1 + c2
y ~ m + x + c1 + c2
"
fit_lavaan <- sem(model = mod, data = dat,
fixed.x = FALSE,
estimator = "MLR")
summary(fit_lavaan)
#> lavaan 0.6-12 ended normally after 1 iterations
#>
#> Estimator ML
#> Optimization method NLMINB
#> Number of model parameters 15
#>
#> Number of observations 100
#>
#> Model Test User Model:
#> Standard Robust
#> Test Statistic 0.000 0.000
#> Degrees of freedom 0 0
#>
#> Parameter Estimates:
#>
#> Standard errors Sandwich
#> Information bread Observed
#> Observed information based on Hessian
#>
#> Regressions:
#> Estimate Std.Err z-value P(>|z|)
#> m ~
#> x 0.935 0.075 12.437 0.000
#> c1 0.198 0.079 2.507 0.012
#> c2 -0.168 0.099 -1.703 0.089
#> y ~
#> m 0.785 0.233 3.363 0.001
#> x 0.508 0.323 1.573 0.116
#> c1 0.140 0.188 0.747 0.455
#> c2 -0.154 0.214 -0.720 0.471
#>
#> Covariances:
#> Estimate Std.Err z-value P(>|z|)
#> x ~~
#> c1 0.026 0.121 0.211 0.833
#> c2 0.100 0.084 1.186 0.235
#> c1 ~~
#> c2 -0.092 0.109 -0.841 0.400
#>
#> Variances:
#> Estimate Std.Err z-value P(>|z|)
#> .m 0.681 0.085 7.976 0.000
#> .y 4.030 0.580 6.944 0.000
#> x 1.102 0.150 7.338 0.000
#> c1 1.218 0.161 7.540 0.000
#> c2 0.685 0.073 9.340 0.000
Suppose we would like to use robust “sandwich” standard errors and confidence intervals provided by MLR for the free parameters, but want to use percentile nonparametric bootstrap confidence interval for the indirect effect. In the call above, we used estimator = "MLR" and did not set se = "boot".
We can then call do_boot() on the output of lavaan::sem() to generate the bootstrap estimates of all free parameters and the implied statistics, such as the variances of m and y, which are not free parameters but are needed to form the confidence interval of the standardized indirect effect.
boot_out_lavaan <- do_boot(fit = fit_lavaan,
R = 100,
ncores = 1)
Usually, just three arguments are needed:
fit: The output of lavaan::sem().
R: The number of bootstrap samples. Should be at least 2000 or even 5000 in real research. 100 is used here just for illustration.
ncores: The number of CPU cores to be used in generating bootstrap estimates in parallel processing.
Parallel processing is enabled by default, and a text progress bar (generated by the package pbapply) will be displayed. If ncores is omitted, the number of cores (ncores) to be used will be decided automatically. Therefore, users usually do not need to use ncores. It is set to 1 here just for illustration.
In real research with a complicated model and moderate to large sample size, even with parallel processing, it may take several minutes, or even over twenty minutes in some cases. Nevertheless, this only need to be conducted once in the workflow of manymome.
If bootstrapping takes an appreciable time to run, it is recommended to save the output using saveRDS() or save():
### Use saveRDS() ###
# Save the output
saveRDS(boot_out_lavaan, file = "boot_out_lavaan.rds")
# Load the output
boot_out_lavaan <- readRDS("boot_out_lavaan.rds")
### Use save() ###
# Save the output
save(boot_out_lavaan, file = "boot_out_lavaan.RData")
# Load the output
load("boot_out_lavaan.RData")
We recommend readRDS() although save() is probably a more popular function.
The Structure of the Output
The output of do_boot() in this case is an object of the class boot_out, which is a list of R lists, each with three elements: est, implied_stats, and ok.
This is the content of est of the first list:
boot_out_lavaan[[1]]$est
#> lhs op rhs est
#> 1 m ~ x 0.966
#> 2 m ~ c1 0.126
#> 3 m ~ c2 0.053
#> 4 y ~ m 0.454
#> 5 y ~ x 0.814
#> 6 y ~ c1 -0.035
#> 7 y ~ c2 0.222
#> 8 m ~~ m 0.736
#> 9 y ~~ y 3.330
#> 10 x ~~ x 1.112
#> 11 x ~~ c1 -0.040
#> 12 x ~~ c2 0.127
#> 13 c1 ~~ c1 1.245
#> 14 c1 ~~ c2 0.004
#> 15 c2 ~~ c2 0.719
#> 16 m r2 m 0.591
#> 17 y r2 y 0.377
The content is just the first four columns of the output of lavaan::parameterEstimates().
This is the content of implied_stats of the first list:
boot_out_lavaan[[1]]$implied_stats
#> $cov
#> m y x c1 c2
#> m 1.800
#> y 1.724 5.345
#> x 1.076 1.423 1.112
#> c1 0.118 -0.022 -0.040 1.245
#> c2 0.162 0.337 0.127 0.004 0.719
#>
#> $mean
#> numeric(0)
#>
#> $mean_lv
#> numeric(0)
It has three elements. cov is the implied variances and covariances of all variables. If a model has latent variables, they will be included too. The other elements, mean and mean_lv, are the implied means of the observed variables and the latent variables (if any), respectively. They are of zero length if mean structure is not in the fitted model.
The last element, ok, denotes whether the solution in a bootstrap sample is admissible or not (determined by lavaan::lavInspect() with what = "post.check"). If not admissible, it will not be used in forming confidence intervals.
Using the Output of do_boot()
When calling indirect_effect() or cond_indirect_effects(), the argument boot_out can be assigned the output of do_bout(). They will then retrieve he stored bootstrap estimates to form the bootstrap confidence intervals, if requested.
out_lavaan <- indirect_effect(x = "x",
y = "y",
m = "m",
fit = fit_lavaan,
boot_ci = TRUE,
boot_out = boot_out_lavaan)
out_lavaan
#>
#> == Indirect Effect ==
#>
#> Path: x -> m -> y
#> Indirect Effect 0.733
#> 95.0% Bootstrap CI: [0.233 to 1.221]
#>
#> Computation Formula:
#> (b.m~x)*(b.y~m)
#> Computation:
#> (0.93469)*(0.78469)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m~x 0.935
#> y~m 0.785
Reusing the bootstrap estimates can ensure that all analysis with bootstrap confidence intervals are based on the same set of bootstrap samples.
Models Fitted by Several Calls to lm()
Suppose we estimate the parameters using multiple regression. We need to fit two regression models, one predicts m and the other predicts y:
# Fit Models
lm_m <- lm(m ~ x + c1 + c2, dat)
lm_y <- lm(y ~ m + x + c1 + c2, dat)
#
# ###### Regression: Predict m ######
summary(lm_m)
#>
#> Call:
#> lm(formula = m ~ x + c1 + c2, data = dat)
#>
#> Residuals:
#> Min 1Q Median 3Q Max
#> -1.82810 -0.56016 -0.08481 0.52524 2.09155
#>
#> Coefficients:
#> Estimate Std. Error t value Pr(>|t|)
#> (Intercept) 9.68941 0.91979 10.534 <2e-16 ***
#> x 0.93469 0.08083 11.563 <2e-16 ***
#> c1 0.19778 0.07678 2.576 0.0115 *
#> c2 -0.16841 0.10305 -1.634 0.1055
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Residual standard error: 0.8425 on 96 degrees of freedom
#> Multiple R-squared: 0.5981, Adjusted R-squared: 0.5855
#> F-statistic: 47.62 on 3 and 96 DF, p-value: < 2.2e-16
#
# ###### Regression: Predict y ######
#
summary(lm_y)
#>
#> Call:
#> lm(formula = y ~ m + x + c1 + c2, data = dat)
#>
#> Residuals:
#> Min 1Q Median 3Q Max
#> -4.1336 -1.3365 -0.1014 1.4597 6.5470
#>
#> Coefficients:
#> Estimate Std. Error t value Pr(>|t|)
#> (Intercept) 4.4152 3.3016 1.337 0.18432
#> m 0.7847 0.2495 3.145 0.00222 **
#> x 0.5077 0.3057 1.661 0.10004
#> c1 0.1405 0.1941 0.724 0.47093
#> c2 -0.1544 0.2554 -0.604 0.54695
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Residual standard error: 2.06 on 95 degrees of freedom
#> Multiple R-squared: 0.3576, Adjusted R-squared: 0.3305
#> F-statistic: 13.22 on 4 and 95 DF, p-value: 1.336e-08
To use do_boot(), we first combine the regression outputs to one object using lm2list(). The output is an lm_list-class object.
fit_lm <- lm2list(lm_m, lm_y)
fit_lm
#>
#> The models:
#> m ~ x + c1 + c2
#> y ~ m + x + c1 + c2
We can now use do_boot() as described above, using the output of lm2list() instead of the output of lavaan::sem():
boot_out_lm <- do_boot(fit = fit_lm,
R = 100,
seed = 98715)
Speed is rarely a concern for a model with parameters estimated by lm(). Therefore, parallel processing is not used. Because the output may not be saved, it is recommended to set the seed of the random number generation using seed, set to 98715 in the above example. The seed can be any integer within the range allowed in R, see set.seed(). Setting the seed ensures that the same R set of bootstrap samples will be generated every time.
The Structure of the Output
The output of do_boot() using the outputs of lm() is identical to that using the output of lavaan::sem(). It is an object of the class boot_out, which is a list of R lists, each with two elements: est and implied_stats.
This is the content of est of the first list:
boot_out_lm[[1]]$est
#> lhs op rhs est
#> 1 m ~ x 0.9583396
#> 2 m ~ c1 0.2808811
#> 3 m ~ c2 -0.3040130
#> 4 m ~1 9.9351030
#> 5 y ~ m 0.3986059
#> 6 y ~ x 0.5626298
#> 7 y ~ c1 0.5010449
#> 8 y ~ c2 -0.3614863
#> 9 y ~1 11.7212742
The content is similar in structure to the output of lavaan::parameterEstimates(). However, the estimates are the estimates based on lm().
This is the content of implied_stats of the first list:
boot_out_lm[[1]]$implied_stats
#> $cov
#> m x c1 c2 y
#> m 1.7489520 0.99463099 0.32168750 -0.15480736 1.4738922
#> x 0.9946310 1.03034065 0.04418569 0.01709202 0.9921266
#> c1 0.3216875 0.04418569 1.13244802 0.12743087 0.6744295
#> c2 -0.1548074 0.01709202 0.12743087 0.68082701 -0.2343517
#> y 1.4738922 0.99212663 0.67442949 -0.23435172 5.4383227
#>
#> $mean
#> m x c1 c2 y
#> 18.487194 9.848009 2.329366 5.065314 23.967238
It has two elements. cov is the variances and covariances of all variables. Unlike the output based on lavaan::sem(), the content is just the sample variances and covariances of the variables in each bootstrap sample, generated using cov(). The other element, mean, stores sample means of all variables in each bootstrap sample.
Using the Output of do_boot()
When calling indirect_effect() or cond_indirect_effects(), we cab set the argument boot_out to the output of do_bout():
out_lm <- indirect_effect(x = "x",
y = "y",
m = "m",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_lm
#>
#> == Indirect Effect ==
#>
#> Path: x -> m -> y
#> Indirect Effect 0.733
#> 95.0% Bootstrap CI: [0.277 to 1.206]
#>
#> Computation Formula:
#> (b.m~x)*(b.y~m)
#> Computation:
#> (0.93469)*(0.78469)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m~x 0.935
#> y~m 0.785