This article is a brief illustration of how to use `indirect_effect()`

from the package manymome to estimate the indirect effects when the model parameters are estimated by ordinary least squares (OLS) multiple regression using `lm()`

.

This is the sample dataset used for illustration:

```
library(manymome)
dat <- data_med_complicated
print(round(head(dat), 2))
#> x1 x2 m11 m12 m2 y1 y2 c1 c2
#> 1 10.16 4.00 5.84 6.78 7.11 6.06 10.38 5.01 8.20
#> 2 10.89 4.79 4.95 5.81 7.92 5.15 8.52 3.92 9.90
#> 3 9.99 5.79 4.95 4.47 8.21 3.25 7.81 5.91 11.36
#> 4 12.36 4.80 5.56 6.21 8.88 6.27 9.41 6.06 10.49
#> 5 10.85 6.39 6.19 5.39 8.76 5.36 9.84 4.28 9.81
#> 6 10.28 4.58 4.88 4.28 8.50 4.57 10.42 4.71 11.38
```

This dataset has 9 variables: 2 predictors (`x1`

and `x2`

), three mediators (`m11`

, `m12`

, and `m2`

), two outcome variables (`y1`

and `y2`

), and two control variables (`c1`

and `c2`

).

Suppose this is the model to be fitted:

Despite the apparent complexity, the path parameters can be estimated by five multiple regression models:

```
lm_m11 <- lm(m11 ~ x1 + x2 + c1 + c2, dat)
lm_m12 <- lm(m12 ~ m11 + x1 + x2 + c1 + c2, dat)
lm_m2 <- lm(m2 ~ x1 + x2 + c1 + c2, dat)
lm_y1 <- lm(y1 ~ m12 + m2 + m11 + x1 + x2 + c1 + c2, dat)
lm_y2 <- lm(y2 ~ m12 + m2 + m11 + x1 + x2 + c1 + c2, dat)
```

These are the regression coefficient estimates of the paths (those of control variables omitted):

```
#> m11 m12 m2 y1 y2
#> x1 0.352 -0.212 0.022 -0.078 0.115
#> x2 -0.045 -0.072 0.289 0.003 0.062
#> m11 0.454 0.147 0.024
#> m12 0.234 0.135
#> m2 -0.433 -0.436
```

Although not mandatory, it is recommended to combine these five models into one object (a system of regression models) using `lm2list()`

:

```
fit_lm <- lm2list(lm_m11, lm_m12, lm_m2, lm_y1, lm_y2)
fit_lm
#>
#> The models:
#> m11 ~ x1 + x2 + c1 + c2
#> m12 ~ m11 + x1 + x2 + c1 + c2
#> m2 ~ x1 + x2 + c1 + c2
#> y1 ~ m12 + m2 + m11 + x1 + x2 + c1 + c2
#> y2 ~ m12 + m2 + m11 + x1 + x2 + c1 + c2
```

Simply use the `lm()`

outputs as arguments. Order does not matter. To ensure that the regression outputs can be validly combined, `lm2list()`

will also check:

whether the same sample is used in all regression analysis (not just same sample size, but the same set of cases), and

whether the models are “connected”, to ensure that the regression outputs can be validly combined.

To form nonparametric bootstrap confidence interval for indirect effects to be computed, `do_boot()`

can be used to generate bootstrap estimates for all regression coefficients first. These estimates can be reused for any indirect effects to be estimated.

Please see `vignette("do_boot")`

or the help page of `do_boot()`

on how to use this function. In real research, `R`

, the number of bootstrap samples, should be set to 2000 or even 5000. The argument `ncores`

can usually be omitted unless users want to manually control the number of CPU cores used in parallel processing.

We can now use `indirect_effect()`

to estimate the indirect effect and form its bootstrap confidence interval for any path in the model. By reusing the generated bootstrap estimates, there is no need to repeat the resampling.

Suppose we want to estimate the indirect effect from `x1`

to `y1`

through `m11`

and `m12`

:

(Refer to `vignette("manymome")`

and the help page of `indirect_effect()`

on the arguments.)

```
out_x1m11m12y1 <- indirect_effect(x = "x1",
y = "y1",
m = c("m11", "m12"),
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x1m11m12y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Indirect Effect 0.037
#> 95.0% Bootstrap CI: [0.003 to 0.077]
#>
#> Computation Formula:
#> (b.m11~x1)*(b.m12~m11)*(b.y1~m12)
#> Computation:
#> (0.35204)*(0.45408)*(0.23402)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m11~x1 0.352
#> m12~m11 0.454
#> y1~m12 0.234
```

The indirect effect is 0.037, with 95% confidence interval [0.003, 0.077].

Similarly, we can estimate the indirect effect from `x2`

to `y2`

through `m2`

:

```
out_x2m2y2 <- indirect_effect(x = "x2",
y = "y2",
m = "m2",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x2m2y2
#>
#> == Indirect Effect ==
#>
#> Path: x2 -> m2 -> y2
#> Indirect Effect -0.126
#> 95.0% Bootstrap CI: [-0.233 to -0.043]
#>
#> Computation Formula:
#> (b.m2~x2)*(b.y2~m2)
#> Computation:
#> (0.28901)*(-0.43598)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m2~x2 0.289
#> y2~m2 -0.436
```

The indirect effect is -0.126, with 95% confidence interval [-0.233, -0.043].

Note that any indirect path in the model can be estimated this way. Suppose, after doing the regression analysis, we want to estimate the indirect effect from `x2`

to `m12`

through `m11`

, we just call `indirect_effect()`

:

```
out_x2m11m12 <- indirect_effect(x = "x2",
y = "m12",
m = "m11",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x2m11m12
#>
#> == Indirect Effect ==
#>
#> Path: x2 -> m11 -> m12
#> Indirect Effect -0.020
#> 95.0% Bootstrap CI: [-0.139 to 0.110]
#>
#> Computation Formula:
#> (b.m11~x2)*(b.m12~m11)
#> Computation:
#> (-0.04471)*(0.45408)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m11~x2 -0.0447
#> m12~m11 0.4541
```

The indirect effect is -0.020, with 95% confidence interval [-0.139, 0.110].

There is no limit on the path to be estimated, as long as all required path coefficients are in the model. `indirect_effect()`

will also check whether a path is valid. Therefore, estimating the effect from `x1`

to `m2`

through `m11`

will result in an error because this path does not exist in the model defined by the regression outputs.

The standardized indirect effect from `x1`

to `y1`

through `m11`

and `m12`

can be estimated by setting `standardized_x`

and `standardized_y`

to `TRUE:

```
std_x1m11m12y1 <- indirect_effect(x = "x1",
y = "y1",
m = c("m11", "m12"),
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm,
standardized_x = TRUE,
standardized_y = TRUE)
std_x1m11m12y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Indirect Effect 0.039
#> 95.0% Bootstrap CI: [0.004 to 0.085]
#>
#> Computation Formula:
#> (b.m11~x1)*(b.m12~m11)*(b.y1~m12)*sd_x1/sd_y1
#> Computation:
#> (0.35204)*(0.45408)*(0.23402)*(1.11605)/(1.06579)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m11~x1 0.352
#> m12~m11 0.454
#> y1~m12 0.234
#>
#> NOTE: The effects of the component paths are from the model, not standardized.
```

The standardized indirect effect is 0.039, with 95% confidence interval [0.004,0.085].

Similarly, we can estimate the standardized indirect effect from `x1`

to `y1`

through `m2`

:

```
std_x1m2y1 <- indirect_effect(x = "x1",
y = "y1",
m = "m2",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm,
standardized_x = TRUE,
standardized_y = TRUE)
std_x1m2y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m2 -> y1
#> Indirect Effect -0.010
#> 95.0% Bootstrap CI: [-0.069 to 0.067]
#>
#> Computation Formula:
#> (b.m2~x1)*(b.y1~m2)*sd_x1/sd_y1
#> Computation:
#> (0.02233)*(-0.43300)*(1.11605)/(1.06579)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m2~x1 0.0223
#> y1~m2 -0.4330
#>
#> NOTE: The effects of the component paths are from the model, not standardized.
```

The standardized indirect effect is -0.010, with 95% confidence interval [-0.069, 0.067].

Note that the results of `indirect_effect()`

can be added using `+`

.

For example, to find the *total* *indirect* effect of `x1`

on `y1`

, we need to compute the indirect effects along the following paths:

`x1`

to`m11`

to`m12`

to`y1`

`x1`

to`m11`

to`y1`

`x1`

to`m12`

to`y1`

`x1`

to`m2`

to`y1`

The indirect effects along Path a has already been computed. We compute the indirect effects along Paths b, c, and d below:

```
out_x1m11y1 <- indirect_effect(x = "x1",
y = "y1",
m = "m11",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x1m11y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> y1
#> Indirect Effect 0.052
#> 95.0% Bootstrap CI: [-0.036 to 0.103]
#>
#> Computation Formula:
#> (b.m11~x1)*(b.y1~m11)
#> Computation:
#> (0.35204)*(0.14694)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m11~x1 0.352
#> y1~m11 0.147
```

```
out_x1m12y1 <- indirect_effect(x = "x1",
y = "y1",
m = "m12",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x1m12y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m12 -> y1
#> Indirect Effect -0.050
#> 95.0% Bootstrap CI: [-0.125 to -0.000]
#>
#> Computation Formula:
#> (b.m12~x1)*(b.y1~m12)
#> Computation:
#> (-0.21182)*(0.23402)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m12~x1 -0.212
#> y1~m12 0.234
```

```
out_x1m2y1 <- indirect_effect(x = "x1",
y = "y1",
m = "m2",
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
out_x1m2y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m2 -> y1
#> Indirect Effect -0.010
#> 95.0% Bootstrap CI: [-0.077 to 0.064]
#>
#> Computation Formula:
#> (b.m2~x1)*(b.y1~m2)
#> Computation:
#> (0.02233)*(-0.43300)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m2~x1 0.0223
#> y1~m2 -0.4330
```

We can now compute the total *indirect* effect:

```
out_x1y1_total <- out_x1m11m12y1 + out_x1m11y1 + out_x1m12y1 + out_x1m2y1
out_x1y1_total
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Path: x1 -> m11 -> y1
#> Path: x1 -> m12 -> y1
#> Path: x1 -> m2 -> y1
#> Function of Effects: 0.030
#> 95.0% Bootstrap CI: [-0.088 to 0.132]
#>
#> Computation of the Function of Effects:
#> (((x1->m11->m12->y1)
#> +(x1->m11->y1))
#> +(x1->m12->y1))
#> +(x1->m2->y1)
#>
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
```

The total effect of `f1`

on `f4`

is 0.030, with 95% confidence interval [-0.088, 0.132].

See `help("math_indirect")`

for further details on addition for `indirect_effect()`

outputs.

Subtraction can also be conducted using `-`

. For example, we can compute the difference between the indirect effect of `x1`

on `y1`

through `m11`

and `m12`

and the indirect effect of `x1`

on `y1`

through `m2`

:

```
out_x1_diff <- out_x1m11m12y1 - out_x1m2y1
out_x1_diff
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Path: x1 -> m2 -> y1
#> Function of Effects: 0.047
#> 95.0% Bootstrap CI: [-0.038 to 0.118]
#>
#> Computation of the Function of Effects:
#> (x1->m11->m12->y1)
#> -(x1->m2->y1)
#>
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
```

The difference in effects is 0.047, with 95% confidence interval [-0.038, 0.118].

See `help("math_indirect")`

for further details on subtraction for `indirect_effect()`

outputs.

If there are several indirect paths in a model, the function `all_indirect_paths()`

can be used to automatically identify all indirect paths (a path with at least one mediator) in a model:

```
all_paths <- all_indirect_paths(fit = fit_lm)
all_paths
#> Call:
#> all_indirect_paths(fit = fit_lm)
#> Path(s):
#> path
#> 1 m11 -> m12 -> y1
#> 2 m11 -> m12 -> y2
#> 3 x1 -> m11 -> m12
#> 4 x1 -> m11 -> m12 -> y1
#> 5 x1 -> m11 -> y1
#> 6 x1 -> m12 -> y1
#> 7 x1 -> m2 -> y1
#> 8 x1 -> m11 -> m12 -> y2
#> 9 x1 -> m11 -> y2
#> 10 x1 -> m12 -> y2
#> 11 x1 -> m2 -> y2
#> 12 x2 -> m11 -> m12
#> 13 x2 -> m11 -> m12 -> y1
#> 14 x2 -> m11 -> y1
#> 15 x2 -> m12 -> y1
#> 16 x2 -> m2 -> y1
#> 17 x2 -> m11 -> m12 -> y2
#> 18 x2 -> m11 -> y2
#> 19 x2 -> m12 -> y2
#> 20 x2 -> m2 -> y2
#> 21 c1 -> m11 -> m12
#> 22 c1 -> m11 -> m12 -> y1
#> 23 c1 -> m11 -> y1
#> 24 c1 -> m12 -> y1
#> 25 c1 -> m2 -> y1
#> 26 c1 -> m11 -> m12 -> y2
#> 27 c1 -> m11 -> y2
#> 28 c1 -> m12 -> y2
#> 29 c1 -> m2 -> y2
#> 30 c2 -> m11 -> m12
#> 31 c2 -> m11 -> m12 -> y1
#> 32 c2 -> m11 -> y1
#> 33 c2 -> m12 -> y1
#> 34 c2 -> m2 -> y1
#> 35 c2 -> m11 -> m12 -> y2
#> 36 c2 -> m11 -> y2
#> 37 c2 -> m12 -> y2
#> 38 c2 -> m2 -> y2
```

The initial list is very long because control variables (`c1`

and `c2`

) are included in the search. Moreover, paths that start from a mediator or end at a mediator are also included. Users can customize the search:

```
all_paths <- all_indirect_paths(fit = fit_lm,
x = c("x1", "x2"),
y = c("y1", "y2"),
exclude = c("c1", "c2"))
all_paths
#> Call:
#> all_indirect_paths(fit = fit_lm, exclude = c("c1", "c2"), x = c("x1",
#> "x2"), y = c("y1", "y2"))
#> Path(s):
#> path
#> 1 x1 -> m11 -> m12 -> y1
#> 2 x1 -> m11 -> y1
#> 3 x1 -> m12 -> y1
#> 4 x1 -> m2 -> y1
#> 5 x1 -> m11 -> m12 -> y2
#> 6 x1 -> m11 -> y2
#> 7 x1 -> m12 -> y2
#> 8 x1 -> m2 -> y2
#> 9 x2 -> m11 -> m12 -> y1
#> 10 x2 -> m11 -> y1
#> 11 x2 -> m12 -> y1
#> 12 x2 -> m2 -> y1
#> 13 x2 -> m11 -> m12 -> y2
#> 14 x2 -> m11 -> y2
#> 15 x2 -> m12 -> y2
#> 16 x2 -> m2 -> y2
```

`x`

is a vector of names. Only paths start from these variables will be included.`y`

is a vector of names. Only paths end at these variables will be included.`exclude`

is a vector of names. Paths that involve these variables will be excluded.

The output is a `all_paths`

-class object. It can be used in `many_indirect_effects()`

```
out_all <- many_indirect_effects(paths = all_paths,
fit = fit_lm,
boot_ci = TRUE,
boot_out = boot_out_lm)
```

The first argument, `paths`

, is the output of `all_indirect_paths()`

. The other arguments will be passed to `indirect_effect()`

.

The output is an `indirect_list`

-class object, which is a list of the outputs of `indirect_effects()`

. If printed, a summary of the indirect effects will be printed:

```
out_all
#>
#> == Indirect Effect(s) ==
#> ind CI.lo CI.hi Sig
#> x1 -> m11 -> m12 -> y1 0.037 0.003 0.077 Sig
#> x1 -> m11 -> y1 0.052 -0.036 0.103
#> x1 -> m12 -> y1 -0.050 -0.125 -0.000 Sig
#> x1 -> m2 -> y1 -0.010 -0.077 0.064
#> x1 -> m11 -> m12 -> y2 0.022 -0.015 0.065
#> x1 -> m11 -> y2 0.009 -0.086 0.093
#> x1 -> m12 -> y2 -0.029 -0.089 0.014
#> x1 -> m2 -> y2 -0.010 -0.074 0.068
#> x2 -> m11 -> m12 -> y1 -0.005 -0.044 0.017
#> x2 -> m11 -> y1 -0.007 -0.055 0.034
#> x2 -> m12 -> y1 -0.017 -0.054 0.049
#> x2 -> m2 -> y1 -0.125 -0.258 -0.031 Sig
#> x2 -> m11 -> m12 -> y2 -0.003 -0.021 0.022
#> x2 -> m11 -> y2 -0.001 -0.021 0.052
#> x2 -> m12 -> y2 -0.010 -0.056 0.045
#> x2 -> m2 -> y2 -0.126 -0.233 -0.043 Sig
#>
#> - [CI.lo to CI.hi] are 95.0% percentile confidence intervals by
#> nonparametric bootstrapping with 100 samples.
#> - The 'ind' column shows the indirect effects.
#>
```

The output of `many_indirect_effects()`

is a named list, names being the path name as appeared in the output. Individual indirect effects can be extracted using either the indices or the path names

An example using index:

```
out1 <- out_all[[1]]
out1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Indirect Effect 0.037
#> 95.0% Bootstrap CI: [0.003 to 0.077]
#>
#> Computation Formula:
#> (b.m11~x1)*(b.m12~m11)*(b.y1~m12)
#> Computation:
#> (0.35204)*(0.45408)*(0.23402)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m11~x1 0.352
#> m12~m11 0.454
#> y1~m12 0.234
```

An example using path name (though not recommended because the name is usually long):

```
out2 <- out_all[["x2 -> m2 -> y2"]]
out2
#>
#> == Indirect Effect ==
#>
#> Path: x2 -> m2 -> y2
#> Indirect Effect -0.126
#> 95.0% Bootstrap CI: [-0.233 to -0.043]
#>
#> Computation Formula:
#> (b.m2~x2)*(b.y2~m2)
#> Computation:
#> (0.28901)*(-0.43598)
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
#>
#> Coefficients of Component Paths:
#> Path Coefficient
#> m2~x2 0.289
#> y2~m2 -0.436
```

The extracted element can be used just like the outputs of `indirect_effect()`

in previous section.

See the help page of `all_indirect_paths()`

and `many_indirect_effects()`

for other arguments available.

The total indirect effect between two variables in a list of paths can be computed by `total_indirect_effect()`

.

```
total_x1_y1 <- total_indirect_effect(out_all,
x = "x1",
y = "y1")
total_x1_y1
#>
#> == Indirect Effect ==
#>
#> Path: x1 -> m11 -> m12 -> y1
#> Path: x1 -> m11 -> y1
#> Path: x1 -> m12 -> y1
#> Path: x1 -> m2 -> y1
#> Function of Effects: 0.030
#> 95.0% Bootstrap CI: [-0.088 to 0.132]
#>
#> Computation of the Function of Effects:
#> (((x1->m11->m12->y1)
#> +(x1->m11->y1))
#> +(x1->m12->y1))
#> +(x1->m2->y1)
#>
#>
#> Percentile confidence interval formed by nonparametric bootstrapping
#> with 100 bootstrap samples.
```

The first argument is the output of `many_indirect_effects()`

or a list of `indirect`

-class object. `x`

is the name of the variable that starts the paths. `y`

is the name of the variable that ends the paths.

For further information on `do_boot()`

and `indirect_effect()`

, please refer to their help pages.