This document will walk you through how to use `birdie`

.
First, load in the package.

For a concrete example, we’ll use some fake voter file data. Our goal is to estimate turnout rates by race.

```
data(pseudo_vf)
print(pseudo_vf)
#> # A tibble: 5,000 × 4
#> last_name zip race turnout
#> <fct> <fct> <fct> <fct>
#> 1 BEAVER 28748 white yes
#> 2 WILLIAMS 28144 black no
#> 3 ROSEN 28270 white yes
#> 4 SMITH 28677 black yes
#> 5 FAY 28748 white no
#> 6 CHURCH 28215 white yes
#> 7 JOHNSON 28212 black yes
#> 8 SZCZYGIEL NA white yes
#> 9 SUMMERS 28152 black yes
#> 10 STARLING 28650 white yes
#> # ℹ 4,990 more rows
```

You’ll notice that we have a `race`

column in our data.
That will allow us to check our work once we’re done. For now, we’ll
generate the *true* distribution of turnout given race, along
with the marginal distribution of each variable.

```
p_xr = prop.table(table(pseudo_vf$turnout, pseudo_vf$race), margin=2)
p_x = prop.table(table(pseudo_vf$turnout))
p_r = prop.table(table(pseudo_vf$race))
```

There are two steps to applying the `birdie`

methodology:

- Generate a first set of individual race probabilities using Bayesian
Improved Surname Geocoding (
`bisg()`

). - For a specific outcome variable of interest, run a Bayesian
Instrumental Regression for Disparity Estimation (
`birdie()`

) model to come up with estimated probabilities conditional on race.

## Generating BISG probabilities

For the first step, you can use any BISG software, including the `wru`

R
package. However, `birdie`

provides its own
`bisg()`

function to make this easy and very computationally
efficient. To use `bisg()`

, you provide a formula that labels
the predictors used. You use `nm()`

to show which variable
contains last names, which must always be provided. ZIP codes and states
can be labeled with `zip()`

and `state()`

. Other
types of geographies can be used as well—just read the documentation for
`bisg()`

.

```
r_probs = bisg(~ nm(last_name) + zip(zip), data=pseudo_vf, p_r=p_r)
print(r_probs)
#> # A tibble: 5,000 × 6
#> pr_white pr_black pr_hisp pr_asian pr_aian pr_other
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.971 0.00517 0.00201 0.000144 0.0136 0.00819
#> 2 0.128 0.860 0.00186 0.000169 0.00104 0.00920
#> 3 0.979 0.00539 0.00436 0.00232 0.000606 0.00837
#> 4 0.521 0.459 0.00535 0.000219 0.00150 0.0124
#> 5 0.989 0.00165 0.00257 0.000319 0.00182 0.00506
#> 6 0.522 0.431 0.0175 0.00125 0.00384 0.0242
#> 7 0.112 0.859 0.0113 0.000720 0.00190 0.0153
#> 8 0.991 0.00794 0.000766 0 0 0
#> 9 0.701 0.283 0.00183 0.000160 0.00136 0.0122
#> 10 0.854 0.133 0.00265 0.000204 0.00241 0.00845
#> # ℹ 4,990 more rows
```

Each row `r_probs`

matches a row in
`pseudo_vf`

. It’s important to note that here we are assuming
that we know the overall racial distribution of our population
(registered voters). Because of that, we provide the
`p_r=p_r`

argument, which gives `bisg()`

the
overall racial distribution. If you don’t know the overall racial
distribution in your context (even a guess is better than nothing), then
you could pass in something like the national distribution of race
(which is conveniently provided by `p_r_natl()`

).

### Alternative race probabilities

Rather than predicting individual race with the standard BISG methodology, you may want to use the improved fully Bayesian Surname Improved Geocoding (fBISG) of Imai et al. (2022). Compared to standard BISG, fBISG accounts for measurement error in the Census counts. This improves the calibration of the probabilities (which is important for accurate disparity estimation), and also improves accuracy among minority populations.

To generate fBISG probabilities, `birdie`

provides the
`bisg_me()`

function, which works just like
`bisg()`

.

Comparing to the standard BISG probabilities, the measurement-error-adjusted probabilities are often more calibrated. One way to see this is to estimate the marginal distribution of race from the probabilities.

```
colMeans(r_probs)
#> pr_white pr_black pr_hisp pr_asian pr_aian pr_other
#> 0.656372686 0.277807934 0.032031532 0.010139008 0.009564482 0.014084358
colMeans(r_probs_me)
#> pr_white pr_black pr_hisp pr_asian pr_aian pr_other
#> 0.7088246 0.2003042 0.0434176 0.0185575 0.0118295 0.0170666
# actual
p_r
#>
#> white black hisp asian aian other
#> 0.7178 0.2078 0.0338 0.0114 0.0102 0.0190
```

The fBISG probabilities are much closer to the actual distribution of race in the data than the standard BISG probabilities are.

### Why aren’t BISG probabilities enough?

At this point, many analyses stop. One can threshold the BISG probabilities to produce a single racial prediction for every individual. Or one can use the BISG probabilities inside weighted averages and weighted regressions.

For example, we could try to estimate turnout rates by race, using the BISG probabilities as weights:

```
est_weighted(r_probs, turnout ~ 1, data=pseudo_vf)
#> Weighted estimator
#> Formula: turnout ~ 1
#> Data: pseudo_vf
#> Number of obs: 5,000; groups: 1
#> Estimated distribution:
#> white black hisp asian aian other
#> no 0.316 0.335 0.385 0.531 0.502 0.341
#> yes 0.684 0.665 0.615 0.469 0.498 0.659
```

However, as discussed in the methodology paper (McCartan et al. 2023), this approach is generally biased. Essentially, it only measures the association between race and turnout which is mediated through names and locations. It doesn’t properly account for other ways in which race could be associated with the outcome. The BIRDiE methodology addresses this problem by relying on a different assumption: that names are independent of outcomes (here, turnout) conditional on location and race. For example, among White voters in a particular ZIP code, this assumption would mean that voters name Smith and those named Jones are both equally likely to vote.

## Estimating distributions by race

We’re now ready to estimate turnout by race. For this we’ll use the
`birdie()`

function, and provide it with a formula describing
our BIRDiE model, including our variable of interest
`turnout`

and our geography variable `zip`

. We
provide `family=cat_mixed()`

to indicate that we want to fit
a Categorical mixed-effects regression model for turnout. Here, we wrap
`zip`

in the `proc_zip()`

function, which, among
other things, recodes missing ZIP codes as “Other” so that the model
doesn’t encounter any missing data. The first argument to
`birdie()`

is `r_probs`

, the racial probabilities.
`birdie`

knows how to handle its columns of because they came
from this package. If you use a different package, the columns may be
named differently. The `prefix`

parameter to
`birdie()`

lets you specify the naming convention for your
probabilities.

```
fit = birdie(r_probs, turnout ~ (1 | proc_zip(zip)), data=pseudo_vf, family=cat_mixed())
#> Using default prior for Pr(Y | R):
#> → Prior scale on intercepts: 2.0
#> → Prior scale on fixed effects coefficients: 0.2
#> → Prior mean of random effects standard deviation: 0.05
#> ⠙ EM iterations 14 done (6.7/s) | 2.1s
#>
#> ⠙ EM iterations 74 done (18/s) | 4.1s
#>
#> This message is displayed once every 8 hours.
print(fit)
#> Categorical mixed-effects BIRDiE model
#> Formula: turnout ~ (1 | proc_zip(zip))
#> Data: pseudo_vf
#> Number of obs: 5,000
#> Estimated distribution:
#> white black hisp asian aian other
#> no 0.293 0.36 0.414 0.594 0.802 0.544
#> yes 0.707 0.64 0.586 0.406 0.198 0.456
```

### Types of BIRDiE Models

The BIRDiE model we just fit is a *mixed-effects* model. It
estimates a different relationship between turnout and race in every
ZIP, but partially pools these estimates towards a common global
estimate of the turnout-race relationship. BIRDiE supports two other
general types of models as well: the complete-pooling and no-pooling
models. The former uses a formula like `turnout ~ 1`

and only
estimates a single, global relationship between turnout and race. The
model therefore assumes that turnout has no association with geography,
after controlling for race. The latter model uses a formula like
`turnout ~ proc_zip(zip)`

. While this model can be more
computationally efficient to fit than the mixed-effects model, its
performance can suffer on smaller datasets like the one used here. We
recommend the mixed-effects model for general use.

### Extracting population and small-area estimates

The `birdie()`

function returns an object of class
`birdie`

, which supports many additional functions. You can
quickly extract the population turnout-race estimates using
`coef()`

or `tidy()`

. The former produces a
matrix, while the latter returns a tidy data frame that may be useful in
plotting or in downstream analyses.

```
tidy(fit)
#> # A tibble: 12 × 3
#> turnout race estimate
#> <chr> <chr> <dbl>
#> 1 no white 0.293
#> 2 yes white 0.707
#> 3 no black 0.360
#> 4 yes black 0.640
#> 5 no hisp 0.414
#> 6 yes hisp 0.586
#> 7 no asian 0.594
#> 8 yes asian 0.406
#> 9 no aian 0.802
#> 10 yes aian 0.198
#> 11 no other 0.544
#> 12 yes other 0.456
```

These estimates are quite close to the true distribution of turnout and race for most racial groups:

```
coef(fit)
#> white black hisp asian aian other
#> no 0.2933854 0.360157 0.4141862 0.5943285 0.8020794 0.5438751
#> yes 0.7066146 0.639843 0.5858138 0.4056715 0.1979206 0.4561249
p_xr # Actual
#>
#> white black hisp asian aian other
#> no 0.3014767 0.3570741 0.4142012 0.4385965 0.6666667 0.5894737
#> yes 0.6985233 0.6429259 0.5857988 0.5614035 0.3333333 0.4105263
```

The estimates suffer here for the smaller racial groups, which each comprise roughly 1-2% of the sample

You can also extract estimates by geography (and other covariates, if
they are present in the model formula) by passing
`subgroup=TRUE`

to either `coef()`

or
`tidy()`

.

### Generating improved individual BISG probabilities

In addition to producing estimates for the whole sample and specific subgroups, BIRDiE yields improved individual race probabilities. The “input” BISG probabilities are for race given surname and location. The “output” probabilities from BIRDiE are for race given surname, location, and also turnout. When the outcome variable is strongly associated with race, these BIRDiE-improved probabilities can be significantly more accurate than the standard BISG probabilities.

Accessing these improved probabilities is simple with the
`fitted()`

function.

```
head(fitted(fit))
#> # A tibble: 6 × 6
#> pr_white pr_black pr_hisp pr_asian pr_aian pr_other
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.987 0.00278 0.00215 0.0000794 0.00237 0.00598
#> 2 0.00321 0.987 0.00100 0.000161 0.00146 0.00677
#> 3 0.978 0.0106 0.00236 0.000227 0.000157 0.00866
#> 4 0.529 0.460 0.00111 0.000109 0.000274 0.00916
#> 5 0.978 0.00377 0.00217 0.000715 0.00595 0.00892
#> 6 0.570 0.389 0.0189 0.000675 0.000552 0.0201
plot(r_probs$pr_white, fitted(fit)$pr_white, cex=0.1)
```

### Bootstrapping standard errors

One drawback of the computationally efficient EM algorithm that
`birdie()`

uses for model fitting is the lack of uncertainty
quantification. The function does however support bootstrapping for some
model types. In general, we recommend bootstrapping a simple
complete-pooling model to understand the rough amount of sampling
variation present. For most datasets, non-sampling error in Census data
and violations of model assumptions will cause much more bias than
sampling variance.

To bootstrap, simply pass a nonzero value of `se_boot`

to
`birdie()`

. This parameter controls the number of bootstrap
replicates. The standard errors are accessible with `$se`

or
using the `vcov()`

generic.

```
fit_boot = birdie(r_probs, turnout ~ 1, data=pseudo_vf, se_boot=200)
#> Using weakly informative empirical Bayes prior for Pr(Y | R)
#> This message is displayed once every 8 hours.
fit_boot$se
#> white black hisp asian aian other
#> no 0.007569618 0.01045631 0.03013438 0.05059397 0.04739559 0.007533608
#> yes 0.007569618 0.01045631 0.03013438 0.05059397 0.04739559 0.007533608
```