srvyr compared to the survey package (original) (raw)

2024-08-19

The srvyr package adds dplyr like syntax to the survey package. This vignette focuses on howsrvyr compares to the survey package, for more information about survey design and analysis, check out the vignettes in the survey package, or Thomas Lumley’s book, Complex Surveys: A Guide to Analysis Using R. (Also see the bottom of this document for some more resources).

Everything that srvyr can do, can also be done insurvey. In fact, behind the scenes the surveypackage is doing all of the hard work for srvyr.srvyr strives to make your code simpler and more easily readable to you, especially if you are already used to thedplyr package.

Motivating example

The dplyr package has made it easy to write code to summarize data. For example, if we wanted to check how the year-to-year change in academic progress indicator score varied by school level and percent of parents were high school graduates, we can do this:

library(survey)
library(ggplot2)
library(dplyr)

data(api)

out <- apistrat %>%
  mutate(hs_grad_pct = cut(hsg, c(0, 20, 100), include.lowest = TRUE,
                           labels = c("<20%", "20+%"))) %>%
  group_by(stype, hs_grad_pct) %>%
  summarize(api_diff = weighted.mean(api00 - api99, pw),
            n = n())

ggplot(data = out, aes(x = stype, y = api_diff, group = hs_grad_pct, fill = hs_grad_pct)) +
  geom_col(stat = "identity", position = "dodge") +
  geom_text(aes(y = 0, label = n), position = position_dodge(width = 0.9), vjust = -1)
## Warning in geom_col(stat = "identity", position = "dodge"): Ignoring unknown
## parameters: `stat`

However, if we wanted to add error bars to the graph to capture the uncertainty due to sampling variation, we have to completely rewrite thedplyr code for the survey package.srvyr allows a more direct translation.

Preparing a survey dataset

as_survey_design(), as_survey_rep() andas_survey_twophase() are analogous tosurvey::svydesign(), survey::svrepdesign() andsurvey::twophase() respectively. Because they are designed to match dplyr’s style of non-standard evaluation, they accept bare column names instead of formulas (~). They also move the data argument first, so that it is easier to use magrittrpipes (%>%).

library(srvyr)

# simple random sample
srs_design_srvyr <- apisrs %>% as_survey_design(ids = 1, fpc = fpc)

srs_design_survey <- svydesign(ids = ~1, fpc = ~fpc, data = apisrs)

The srvyr functions also acceptdplyr::select()’s special selection functions (such asstarts_with(), one_of(), etc.), so these functions are analogous:

# selecting variables to keep in the survey object (stratified example)
strat_design_srvyr <- apistrat %>%
  as_survey_design(1, strata = stype, fpc = fpc, weight = pw,
                variables = c(stype, starts_with("api")))

strat_design_survey <- svydesign(~1, strata = ~stype, fpc = ~fpc,
                                 variables = ~stype + api99 + api00 + api.stu,
                                 weight = ~pw, data = apistrat)

The function as_survey() will automatically choose between the three as_survey_* functions based on the arguments, so you can save a few keystrokes.

# simple random sample (again)
srs_design_srvyr2 <- apisrs %>% as_survey(ids = 1, fpc = fpc)

Data manipulation

Once you’ve set up your survey data, you can use dplyrverbs such as mutate(), select(),filter() and rename().

strat_design_srvyr <- strat_design_srvyr %>%
  mutate(api_diff = api00 - api99) %>%
  rename(api_students = api.stu)

strat_design_survey$variables$api_diff <- strat_design_survey$variables$api00 -
  strat_design_survey$variables$api99
names(strat_design_survey$variables)[names(strat_design_survey$variables) == "api.stu"] <- "api_students"

Note that arrange() is not available, because thesrvyr object expects to stay in the same order. Nor are two-table verbs such as full_join(),bind_rows(), etc. available to srvyr objects either because they may have implications on the survey design. If you need to use these functions, you should use them earlier in your analysis pipeline, when the objects are still stored asdata.frames.

Summary statistics

Of the entire population

srvyr also provides summarize() and several survey-specific functions that calculate summary statistics on numeric variables: survey_mean(), survey_total(),survey_quantile() and survey_ratio(). These functions differ from their counterparts in survey because they always return a data.frame in a consistent format. As such, they do not return the variance-covariance matrix, and so are not as flexible.

# Using srvyr
out <- strat_design_srvyr %>%
  summarize(api_diff = survey_mean(api_diff, vartype = "ci"))

out
## # A tibble: 1 × 3
##   api_diff api_diff_low api_diff_upp
##      <dbl>        <dbl>        <dbl>
## 1     32.9         28.8         36.9
# Using survey
out <- svymean(~api_diff, strat_design_survey)

out
##            mean     SE
## api_diff 32.893 2.0511
##             2.5 %   97.5 %
## api_diff 28.87241 36.91262

By group

srvyr also allows you to calculate statistics on numeric variables by group, using group_by().

# Using srvyr
strat_design_srvyr %>%
  group_by(stype) %>%
  summarize(api_increase = survey_total(api_diff >= 0),
            api_decrease = survey_total(api_diff < 0))
## # A tibble: 3 × 5
##   stype api_increase api_increase_se api_decrease api_decrease_se
##   <fct>        <dbl>           <dbl>        <dbl>           <dbl>
## 1 E            4067.           119.         354.            119. 
## 2 H             498.            49.4        257.             49.4
## 3 M             998.            19.9         20.4            19.9
# Using survey
svyby(~api_diff >= 0, ~stype, strat_design_survey, svytotal)
##   stype api_diff >= 0FALSE api_diff >= 0TRUE se.api_diff >= 0FALSE
## E     E             353.68           4067.32             119.17185
## H     H             256.70            498.30              49.37208
## M     M              20.36            997.64              19.85371
##   se.api_diff >= 0TRUE
## E            119.17185
## H             49.37208
## M             19.85371

Proportions by group

You can also calculate the proportion or count in each group of a factor or character variable by leaving x empty insurvey_mean() or survey_total().

# Using srvyr
srs_design_srvyr %>%
  group_by(awards) %>%
  summarize(proportion = survey_mean(),
            total = survey_total())
## # A tibble: 2 × 5
##   awards proportion proportion_se total total_se
##   <fct>       <dbl>         <dbl> <dbl>    <dbl>
## 1 No           0.38        0.0338 2354.     210.
## 2 Yes          0.62        0.0338 3840.     210.
# Using survey
svymean(~awards, srs_design_survey)
##           mean     SE
## awardsNo  0.38 0.0338
## awardsYes 0.62 0.0338
svytotal(~awards, srs_design_survey)
##            total     SE
## awardsNo  2353.7 209.65
## awardsYes 3840.3 209.65

Unweighted calculations

Finally, the unweighted() function can act as an escape hatch to calculate unweighted calculations on the dataset.

# Using srvyr
strat_design_srvyr %>%
  group_by(stype) %>%
  summarize(n = unweighted(n()))
## # A tibble: 3 × 2
##   stype     n
##   <fct> <int>
## 1 E       100
## 2 H        50
## 3 M        50
# Using survey
svyby(~api99, ~stype, strat_design_survey, unwtd.count)
##   stype counts se
## E     E    100  0
## H     H     50  0
## M     M     50  0

Back to the example

So now, we have all the tools needed to create the first graph and add error bounds. Notice that the data manipulation code is nearly identical to the dplyr code, with a little extra set up, and replacing weighted.mean() withsurvey_mean.

strat_design <- apistrat %>%
  as_survey_design(strata = stype, fpc = fpc, weight  = pw)

out <- strat_design %>%
  mutate(hs_grad_pct = cut(hsg, c(0, 20, 100), include.lowest = TRUE,
                           labels = c("<20%", "20+%"))) %>%
  group_by(stype, hs_grad_pct) %>%
  summarize(api_diff = survey_mean(api00 - api99, vartype = "ci"),
            n = unweighted(n()))

ggplot(data = out, aes(x = stype, y = api_diff, group = hs_grad_pct, fill = hs_grad_pct,
                       ymax = api_diff_upp, ymin = api_diff_low)) +
  geom_col(stat = "identity", position = "dodge") +
  geom_errorbar(position = position_dodge(width = 0.9), width = 0.1) +
  geom_text(aes(y = 0, label = n), position = position_dodge(width = 0.9), vjust = -1)
## Warning in geom_col(stat = "identity", position = "dodge"): Ignoring unknown
## parameters: `stat`

Comparison to the survey package (Degrees of freedom)

For the most part, srvyr tries to be a drop-in replacement for the survey package, only changing the syntax that you wrote. However, the way that calculations of degrees of freedom when calculating confidence intervals is different.

srvyr assumes that you want to use the true degrees of freedom by default, but the survey package usesInf as the default. You can use the argumentdf to get the same result as the survey package.

# Set pillar print methods so tibble has more decimal places
old_sigfig <- options("pillar.sigfig")
options("pillar.sigfig" = 5)

# survey default
estimate <- svymean(~api99, strat_design)
confint(estimate)
##          2.5 %   97.5 %
## api99 609.8659 648.9238
# srvyr default
strat_design %>%
  summarize(x = survey_mean(api99, vartype = "ci"))
## # A tibble: 1 × 3
##        x  x_low  x_upp
##    <dbl>  <dbl>  <dbl>
## 1 629.39 609.75 649.04
# setting the degrees of freedom so srvyr matches survey default
strat_design %>%
  summarize(x = survey_mean(api99, vartype = "ci", df = Inf)) %>%
  print()
## # A tibble: 1 × 3
##        x  x_low  x_upp
##    <dbl>  <dbl>  <dbl>
## 1 629.39 609.87 648.92
# setting the degrees of freedom so survey matches survey default
confint(estimate, df = degf(strat_design))
##          2.5 %   97.5 %
## api99 609.7452 649.0445
# reset significant figures
options("pillar.sigfig" = old_sigfig)

Grab Bag

Using survey functions on srvyrobjects

Because srvyr objects are just surveyobjects with some extra structure, all of the functions fromsurvey will still work with them. If you need to calculate something beyond simple summary statistics, you can usesurvey functions.

glm <- svyglm(api00 ~ ell + meals + mobility, design = strat_design)
summary(glm)
## 
## Call:
## svyglm(formula = api00 ~ ell + meals + mobility, design = strat_design)
## 
## Survey design:
## Called via srvyr
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 820.8873    10.0777  81.456   <2e-16 ***
## ell          -0.4806     0.3920  -1.226    0.222    
## meals        -3.1415     0.2839 -11.064   <2e-16 ***
## mobility      0.2257     0.3932   0.574    0.567    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for gaussian family taken to be 5171.966)
## 
## Number of Fisher Scoring iterations: 2

Using expressions to create variables on the fly

Like dplyr, srvyr allows you to use expressions in the arguments, allowing you to create variables in a single step. For example, you can use expressions:

  1. as the arguments inside the survey statistic functions likesurvey_mean
strat_design %>%
  summarize(prop_api99_over_700 = survey_mean(api99 > 700))
## # A tibble: 1 × 2
##   prop_api99_over_700 prop_api99_over_700_se
##                 <dbl>                  <dbl>
## 1               0.306                 0.0356
  1. as an argument to summarize
strat_design %>%
  group_by(awards) %>%
  summarize(percentage = 100 * survey_mean())
## # A tibble: 2 × 3
##   awards percentage percentage_se
##   <fct>       <dbl>         <dbl>
## 1 No           36.1          3.44
## 2 Yes          63.9          3.44
  1. and you can even create variables inside ofgroup_by
strat_design %>%
  group_by(api99_above_700 = api99 > 700) %>%
  summarize(api00_mn = survey_mean(api00))
## # A tibble: 2 × 3
##   api99_above_700 api00_mn api00_mn_se
##   <lgl>              <dbl>       <dbl>
## 1 FALSE               599.        7.88
## 2 TRUE                805.        7.15

Though on-the-fly expressions are syntactically valid, it is possible to make statistically invalid numbers from them. For example, though the standard error and confidence intervals can be multiplied by a scalar (like 100), the variance does not scale the same way, so the following is invalid:

# BAD DON'T DO THIS!
strat_design %>%
  group_by(awards) %>%
  summarize(percentage = 100 * survey_mean(vartype = "var"))
# VARIANCE IS WRONG

Non-Standard evaluation

Srvyr supports the non-standard evaluation conventions that dplyr uses. If you’d like to use a function programmatically, you can use the functions from rlang like the {{ operator (aka “curly curly”) from rlang.

Here’s a quick example, but please see the dplyr vignette vignette("programming", package = "dplyr")for more details.

mean_with_ci <- function(.data, var) {
  summarize(.data, mean = survey_mean({{var}}, vartype = "ci"))
}

srs_design_srvyr <- apisrs %>% as_survey_design(fpc = fpc)

mean_with_ci(srs_design_srvyr, api99)
## # A tibble: 1 × 3
##    mean mean_low mean_upp
##   <dbl>    <dbl>    <dbl>
## 1  625.     606.     643.

Srvyr will also follow dplyr’s lead on deprecating the old methods of NSE, such as rlang::quo, and !!, in addition to the so-called “underscore functions” (like summarize_). Currently, they have been soft-deprecated, they may be removed altogether in some future version of srvyr.

Working column-wise

As of version 1.0 of srvyr, it supports dplyr’s across function, so when you want to calculate a statistic on more than one variable, it is easy to do so. See vignette("colwise", package = "dplyr")for more details, but here is another quick example:

# Calculate survey mean for all variables that have names starting with "api"
strat_design %>%
  summarize(across(starts_with("api"), survey_mean))
## # A tibble: 1 × 6
##   api00 api00_se api99 api99_se api.stu api.stu_se
##   <dbl>    <dbl> <dbl>    <dbl>   <dbl>      <dbl>
## 1  662.     9.41  629.     9.96    498.       16.1

Srvyr also supports older methods of working column-wise, the “scoped variants”, such as summarize_at, summarize_if,summarize_all and summarize_each. Again, these are maintained for backwards compatibility, matching what the tidyverse team has done, but may be removed from a future version.

Calculating proportions in groups

You can calculate the weighted proportion that falls into a group using the survey_prop() function (or thesurvey_mean() function with no x argument). The proportion is calculated by “unpeeling” the last variable used ingroup_by() and then calculating the proportion within the other groups that fall into the last group (so that the proportion within each group that was unpeeled sums to 100%).

# Calculate the proportion that falls into each category of `awards` per `stype`
strat_design %>%
  group_by(stype, awards) %>%
  summarize(prop = survey_prop())
## When `proportion` is unspecified, `survey_prop()` now defaults to `proportion = TRUE`.
## ℹ This should improve confidence interval coverage.
## This message is displayed once per session.
## # A tibble: 6 × 4
## # Groups:   stype [3]
##   stype awards  prop prop_se
##   <fct> <fct>  <dbl>   <dbl>
## 1 E     No     0.270  0.0441
## 2 E     Yes    0.730  0.0441
## 3 H     No     0.680  0.0644
## 4 H     Yes    0.320  0.0644
## 5 M     No     0.520  0.0696
## 6 M     Yes    0.480  0.0696

If you want to calculate the proportion for groups from multiple variables at the same time that add up to 100%, theinteract function can help. The interactfunction creates a variable that is automatically split apart so that more than one variable can be unpeeled.

# Calculate the proportion that falls into each category of both `awards` and `stype`
strat_design %>%
  group_by(interact(stype, awards)) %>%
  summarize(prop = survey_prop())
## # A tibble: 6 × 4
##   stype awards   prop prop_se
##   <fct> <fct>   <dbl>   <dbl>
## 1 E     No     0.193  0.0315 
## 2 E     Yes    0.521  0.0315 
## 3 H     No     0.0829 0.00785
## 4 H     Yes    0.0390 0.00785
## 5 M     No     0.0855 0.0114 
## 6 M     Yes    0.0789 0.0114

Learning More

Here are some free resources put together by the community about srvyr:

Still need help?

I think the best way to get help is to form a specific question and ask it in some place like posit’s community website (known for it’s friendly community) or stackoverflow.com (maybe not known for being quite as friendly, but probably has more people). If you think you’ve found a bug in srvyr’s code, please file an issue on GitHub, but note that I’m not a great resource for helping specific issue, both because I have limited capacity but also because I do not consider myself an expert in the statistical methods behind survey analysis.

Have something to add?

These resources were mostly found via vanity searches on twitter & github. If you know of anything I missed, or have written something yourself, please let me know in this GitHub issue!