srvyr survey_quantile - no output when using ci

StatSteph · March 7, 2021, 11:01pm

I am not getting any output (0 rows) when specifying confidence interval with quantiles. Any ideas? Here's a reprex:

library(tidyverse) # for tidyverse
library(here) # for file paths
#> here() starts at C:/Users/sazimmer/AppData/Local/Temp/RtmpyMdwWk/reprex5a68704646a1
library(survey) # for some survey analysis
#> Loading required package: grid
#> Loading required package: Matrix
#> 
#> Attaching package: 'Matrix'
#> The following objects are masked from 'package:tidyr':
#> 
#>     expand, pack, unpack
#> Loading required package: survival
#> 
#> Attaching package: 'survey'
#> The following object is masked from 'package:graphics':
#> 
#>     dotchart
library(srvyr) # for tidy survey analysis
#> 
#> Attaching package: 'srvyr'
#> The following object is masked from 'package:stats':
#> 
#>     filter

# recs <- read_rds(here("Data", "recs.rds"))
# 
# recs %>%
#    select(NWEIGHT, BRRWT1:BRRWT20, TOTALDOL) %>%
#    mutate_if(is.numeric, round, 1) %>%
#    slice(1:10) %>%
#    dput()

recs <- structure(list(NWEIGHT = c(12085.2, 14410.2, 23326, 12165.3, 
                                   16717.7, 26058.9, 45952.8, 15281, 14034.7, 43359.2), BRRWT1 = c(16555.3, 
                                                                                                   21486.3, 12297.4, 18554, 8075.7, 37004.1, 28077.4, 22962.3, 6989.9, 
                                                                                                   73353.8), BRRWT2 = c(5938, 19147, 36659.8, 5209.1, 8427.3, 34907.2, 
                                                                                                                        71118.6, 7067.5, 6954.7, 19161.1), BRRWT3 = c(17725.6, 7320.4, 
                                                                                                                                                                      10476.2, 18041.5, 8335.6, 15314.9, 20106.9, 25747.7, 7097.5, 
                                                                                                                                                                      16672.1), BRRWT4 = c(17635.6, 23567.9, 10101.9, 5441.8, 23666.4, 
                                                                                                                                                                                           33343, 68172.2, 23842.5, 20873, 18551), BRRWT5 = c(6032.8, 21926.6, 
                                                                                                                                                                                                                                              10291.1, 5815.6, 7674.5, 15332.5, 64424.8, 7951.1, 8224.2, 81545.2
                                                                                                                                                                                           ), BRRWT6 = c(17095.4, 7477.4, 39732, 4936, 25586.8, 14433.9, 
                                                                                                                                                                                                         56769.9, 26022.5, 19524.2, 63728), BRRWT7 = c(6003.4, 21544, 
                                                                                                                                                                                                                                                       11547.8, 22136.1, 23442, 14590.9, 22868.6, 7984.6, 21250.8, 67869
                                                                                                                                                                                                         ), BRRWT8 = c(5994.1, 8189.4, 12678.5, 18412.7, 26866.4, 32685.3, 
                                                                                                                                                                                                                       18690.8, 6924.7, 19723.2, 19365.2), BRRWT9 = c(5403, 6616.4, 
                                                                                                                                                                                                                                                                      38550.9, 18910.6, 8263.6, 34548.4, 27477.9, 6676.5, 5853.1, 69789.9
                                                                                                                                                                                                                       ), BRRWT10 = c(17569.6, 7260.4, 10754.5, 6621.4, 8210.5, 33987.8, 
                                                                                                                                                                                                                                      84209.8, 23981.8, 6368.9, 64151.3), BRRWT11 = c(16621, 21417, 
                                                                                                                                                                                                                                                                                      44738.6, 20070.6, 8292.4, 14716.9, 22968.8, 23687.5, 7158.6, 
                                                                                                                                                                                                                                                                                      22341.6), BRRWT12 = c(18815.8, 21356.5, 36050.6, 23333.1, 25607.7, 
                                                                                                                                                                                                                                                                                                            32993.5, 24615.3, 24816.2, 22569.4, 67045.8), BRRWT13 = c(5660.4, 
                                                                                                                                                                                                                                                                                                                                                                      7196.1, 12305.6, 18647.6, 24152.6, 36403.8, 61313.4, 22493.8, 
                                                                                                                                                                                                                                                                                                                                                                      22462.3, 19394.3), BRRWT14 = c(20846.4, 8036.6, 36765.3, 5191.9, 
                                                                                                                                                                                                                                                                                                                                                                                                     25632.3, 34958.6, 24262.1, 6726.5, 22151.8, 77443.7), BRRWT15 = c(7251.4, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       21021.6, 10564.8, 17992.9, 27171.8, 14994.7, 55610, 25790, 19986.2, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       83486.3), BRRWT16 = c(6305.8, 6465.2, 10107.8, 5299.3, 7484.6, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             33526.7, 31353, 24029.8, 7626.1, 75868), BRRWT17 = c(17556.9, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  7067.4, 10337, 5938.8, 24470.2, 15120.5, 22056.8, 6785.7, 23286.2, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  17688.3), BRRWT18 = c(5502.9, 19909.7, 40280.8, 4850.4, 8446.1, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        14267, 21275.6, 26481.6, 6040, 22775.7), BRRWT19 = c(17874.9, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             7107.3, 11448.9, 21861.2, 7888.2, 14766.8, 74685.1, 7270.7, 6770.2, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             21210.8), BRRWT20 = c(17451.2, 19018.8, 12917.4, 18002.6, 8830.7, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   32376.9, 80576.5, 6998.6, 7081.4, 74481), TOTALDOL = c(1406.1, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          1366, 2828.8, 2103, 910.9, 1040, 1015.2, 2384.1, 2485, 1973.7
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   )), row.names = c(NA, -10L), class = c("tbl_df", "tbl", "data.frame"
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ))

recs_des <- recs %>%
   as_survey_rep(weights=NWEIGHT,
                 repweights=starts_with("BRRWT"),
                 type="Fay",
                 rho=0.5,
                 mse=TRUE)


### no output?
recs_des %>%
   summarize(
      Spent=survey_quantile(
         x = TOTALDOL,
         quantiles = c(.25, .75),
         vartype = "ci"
      )
   )
#> [1] Spent_q25     Spent_q75     Spent_q25_low Spent_q75_low Spent_q25_upp
#> [6] Spent_q75_upp
#> <0 rows> (or 0-length row.names)

recs_des %>%
   summarize(
      Spent=survey_quantile(
         x = TOTALDOL,
         quantiles = c(.25, .75),
         vartype = "se"
      )
   )
#>   Spent_q25 Spent_q75 Spent_q25_se Spent_q75_se
#> 1  999.7143  2068.924     20.65815     399.1772


recs_des %>%
   summarize(
      Spent=survey_mean(
         x = TOTALDOL,
         vartype = "ci"
      )
   )
#>      Spent Spent_low Spent_upp
#> 1 1674.696  1110.019  2239.373

^{Created on 2021-03-07 by the reprex package (v1.0.0)}

technocrat · March 8, 2021, 12:08am

class(recs_des)
[1] "tbl_svy"       "svyrep.design"
 print(recs_des)
Call: Called via srvyr
Fay's variance method (rho= 0.5 ) with 20 replicates and MSE variances.
Sampling variables:
 - repweights: `BRRWT1 + BRRWT2 + BRRWT3 + BRRWT4 + BRRWT5 + BRRWT6 + BRRWT7 + BRRWT8 + BRRWT9 + BRRWT10 + BRRWT11 + BRRWT12 + BRRWT13 + BRRWT14 + BRRWT15 + BRRWT16 + BRRWT17 + BRRWT18 + BRRWT19 + BRRWT20`
 - weights: NWEIGHT
Data variables: NWEIGHT (dbl), BRRWT1 (dbl), BRRWT2 (dbl), BRRWT3 (dbl), BRRWT4 (dbl),
  BRRWT5 (dbl), BRRWT6 (dbl), BRRWT7 (dbl), BRRWT8 (dbl), BRRWT9 (dbl), BRRWT10 (dbl),
  BRRWT11 (dbl), BRRWT12 (dbl), BRRWT13 (dbl), BRRWT14 (dbl), BRRWT15 (dbl), BRRWT16
  (dbl), BRRWT17 (dbl), BRRWT18 (dbl), BRRWT19 (dbl), BRRWT20 (dbl), TOTALDOL (dbl)

doesn't have an implicit print method.

StatSteph · March 8, 2021, 12:15am

That's not the issue - you can see it returns something with 0 rows and I expect 1 row. I found a bug on github so there's no solution.

github.com/gergness/srvyr

survey_quantile on a svy_rep

opened 10:07PM - 23 Sep 20 UTC

closed 07:51PM - 28 Aug 21 UTC

Hanzzman

survey_quantile (and the related survey_median) gives an error when called for a… survey object with replicated weights, but not on a common survey object, when i ask for confidence intervals ``` dis<-data%>% as_survey_design(... dis_rep<- dis %>% as_survey_rep(replicates=2000... dis%>%summarise(ing=survey_median(... #it runs but it is not what i need... dis_rep %>% summarise(ing=survey_median(... #error. >Error in names(ci) <- paste0(qnames, rep(c("_low", "_upp"), each = out_width)) : el atributo 'names' [2] debe tener la misma longitud que el vector [0] ``` The error looks like it comes from the function get_var_est_quantile() if i use vartype=c("se"), there is no error. so, that is my current fix. i am a basic R user, sorry if i cant provide a sample code.

technocrat · March 8, 2021, 12:29am

OP code is consistent with the help(as_survey_rep) example, which shows a class list` return value.

suppressPackageStartupMessages({
  library(dplyr)
  library(survey)
  library(srvyr)
})

data(scd)
# use BRR replicate weights from Levy and Lemeshow
scd <- scd %>%
  mutate(rep1 = 2 * c(1, 0, 1, 0, 1, 0),
         rep2 = 2 * c(1, 0, 0, 1, 0, 1),
         rep3 = 2 * c(0, 1, 1, 0, 0, 1),
         rep4 = 2 * c(0, 1, 0, 1, 1, 0))

scdrep <- scd %>%
  as_survey_rep(type = "BRR", repweights = starts_with("rep"),
                combined_weights = FALSE)
#> Warning in svrepdesign.default(variables = variables, repweights = repweights, :
#> No sampling weights provided: equal probability assumed

print(scdrep)
#> Call: Called via srvyr
#> Balanced Repeated Replicates with 4 replicates.
#> Sampling variables:
#>  - repweights: `rep1 + rep2 + rep3 + rep4`
#> Data variables: ESA (int), ambulance (int), arrests (dbl), alive (dbl), rep1
#>   (dbl), rep2 (dbl), rep3 (dbl), rep4 (dbl)

str(scdrep)
#> List of 11
#>  $ type            : chr "BRR"
#>  $ scale           : num 0.25
#>  $ rscales         : num [1:4] 1 1 1 1
#>  $ rho             : NULL
#>  $ call            : 'quoteless_text' chr "Called via srvyr"
#>  $ combined.weights: logi FALSE
#>  $ variables       : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
#>   ..$ ESA      : int [1:6] 1 1 2 2 3 3
#>   ..$ ambulance: int [1:6] 1 2 1 2 1 2
#>   ..$ arrests  : num [1:6] 120 78 185 228 670 530
#>   ..$ alive    : num [1:6] 25 24 30 49 80 70
#>   ..$ rep1     : num [1:6] 2 0 2 0 2 0
#>   ..$ rep2     : num [1:6] 2 0 0 2 0 2
#>   ..$ rep3     : num [1:6] 0 2 2 0 0 2
#>   ..$ rep4     : num [1:6] 0 2 0 2 2 0
#>  $ pweights        : num [1:6] 1 1 1 1 1 1
#>  $ repweights      :'data.frame':    6 obs. of  4 variables:
#>   ..$ rep1: num [1:6] 2 0 2 0 2 0
#>   ..$ rep2: num [1:6] 2 0 0 2 0 2
#>   ..$ rep3: num [1:6] 0 2 2 0 0 2
#>   ..$ rep4: num [1:6] 0 2 0 2 2 0
#>   ..- attr(*, "terms")=Classes 'terms', 'formula'  language ~rep1 + rep2 + rep3 + rep4
#>   .. .. ..- attr(*, "variables")= language list(rep1, rep2, rep3, rep4)
#>   .. .. ..- attr(*, "factors")= int [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : chr [1:4] "rep1" "rep2" "rep3" "rep4"
#>   .. .. .. .. ..$ : chr [1:4] "rep1" "rep2" "rep3" "rep4"
#>   .. .. ..- attr(*, "term.labels")= chr [1:4] "rep1" "rep2" "rep3" "rep4"
#>   .. .. ..- attr(*, "order")= int [1:4] 1 1 1 1
#>   .. .. ..- attr(*, "intercept")= int 1
#>   .. .. ..- attr(*, "response")= int 0
#>   .. .. ..- attr(*, ".Environment")=<environment: 0x55e0245b7488> 
#>   .. .. ..- attr(*, "predvars")= language list(rep1, rep2, rep3, rep4)
#>   .. .. ..- attr(*, "dataClasses")= Named chr [1:4] "numeric" "numeric" "numeric" "numeric"
#>   .. .. .. ..- attr(*, "names")= chr [1:4] "rep1" "rep2" "rep3" "rep4"
#>  $ degf            : num 3
#>  $ mse             : logi FALSE
#>  - attr(*, "class")= chr [1:2] "tbl_svy" "svyrep.design"
#>  - attr(*, "survey_vars")=List of 3
#>   ..$ repweights:List of 1
#>   .. ..$ : symbol rep1 + rep2 + rep3 + rep4
#>   ..$ weights   : NULL
#>   ..$ fpc       : NULL
#>   ..- attr(*, "class")= chr "survey_vars"

StatSteph · March 8, 2021, 1:26pm

I think you missed the question. It's about when getting quantile estimates and requesting confidence intervals and is related to this issue: https://github.com/gergness/srvyr/issues/101

suppressPackageStartupMessages({
   library(dplyr)
   library(survey)
   library(srvyr)
})

data(scd)
# use BRR replicate weights from Levy and Lemeshow
scd <- scd %>%
   mutate(rep1 = 2 * c(1, 0, 1, 0, 1, 0),
          rep2 = 2 * c(1, 0, 0, 1, 0, 1),
          rep3 = 2 * c(0, 1, 1, 0, 0, 1),
          rep4 = 2 * c(0, 1, 0, 1, 1, 0))

scdrep <- scd %>%
   as_survey_rep(type = "BRR", repweights = starts_with("rep"),
                 combined_weights = FALSE)
#> Warning in svrepdesign.default(variables = variables, repweights = repweights, :
#> No sampling weights provided: equal probability assumed

scdrep %>%
   summarise(
      arrest=survey_quantile(
         arrests,
         quantiles = c(.25, .75),
         vartype = "ci"
      )
   )
#> [1] arrest_q25     arrest_q75     arrest_q25_low arrest_q75_low arrest_q25_upp
#> [6] arrest_q75_upp
#> <0 rows> (or 0-length row.names)

^{Created on 2021-03-08 by the reprex package (v1.0.0)}

technocrat · March 8, 2021, 7:37pm

Yup. Sure did. Thanks on behalf of posterity.

system · March 15, 2021, 7:37pm

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