R Under development (unstable) (2024-03-07 r86063 ucrt) -- "Unsuffered Consequences"
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> library(survey)
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart

> options(warn=2)
> 
> ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob)
> data(api)
> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
> svyby(~api99, ~stype, dclus1, svymean )
  stype    api99       se
E     E 607.7917 22.81660
H     H 595.7143 41.76400
M     M 608.6000 32.56064
> 
> set.seed(123)
> apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA
> dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
> 
> # subsetting w/ na.rm = FALSE...
> svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE )
      mean SE
api99   NA NA
> svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE )
        mean     SE
api99 595.71 41.764
> svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE )
      mean SE
api99   NA NA
> 
> # ... looks like this:
> svyby(~api99, ~stype, dclus1.na , svymean )
  stype    api99     se
E     E       NA     NA
H     H 595.7143 41.764
M     M       NA     NA
> 
> # subsetting w/ na.rm = TRUE...
> svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE )
        mean     SE
api99 606.53 22.901
> svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE )
        mean     SE
api99 595.71 41.764
> svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE )
        mean     SE
api99 613.39 33.224
> 
> # ... looks like this
> svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE )
  stype    api99       se
E     E 606.5319 22.90084
H     H 595.7143 41.76400
M     M 613.3913 33.22358
> 
> # Without missing values, this works:
> svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE )
  stype    api99       se
E     E 607.7917 22.81660
H     H 595.7143 41.76400
M     M 608.6000 32.56064
> 
> # ... but this breaks!
> svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE )
  stype    api99       se
E     E 606.5319 22.90084
H     H 595.7143 41.76400
M     M 613.3913 33.22358
> 
> # ... and i don't think this is the expected behavior
> svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE )
  stype    api99     se
E     E       NA     NA
H     H 595.7143 41.764
M     M       NA     NA
> svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE )
  stype    api99       se
E     E 606.5319 22.90084
H     H 595.7143 41.76400
M     M 613.3913 33.22358
> 
> 
> ## <TL> Now some more as tests
> svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE )
  stype     api99       se
E     E 2894629.0 792809.8
H     H  282283.9 101492.9
M     M  477513.4 107555.5
> svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE )
  stype api99/api00 se.api99/api00
E     E   0.9367750    0.006365702
H     H   0.9630485    0.010520785
M     M   0.9682246    0.009390982
> 
> ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...)
> svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE )
  stype (Intercept) se.(Intercept)
E     E    606.5319       22.90084
H     H    595.7143       41.76400
M     M    613.3913       33.22358
> 
> proc.time()
   user  system elapsed 
   1.18    0.14    1.32