如何获取用于大型调查数据集的 svydb R 包以返回标准错误 [英] How to get svydb R package for large survey data sets to return standard errors

问题描述

很高兴看到 Charco Hui 将 Thomas Lumley 的实验性 sqlsurvey 包复活为 svydb.可能是在 R 中处理大型调查数据集的绝佳工具.

Excited to see Charco Hui resurrected Thomas Lumley's experimental sqlsurvey package as svydb. Potentially a great tool for working with large survey data sets in R.

虽然在 svydb 计算标准误差时遇到了一些问题.这个问题与我在 sqlsurvey 中遇到的问题非常相似.在运行 Mojave、R 版本 3.5.1 和 MonetDB Aug 2018-SP1 Release 的 Mac Pro 上进行的定期调查中，类似的程序运行良好

Have though run into some problems with svydb calculating standard errors. This issue is very similar to one I encountered with sqlsurvey. The analogous procedures work fine in regular survey working on a Mac Pro running Mojave, R version 3.5.1, and MonetDB Aug 2018-SP1 Release

对于健康研究人员和流行病学家来说，该软件包可能是一个非常重要的工具，所以希望我做的事情显然是错误的，并且很容易解决这个问题.

The package is potentially a very important tool for health researchers and epidemiologists, so hoping I am doing something obviously wrong and will be easy to sort this out.

以下是一个基于 BRFSS 数据集随机抽取的可重现示例.

Below is a reproducible example based on some random draws from a BRFSS data set.

# create data
dat<-data.frame(var1=c(6, 5, 6, 6, 6, 6, 3, 3, 2, 6, 3, 4, 6, 6, 3, 6, 5, 5, 4, 5, 4, 4, 6, 6, 4, 3, 4, 4, 3, 5, 5, 3, 6, 1, 6, 3, 5, 3, 4, 2, 5, 2, 6, 5, 6, 2, 2, 4, 3, 6, 6, 6, 3, 6, 2, 3, 4, 1, 4, 4, 2, 6, 5, 4, 6, 2, 6, 2, 6, 6, 6, 5, 4, 2, 5, 3, 4, 4, 5, 1, 2, 6, 6, 6, 2, 6, 4, 4, 2, 3, 6, 3, 3, 6, 2, 6, 5, 4, 6, 2),
var2=c(NA, NA, 88, 88, 88, NA, 1, 88, 88, NA, NA, 2, NA, NA, 88, NA, NA, 88, NA, 88, 88, 88, 88, NA, 88, 88, 88, NA, 88, NA, NA, 88, NA, NA, NA, 88, NA, NA, 4, NA, 88, NA, NA, 8, NA, NA, NA, 88, 88, NA, NA, NA, NA, NA, 88, NA, 88, 88, NA, 88, NA, 88, NA, 11, NA, 1, NA, 4, 88, 7, NA, 88, NA, NA, 88, 88, NA, 88, NA, 88, 1, 88, 88, NA, 88, NA, NA, 88, 29, 88, 88, NA, 88, NA, 88, NA, 88, NA, NA, 88),
strat=c(25011, 12032, 19101, 22011, 24011, 53311, 8011, 25061, 8012, 35031, 32022, 18022, 34101, 19061, 5011, 24011, 34101, 24011, 19021, 31031, 37111, 5012, 25011, 53201, 15052, 22011, 37261, 27011, 30031, 44031, 26011, 42011, 37121, 25041, 39082, 24032, 38011, 15012, 24012, 35062, 16071, 42042, 27011, 45062, 50011, 25041, 56012, 25041, 9022, 55031, 55021, 19091, 35022, 28011, 34101, 40021, 9021, 23031, 34041, 78021, 2021, 30021, 1011, 9012, 40032, 18042, 20011, 49041, 24011, 53111, 16012, 20011, 22011, 25042, 49122, 53352, 53091, 9021, 19071, 29021, 18021, 37131, 46041, 8011, 42031, 47121, 46051, 17011, 42021, 72061, 34101, 25062, 35062, 37061, 55062, 46031, 45041, 28011, 37211, 12021),
psu=c(2006092024, 2006018204, 2006024879, 2006009844, 2006054713, 2006074840, 2006014252, 2006022459, 2006030518, 2006033744, 2006004188, 2006029456, 2006028186, 2006021413, 2006049813, 2006007831, 2006166137, 2006030867, 2006027180, 2006027225, 2006029188, 2006004573, 2006000994, 2006064527, 2006011204, 2006007744, 2006016792, 2006020891, 2006039237, 2006007268, 2006019976, 2006065941, 2006074498, 2006008616, 2006018805, 2006046669, 2006018600, 2006013675, 2006075607, 2006008605, 2006020846, 2006022428, 2006033687, 2006020260, 2006035555, 2006009957, 2006006278, 2006103150, 2006048853, 2006015663, 2006001191, 2006023333, 2006002411, 2006035682, 2006041137, 2006011947, 2006042893, 2006025836, 2006099337, 2006036076, 2006016300, 2006028942, 2006013850, 2006064497, 2006026877, 2006020508, 2006020272, 2006023852, 2006012831, 2006051597, 2006033700, 2006044908, 2006003444, 2006072406, 2006021862, 2006081285, 2006133751, 2006019507, 2006031458, 2006019504, 2006002030, 2006075571, 2006020267, 2006040619, 2006125145, 2006008496, 2006051043, 2006031048, 2006106217, 2006004721, 2006148449, 2006017795, 2006008827, 2006003243, 2006009762, 2006044530, 2006029068, 2006019002, 2006013326, 2006015464),
wt= c(131.167091, 1135.222016, 462.911082, 237.434588, 222.090249, 8.867523, 367.057462, 635.047502, 734.512583, 168.266313, 237.236438, 794.324159, 896.016179, 453.886381, 516.676601, 222.090249, 370.880284, 266.860031, 178.231943, 127.053275, 286.216069, 212.409224, 196.986648, 52.223519, 13.850239, 176.044166, 290.372567, 517.028007, 79.796161, 174.701770, 829.008988, 2514.492945, 177.300719, 190.845451, 270.146986, 261.739684, 45.144276, 276.447180, 1704.022745, 102.473540, 168.798958, 42.614573, 321.460974, 139.006541, 22.110006, 50.144119, 60.941799, 42.225301, 704.172192, 1094.072745, 423.243864, 424.056478, 256.796474, 222.921805, 940.041214, 191.560779, 280.303505, 959.310457, 401.479694, 27.638152, 84.411858, 111.955653, 661.796967, 72.884007, 118.783933, 1905.071998, 214.932923, 539.094181, 415.230283, 91.327212, 217.747861, 366.950758, 378.620855, 150.430028, 594.726292, 189.966155, 74.510093, 280.303505, 474.297391, 5389.787617, 753.892676, 502.921582, 59.307656, 444.877512, 51.007590, 446.469588, 32.298617, 2518.461812, 76.319144, 819.303078, 396.857545, 476.354501, 97.705354, 168.923737, 1179.296136, 34.909445, 275.003257, 410.288302, 147.335207, 723.221948))

# analysis in survey works
library(survey)
options(survey.lonely.psu="remove")
svyDat1<-
svydesign(
id=~psu,
strata=~strat,
data=dat,
weights=~wt,
)


svymean(~var1, svyDat1, se=T, na.rm=T)
#          mean     SE
# numVar 79.286 0.3439

svymean(~var2, svyDat1, se=T, na.rm=T)
#        mean     SE
# var2 70.171 1.0314

# analysis in svydb does not work
library(devtools)
install_github("chrk623/svydb")
library(svydb)

svyDat2 = svydbdesign(st="strat", wt="wt", id="psu", data=dat)
svydbmean(x = var1, design = svyDat2 , num = T)
#        Mean SE
# var1 3.6063 NA
svydbmean(x = var2, design = svyDat2 , num = T)
#        Mean SE
# var2 70.171 NA


# try with database connection returns more informative (?) error message 
require(MonetDBLite)
require(DBI)
require(dbplyr)
con = dbConnect(MonetDBLite())
dbWriteTable(con, "dat", dat)
dat.db = tbl(con, "dat")
svyDat3 = svydbdesign(st = strat , wt = wt,id = psu , data = dat.db)
svydbmean(x = var1, design = svyDat3 , num = T)
# Error in .local(conn, statement, ...) :
#   Unable to execute statement 'CREATE TEMPORARY TABLE "auugiyqyip" AS SELECT "sum(scaled)"
# FROM (SELECT SUM("scaled") AS "sum(scale...'.
# Server says 'MALException:batcalc./:22012!division by zero. '.
# In addition: There were 12 warnings (use warnings() to see them)

svydbmean(x = var2, design = svyDat3 , num = T)
# Error in .local(conn, statement, ...) :
#   Unable to execute statement 'CREATE TEMPORARY TABLE "yxqvidpdbx" AS SELECT "sum(scaled)"
# FROM (SELECT SUM("scaled") AS "sum(scale...'.
# Server says 'MALException:batcalc./:22012!division by zero. '.

推荐答案

正如程序作者 Charco Hui 所指出的，svydb 已更新为允许 svydb.lonely.psu = "remove" 作为一个选项.这解决了问题.

As noted by Charco Hui, the author of the program, svydb has been updated to allow svydb.lonely.psu = "remove" as an option. This solved the problem.

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