Error in (function (object, ...) : missing values in `weights'

popy · November 15, 2022, 2:14pm

Hi there,

I'm using 4 survey cycles (2006 - 2013) of the Nhanes data (N=40,617) and am interested in pregnant women (n= 247) who are black and Hispanic. I am trying to correct for survey design, non-response, etc., per Nhanes by applying weights as in the code below. However, I keep getting the above error message that I'm not sure how to correct.

Demo_Metals <- left_join(DEMO_BMX, Metals_0613, by="SEQN")%>%
mutate(. ,
# Generating 8-year subsample weights (Dividing weights by 4 because we are appending 4 survey cycles). Using the subsample weights (WTSA2YR), per the analytic notes on the metals documentation
WTSA8YR = WTSA2YR/4,
# Defining indicator for analysis pop
inAnalysis= (RIDEXPRG=1 & RIDRETH1 != c(3, 5) & !is.na(WTSA2YR)))%>%

#' ## Defining survey design for overall dataset
NHANES_all <- svydesign(data=Demo_Metals, id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTSA8YR, nest=TRUE)

#Creating a survey design object for the subset of interest - pregnant, black, and Hispanic women.

# Subsetting the original survey design object to keep the design information about the number of cluster, and strata

NHANES <- subset(NHANES_all, inAnalysis)

This is a sample of the data frame

dput(head(Demo_Metals, 10))
structure(list(SEQN = c(41475, 41476, 41477, 41478, 41479, 41480,
41481, 41482, 41483, 41484), DMDEDUC2 = c(3, NA, 3, NA, 1, NA,
3, 2, 4, NA), INDFMIN2 = c(6, 15, 5, 3, 8, 4, 6, 15, 5, 3), RIDRETH1 = c(5,
5, 3, 3, 1, 1, 4, 1, 4, 3), RIDAGEYR = c(62, 6, 71, 1, 52, 6,
21, 64, 66, 0), RIDEXPRG = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_),
SDMVSTRA = c(60, 70, 67, 59, 70, 69, 68, 65, 66, 59), SDMVPSU = c(1,
1, 1, 2, 1, 2, 2, 2, 2, 2), WTMEC2YR = c(60045.772497, 35353.21044,
10074.150074, 14560.472652, 9234.055759, 7297.067503, 24655.376656,
11602.178638, 7920.812275, 9259.270099), BMXBMI = c(58.04,
15.18, 30.05, NA, 27.56, 17.93, 23.34, 33.64, 44.06, NA),
LBXBCD = c(0.2, 0.14, 0.14, 0.14, 0.14, NA, NA, 0.42, 0.57,
NA), LBDBCDSI = c(1.78, 1.25, 1.25, 1.25, 1.25, NA, NA, 3.74,
5.07, NA), LBXBPB = c(1.1, 1.94, 0.9, 2.28, 1.7, NA, NA,
0.99, 2.17, NA), LBDBPBSI = c(0.053, 0.094, 0.043, 0.11,
0.082, NA, NA, 0.048, 0.105, NA), LBXTHG = c(0.2, 2.6, 1.31,
0.2, 1.22, NA, NA, 0.64, 0.65, NA), LBDTHGSI = c(1, 13, 6.5,
1, 6.1, NA, NA, 3.2, 3.2, NA), LBDTHGLC = c(1, 0, 0, 1, 0,
NA, NA, 0, 0, NA), Matrix.x = c("Blood", "Blood", "Blood",
"Blood", "Blood", "Blood", "Blood", "Blood", "Blood", NA),
WTSA2YR.x = c(NA, NA, 28753.7444494525, NA, NA, 23899.3095881372,
75774.2128638516, 34222.0864226224, NA, NA), URXUCR.x = c(NA,
NA, 135, NA, NA, 33, 366, 130, NA, NA), URXUAS = c(NA, NA,
98.88, NA, NA, 6.57, 9.49, 6.17, NA, NA), URDUASLC = c(NA,
NA, 0, NA, NA, 0, 0, 0, NA, NA), URXUAS3 = c(NA, NA, 0.85,
NA, NA, 0.85, 0.85, 0.85, NA, NA), URDUA3LC = c(NA, NA, 1,
NA, NA, 1, 1, 1, NA, NA), URXUAS5 = c(NA, NA, 0.71, NA, NA,
0.71, 0.71, 0.71, NA, NA), URDUA5LC = c(NA, NA, 1, NA, NA,
1, 1, 1, NA, NA), URXUAB = c(NA, NA, 72.2, NA, NA, 0.61,
2.19, 0.28, NA, NA), URDUABLC = c(NA, NA, 0, NA, NA, 0, 0,
1, NA, NA), URXUAC = c(NA, NA, 0.42, NA, NA, 0.42, 0.42,
0.42, NA, NA), URDUACLC = c(NA, NA, 1, NA, NA, 1, 1, 1, NA,
NA), URXUDMA = c(NA, NA, 5, NA, NA, 4.56, 4.48, 3.53, NA,
NA), URDUDALC = c(NA, NA, 0, NA, NA, 0, 0, 0, NA, NA), URXUMMA = c(NA,
NA, 0.64, NA, NA, 0.64, 1.09, 0.64, NA, NA), URDUMMAL = c(NA,
NA, 1, NA, NA, 1, 0, 1, NA, NA), URXUTM = c(NA, NA, 0.71,
NA, NA, 0.71, 0.71, 0.71, NA, NA), URDUTMLC = c(NA, NA, 1,
NA, NA, 1, 1, 1, NA, NA), Matrix.y = c(NA, NA, "Urine", NA,
NA, "Urine", "Urine", "Urine", NA, NA), WTSA2YR.y = c(NA,
NA, 28753.7444494525, NA, NA, 23899.3095881372, 75774.2128638516,
34222.0864226224, NA, NA), URXUCR.y = c(NA, NA, 135, NA,
NA, 33, 366, 130, NA, NA), URXUBA = c(NA, NA, 4.64, NA, NA,
0.52, 1.54, 2.19, NA, NA), URDUBALC = c(NA, NA, 0, NA, NA,
0, 0, 0, NA, NA), URXUBE = c(NA, NA, 0.051, NA, NA, 0.051,
0.051, 0.051, NA, NA), URDUBELC = c(NA, NA, 1, NA, NA, 1,
1, 1, NA, NA), URXUCD = c(NA, NA, 0.218, NA, NA, 0.03, 0.24,
1.03, NA, NA), URDUCDLC = c(NA, NA, 0, NA, NA, 1, 0, 0, NA,
NA), URXUCO = c(NA, NA, 0.639, NA, NA, 0.128, 0.561, 0.373,
NA, NA), URDUCOLC = c(NA, NA, 0, NA, NA, 0, 0, 0, NA, NA),
URXUCS = c(NA, NA, 6.74, NA, NA, 6.34, 7.6, 4.81, NA, NA),
URDUCSLC = c(NA, NA, 0, NA, NA, 0, 0, 0, NA, NA), URXUMO = c(NA,
NA, 52.3, NA, NA, 49.2, 74.6, 161, NA, NA), URDUMOLC = c(NA,
NA, 0, NA, NA, 0, 0, 0, NA, NA), URXUPB = c(NA, NA, 0.53,
NA, NA, 0.37, 0.73, 0.56, NA, NA), URDUPBLC = c(NA, NA, 0,
NA, NA, 0, 0, 0, NA, NA), URXUPT = c(NA, NA, 0.006, NA, NA,
0.006, 0.006, 0.006, NA, NA), URDUPTLC = c(NA, NA, 1, NA,
NA, 1, 1, 1, NA, NA), URXUSB = c(NA, NA, 0.066, NA, NA, 0.059,
0.115, 0.056, NA, NA), URDUSBLC = c(NA, NA, 0, NA, NA, 0,
0, 0, NA, NA), URXUTL = c(NA, NA, 0.235, NA, NA, 0.115, 0.179,
0.186, NA, NA), URDUTLLC = c(NA, NA, 0, NA, NA, 0, 0, 0,
NA, NA), URXUTU = c(NA, NA, 0.104, NA, NA, 0.107, 0.506,
0.021, NA, NA), URDUTULC = c(NA, NA, 0, NA, NA, 0, 0, 0,
NA, NA), URXUUR = c(NA, NA, 0.0137, NA, NA, 0.0055, 0.0126,
0.01, NA, NA), URDUURLC = c(NA, NA, 0, NA, NA, 0, 0, 0, NA,
NA), Matrix = c(NA, NA, "Urine", NA, NA, "Urine", "Urine",
"Urine", NA, NA), LBDBCDLC = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), LBDBPBLC = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
), LBXBSE = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), LBDBSESI = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_), LBDBSELC = c(NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_), LBXBMN = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), LBDBMNSI = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
), LBDBMNLC = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), URXUMN = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_), URDUMNLC = c(NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_), URXUSN = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), URDUSNLC = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
), URXUSR = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), URDUSRLC = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_), Matrix.x.x = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), WTSA2YR = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), URXUCR = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
), LBXSCU = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), LBDSCUSI = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_), LBXSSE = c(NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_), LBDSSESI = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), LBXSZN = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
), LBDSZNSI = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), Matrix.y.y = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), WTSH2YR = c(NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_)), row.names = c(NA, 10L), class = "data.frame")

I'm new to R so I may be missing the obvious. Happy to provide any further information as needed so that I can go past this error message. Thanks.

technocrat · November 15, 2022, 10:26pm

What function in which library is producing the error?

popy · November 15, 2022, 10:32pm

I'm not sure, but I'm using the following:
library(dplyr)
library(survey)
library(extraoperators)

technocrat · November 15, 2022, 10:35pm

The function will be the one that was called before the error

... # your preceding script
some_function(...) # calling function and it's arguments
... # one or more lines
ERROR message

popy · November 15, 2022, 10:41pm

I ran the whole code as posted and obtained the error just as posted and so I'm not sure. If I run the code to the level of the svdesign function I get the error "Error in eval(predvars, data, env) : object 'WTSA8YR' not found"

technocrat · November 15, 2022, 10:48pm

See the FAQ: How to do a minimal reproducible example reprex for beginners. That error message might arise from svydesign(), probably not from subset(), but it's impossible to tell. There's not even a complete error message error provided. Up to the user to provide what's needed to make it possible for the community here (we're almost all unpaid volunteers) to help the user.

system · December 27, 2022, 10:48pm

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