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Warnings/error with 'multimed' 'argument is not numeric or logical: returning NA'? #42

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kristyrobledo opened this issue May 18, 2022 · 0 comments
Open

Warnings/error with 'multimed' 'argument is not numeric or logical: returning NA'? #42

kristyrobledo opened this issue May 18, 2022 · 0 comments

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@kristyrobledo
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Hi,
Im trying to use the multimed function.
I can run the example code for multimed, but when I run it on my dataset, or this 'fake' dataset, it errors (see below).
treat is a 0/1 numeric variable.

What am I doing wrong? I assume its user error?
thanks!

library(palmerpenguins)
library(mediation)
#> Loading required package: MASS
#> Loading required package: Matrix
#> Loading required package: mvtnorm
#> Loading required package: sandwich
#> mediation: Causal Mediation Analysis
#> Version: 4.5.0
library(tidyverse)
library(reprex)

create a fake dataset to show example of error

glimpse(penguins)
#> Rows: 344
#> Columns: 8
#> $ species Adelie, Adelie, Adelie, Adelie, Adelie, Adelie, Adel~
#> $ island Torgersen, Torgersen, Torgersen, Torgersen, Torgerse~
#> $ bill_length_mm 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1, ~
#> $ bill_depth_mm 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6, 18.1, ~
#> $ flipper_length_mm 181, 186, 195, NA, 193, 190, 181, 195, 193, 190, 186~
#> $ body_mass_g 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675, 3475, ~
#> $ sex male, female, female, NA, female, male, female, male~
#> $ year 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007~

penguins %>%
filter(species!="Gentoo") %>%
mutate(treat = as.numeric(rbernoulli(n=220, 0.5))) %>%
drop_na()->df

summary(df)
#> species island bill_length_mm bill_depth_mm
#> Adelie :146 Biscoe : 44 Min. :32.1 Min. :15.50
#> Chinstrap: 68 Dream :123 1st Qu.:37.8 1st Qu.:17.50
#> Gentoo : 0 Torgersen: 47 Median :40.6 Median :18.40
#> Mean :42.0 Mean :18.37
#> 3rd Qu.:46.0 3rd Qu.:19.10
#> Max. :58.0 Max. :21.50
#> flipper_length_mm body_mass_g sex year treat
#> Min. :172.0 Min. :2700 female:107 Min. :2007 Min. :0.000
#> 1st Qu.:187.0 1st Qu.:3400 male :107 1st Qu.:2007 1st Qu.:0.000
#> Median :191.0 Median :3700 Median :2008 Median :1.000
#> Mean :191.9 Mean :3715 Mean :2008 Mean :0.514
#> 3rd Qu.:196.0 3rd Qu.:3994 3rd Qu.:2009 3rd Qu.:1.000
#> Max. :212.0 Max. :4800 Max. :2009 Max. :1.000

test<-multimed(outcome = "bill_length_mm",
med.main = "flipper_length_mm",
med.alt = "bill_depth_mm",
treat = "treat",
covariates = "year",
data=df, sims=100)
#> Warning in mean.default(data.1[, treat] * data.1[, med.main]^2): argument is not
#> numeric or logical: returning NA
#> Warning in ETM2 * sigma^2/VY: Recycling array of length 1 in vector-array arithmetic is deprecated.
#> Use c() or as.vector() instead.
#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA

#> Warning in mean.default(data.b[, treat]): argument is not numeric or logical:
#> returning NA
Created on 2022-05-18 by the reprex package (v2.0.1)
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@kristyrobledo