Hello all, I am getting an error when asking the computation of the chisquare, any suggestion please?

ds.table(rvar="ext_pcbin_df$prepreg_dep",

cvar="ext_pcbin_df$eusilc_income_quintiles",

report.chisq.tests = TRUE,

exclude =c("NaN", "NA"),

useNA= "no")
Data in all studies were valid
Study 1 : No errors reported from this study
Study 2 : No errors reported from this study
Study 3 : No errors reported from this study
Study 4 : No errors reported from this study
Study 5 : No errors reported from this study
Study 6 : No errors reported from this study
Study 7 : No errors reported from this study
 Error in stats::chisq.test(input.array.source.specific) :
at least one entry of ‘x’ must be positive
Thanks
Hi Gabriella,
Could you let us know which version of dsBase and dsBaseClient you are using?
Regards,
Stuart
Hi Stuart,
I have the following:
dsBaseClient_6.1.0
DSOpal_1.1.0
DSI_1.1.0
R6_2.4.0
progress_1.2.2
opalr_1.4.1
httr_1.4.2
but cannot see dsBase…
Thanks,
Gabriella
Hi Gabriella,
Here are the 1D tables for each one of those variables:
study
nonrep$prepreg_dep 1 2 3 4 5 6 7 8
0 7057 96911 0 0 0 0 0 11458
1 237 6791 0 0 0 0 0 1136
NA 348 2343 96825 1678 18329 2868 2270 3051
study
nonrep$eusilc_income_quintiles 1 2 3 4 5 6 7 8
1 1402 18249 16368 308 2708 0 383 2158
2 1402 18058 16470 304 2709 0 387 2166
3 1402 17436 16370 304 2709 0 387 2152
4 1401 19287 16417 304 2709 0 385 2187
5 1404 0 16417 303 2709 0 385 2126
NA 631 33015 14783 155 4785 2868 343 4856
As you can see prepreg_dep includes only NAs in studies 3 to 7 (those are dnbc, chop, elfe, raine, and inma in that order). So if you do a 2D table of the two variables for the other 3 studies (ninfea, moba and alspac) you can then get the results of the chisquared test:
$chisq.tests
$chisq.tests$chisq.test_TABLE.STUDY.1_counts
Pearson's Chisquared test
data: input.array.source.specific
Xsquared = 16.747, df = 4, pvalue = 0.002165
$chisq.tests$chisq.test_TABLE.STUDY.2_counts
Pearson's Chisquared test
data: input.array.source.specific
Xsquared = NaN, df = 4, pvalue = NA
$chisq.tests$chisq.test_TABLE.STUDY.3_counts
Pearson's Chisquared test
data: input.array.source.specific
Xsquared = 231.13, df = 4, pvalue < 2.2e16
$chisq.tests$chisq.test_TABLES.COMBINED_all.sources_counts
Pearson's Chisquared test
data: combine.array.all.sources
Xsquared = 154.81, df = 4, pvalue < 2.2e16
$validity.message
[1] "Data in all studies were valid"
Great, thanks! I thought I was factoring out NAs through the commands exclude and useNA, but nope! Thanks again
thanks for the awesome information.