Sorkin, John
2023-Oct-25 19:23 UTC
[R] Error running gee function. I neither understand the error message, nor know what needs to be done the get the gee to run
Colleagues, I am receiving several error messages from the gee function. I don't understand the ides the error messages are trying to impart, and I don't know how to debug or correct the error. The error messages follow:> fitgee <- gee(HipFlex ~ StepHeight,data=datashort,id=PID,corstr="exchangeable",na.action=na.omit)Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) StepHeight 1.400319 58.570236 Error in gee(HipFlex ~ StepHeight, data = datashort, id = PID, corstr = "exchangeable", : NA/NaN/Inf in foreign function call (arg 3) In addition: Warning message: In gee(HipFlex ~ StepHeight, data = datashort, id = PID, corstr = "exchangeable", : NAs introduced by coercion Of note, when the analysis is run using lm, there is no problem. My fully data and code follow: Thank you, John CODE: if (!require(gee)) {install.packages("gee")} library(gee) datashort <- structure(list(HipFlex = c(1.95, 2.07, 1.55, 0.44, 0.23, 0.41, 0.22, 4.61, 10.02, 1.08, 1.43, 1.82, 0.34, 0.77, 0.22, 1.06, 0.13, 0.36, 2.84, 5.2, 12.27, 1.37, 2.33, 3.48, 4.76, 1.92, 2.09, 4.67, 2.94, 0.75, 0.11, 3.56, 1.63, 0.8, 1.54, 5.06, NA, 5.41, 6.18, 3.75, 3.12, 17.43, 3.18, 0.85, 14.54, 14.34, 21.92, 4.91, 1.52, 0.38, 0.43, 0.47, 0.56, 6.4, 12.4, 3.98, 0.57, 1.84, 12.06, 0.45, 8.16, 0.02, 0, 0.05, 0.52, 0.11, 0.48, 1.5, 3.29, 2.58, 2.07, 6.06, 1.46, 1.06, 3.82, 1.09, 2.86, 3.47, 2.22, 1.89, NA, 3.48, 6.38, 3.58, 1.83, 2.8, 8.28, 7.15, 4.77, 4.93, 0, 0.11, 1.99, 2.01, 2.3, 1.24, 1.33, 2, 1.01), PID = c("HIPS004", "HIPS004", "HIPS005", "HIPS005", "HIPS005", "HIPS006", "HIPS006", "HIPS008", "HIPS010", "HIPS024", "HIPS024", "HIPS024", "HIPS025", "HIPS028", "HIPS028", "HIPS030", "HIPS030", "HIPS030", "HIPS035", "HIPS035", "HIPS035", "HIPS036", "HIPS036", "HIPS037", "HIPS044", "HIPS047", "HIPS047", "HIPS056", "HIPS056", "HIPS057", "HIPS057", "HIPS057", "HIPS058", "HIPS059", "HIPS059", "HIPS061", "HIPS062", "HIPS062", "HIPS062", "HIPS064", "HIPS074", "HIPS079", "HIPS084", "HIPS089", "HIPS090", "HIPS090", "HIPS090", "HIPS091", "HIPS091", "HIPS092", "HIPS092", "HIPS092", "HIPS001", "HIPS001", "HIPS001", "HIPS004", "HIPS004", "HIPS004", "HIPS005", "HIPS005", "HIPS005", "HIPS006", "HIPS006", "HIPS008", "HIPS022", "HIPS024", "HIPS028", "HIPS030", "HIPS035", "HIPS036", "HIPS036", "HIPS039", "HIPS044", "HIPS047", "HIPS051", "HIPS056", "HIPS058", "HIPS058", "HIPS059", "HIPS059", "HIPS062", "HIPS062", "HIPS062", "HIPS069", "HIPS069", "HIPS071", "HIPS074", "HIPS079", "HIPS084", "HIPS084", "HIPS085", "HIPS089", "HIPS090", "HIPS091", "HIPS091", "HIPS091", "HIPS092", "HIPS092", "HIPS093"), StepHeight = c(0.005, 0.008, 0.072, 0.003, 0.014, 0.01, 0.027, 0.074, 0.128, 0.048, 0.036, 0.024, 0.021, 0.026, 0.03, 0.004, 0.006, 0.006, 0.011, 0.006, 0.053, 0.028, 0.073, 0.041, 0.005, 0.007, 0.013, 0.012, 0.021, 0.053, 0.013, 0.071, 0.012, 0.016, 0.023, 0.024, 0.011, 0.019, 0.014, 0.022, 0.011, 0.129, 0.03, 0.012, 0.062, 0.145, 0.077, 0.028, 0.006, 0.019, 0.008, 0.006, 0.034, 0.109, 0.09, 0.005, 0.016, 0.005, 0.257, 0.011, 0.205, 0.01, 0.017, 0.039, 0.01, 0.016, 0.043, 0.004, 0.008, 0.04, 0.068, 0.006, 0.008, 0.005, 0.097, 0.015, 0.016, 0.01, 0.021, 0.008, 0.01, 0.006, 0.016, 0.021, 0.012, 0.009, 0.032, 0.055, 0.006, 0.066, 0.018, 0.01, 0.018, 0.017, 0.015, 0.01, 0.017, 0.02, 0.022)), class = "data.frame", row.names = c(4L, 5L, 6L, 7L, 8L, 10L, 12L, 14L, 19L, 29L, 30L, 31L, 33L, 41L, 43L, 44L, 45L, 46L, 47L, 48L, 51L, 52L, 53L, 58L, 62L, 65L, 67L, 70L, 72L, 74L, 75L, 77L, 79L, 82L, 83L, 86L, 88L, 89L, 90L, 93L, 109L, 114L, 117L, 129L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, 152L, 155L, 165L, 167L, 172L, 173L, 174L, 176L, 178L, 179L, 185L, 186L, 188L, 192L, 193L, 195L, 197L, 199L, 202L, 203L, 204L, 214L, 216L, 221L, 225L, 234L, 236L, 237L, 238L, 250L, 252L, 255L, 256L, 257L, 258L, 260L, 261L)) datashort # This does not work: fitgee <- gee(HipFlex ~ StepHeight,data=datashort,id=PID,corstr="exchangeable",na.action=na.omit) summary(fitgee) # This works. fitlm <- lm(HipFlex ~ StepHeight,data=datashort) summary(fitlm) John David Sorkin M.D., Ph.D. Professor of Medicine, University of Maryland School of Medicine; Associate Director for Biostatistics and Informatics, Baltimore VA Medical Center Geriatrics Research, Education, and Clinical Center; PI Biostatistics and Informatics Core, University of Maryland School of Medicine Claude D. Pepper Older Americans Independence Center; Senior Statistician University of Maryland Center for Vascular Research; Division of Gerontology and Paliative Care, 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 Cell phone 443-418-5382 [[alternative HTML version deleted]]
Duncan Murdoch
2023-Oct-25 19:38 UTC
[R] Error running gee function. I neither understand the error message, nor know what needs to be done the get the gee to run
I don't see it documented, but it appears that the gee() function assumes the id variable can be coerced to a number. Your ids are in PID, and are strings like "HIPS004", etc. Change that to "004" or a numeric 4 and the error goes away. Duncan Murdoch On 25/10/2023 3:23 p.m., Sorkin, John wrote:> Colleagues, > > I am receiving several error messages from the gee function. I don't understand the ides the error messages are trying to impart, and I don't know how to debug or correct the error. The error messages follow: > > >> fitgee <- gee(HipFlex ~ StepHeight,data=datashort,id=PID,corstr="exchangeable",na.action=na.omit) > > Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 > > running glm to get initial regression estimate > > (Intercept) StepHeight > > 1.400319 58.570236 > > Error in gee(HipFlex ~ StepHeight, data = datashort, id = PID, corstr = "exchangeable", : > > NA/NaN/Inf in foreign function call (arg 3) > > In addition: Warning message: > > In gee(HipFlex ~ StepHeight, data = datashort, id = PID, corstr = "exchangeable", : > > NAs introduced by coercion > > Of note, when the analysis is run using lm, there is no problem. My fully data and code follow: > Thank you, > John > > > CODE: > > if (!require(gee)) {install.packages("gee")} > library(gee) > > datashort <- structure(list(HipFlex = c(1.95, 2.07, 1.55, 0.44, 0.23, 0.41, > 0.22, 4.61, 10.02, 1.08, 1.43, 1.82, 0.34, 0.77, 0.22, 1.06, > 0.13, 0.36, 2.84, 5.2, 12.27, 1.37, 2.33, 3.48, 4.76, 1.92, 2.09, > 4.67, 2.94, 0.75, 0.11, 3.56, 1.63, 0.8, 1.54, 5.06, NA, 5.41, > 6.18, 3.75, 3.12, 17.43, 3.18, 0.85, 14.54, 14.34, 21.92, 4.91, > 1.52, 0.38, 0.43, 0.47, 0.56, 6.4, 12.4, 3.98, 0.57, 1.84, 12.06, > 0.45, 8.16, 0.02, 0, 0.05, 0.52, 0.11, 0.48, 1.5, 3.29, 2.58, > 2.07, 6.06, 1.46, 1.06, 3.82, 1.09, 2.86, 3.47, 2.22, 1.89, NA, > 3.48, 6.38, 3.58, 1.83, 2.8, 8.28, 7.15, 4.77, 4.93, 0, 0.11, > 1.99, 2.01, 2.3, 1.24, 1.33, 2, 1.01), PID = c("HIPS004", "HIPS004", > "HIPS005", "HIPS005", "HIPS005", "HIPS006", "HIPS006", "HIPS008", > "HIPS010", "HIPS024", "HIPS024", "HIPS024", "HIPS025", "HIPS028", > "HIPS028", "HIPS030", "HIPS030", "HIPS030", "HIPS035", "HIPS035", > "HIPS035", "HIPS036", "HIPS036", "HIPS037", "HIPS044", "HIPS047", > "HIPS047", "HIPS056", "HIPS056", "HIPS057", "HIPS057", "HIPS057", > "HIPS058", "HIPS059", "HIPS059", "HIPS061", "HIPS062", "HIPS062", > "HIPS062", "HIPS064", "HIPS074", "HIPS079", "HIPS084", "HIPS089", > "HIPS090", "HIPS090", "HIPS090", "HIPS091", "HIPS091", "HIPS092", > "HIPS092", "HIPS092", "HIPS001", "HIPS001", "HIPS001", "HIPS004", > "HIPS004", "HIPS004", "HIPS005", "HIPS005", "HIPS005", "HIPS006", > "HIPS006", "HIPS008", "HIPS022", "HIPS024", "HIPS028", "HIPS030", > "HIPS035", "HIPS036", "HIPS036", "HIPS039", "HIPS044", "HIPS047", > "HIPS051", "HIPS056", "HIPS058", "HIPS058", "HIPS059", "HIPS059", > "HIPS062", "HIPS062", "HIPS062", "HIPS069", "HIPS069", "HIPS071", > "HIPS074", "HIPS079", "HIPS084", "HIPS084", "HIPS085", "HIPS089", > "HIPS090", "HIPS091", "HIPS091", "HIPS091", "HIPS092", "HIPS092", > "HIPS093"), StepHeight = c(0.005, 0.008, 0.072, 0.003, 0.014, > 0.01, 0.027, 0.074, 0.128, 0.048, 0.036, 0.024, 0.021, 0.026, > 0.03, 0.004, 0.006, 0.006, 0.011, 0.006, 0.053, 0.028, 0.073, > 0.041, 0.005, 0.007, 0.013, 0.012, 0.021, 0.053, 0.013, 0.071, > 0.012, 0.016, 0.023, 0.024, 0.011, 0.019, 0.014, 0.022, 0.011, > 0.129, 0.03, 0.012, 0.062, 0.145, 0.077, 0.028, 0.006, 0.019, > 0.008, 0.006, 0.034, 0.109, 0.09, 0.005, 0.016, 0.005, 0.257, > 0.011, 0.205, 0.01, 0.017, 0.039, 0.01, 0.016, 0.043, 0.004, > 0.008, 0.04, 0.068, 0.006, 0.008, 0.005, 0.097, 0.015, 0.016, > 0.01, 0.021, 0.008, 0.01, 0.006, 0.016, 0.021, 0.012, 0.009, > 0.032, 0.055, 0.006, 0.066, 0.018, 0.01, 0.018, 0.017, 0.015, > 0.01, 0.017, 0.02, 0.022)), class = "data.frame", row.names = c(4L, > 5L, 6L, 7L, 8L, 10L, 12L, 14L, 19L, 29L, 30L, 31L, 33L, 41L, > 43L, 44L, 45L, 46L, 47L, 48L, 51L, 52L, 53L, 58L, 62L, 65L, 67L, > 70L, 72L, 74L, 75L, 77L, 79L, 82L, 83L, 86L, 88L, 89L, 90L, 93L, > 109L, 114L, 117L, 129L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, > 138L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 149L, 150L, 151L, > 152L, 155L, 165L, 167L, 172L, 173L, 174L, 176L, 178L, 179L, 185L, > 186L, 188L, 192L, 193L, 195L, 197L, 199L, 202L, 203L, 204L, 214L, > 216L, 221L, 225L, 234L, 236L, 237L, 238L, 250L, 252L, 255L, 256L, > 257L, 258L, 260L, 261L)) > > datashort > > # This does not work: > fitgee <- gee(HipFlex ~ StepHeight,data=datashort,id=PID,corstr="exchangeable",na.action=na.omit) > summary(fitgee) > > # This works. > fitlm <- lm(HipFlex ~ StepHeight,data=datashort) > summary(fitlm) > > > John David Sorkin M.D., Ph.D. > Professor of Medicine, University of Maryland School of Medicine; > > Associate Director for Biostatistics and Informatics, Baltimore VA Medical Center Geriatrics Research, Education, and Clinical Center; > > PI Biostatistics and Informatics Core, University of Maryland School of Medicine Claude D. Pepper Older Americans Independence Center; > > Senior Statistician University of Maryland Center for Vascular Research; > > Division of Gerontology and Paliative Care, > 10 North Greene Street > GRECC (BT/18/GR) > Baltimore, MD 21201-1524 > Cell phone 443-418-5382 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.