getting Error in svd(X) : infinite or missing values in 'x' when using summary of regression model

Question

I am getting an error

Error in svd(X) : infinite or missing values in 'x'

while doing summary of ordinal regression model. This is my code ..

library(MASS)
a <- dget('dput.txt')
lep <- polr(bmicat2 ~ Leptin, data = a,Hess = TRUE)
summary(lep)
Error in svd(X) : infinite or missing values in 'x'

sample data is given to replicate the error. Can someone please help.

structure(list(bmicat2 = structure(c(1L, 3L, 2L, 1L, 1L, 1L, 
1L, 1L, 3L, 3L, 3L, 3L, 3L, 1L, 2L, 3L, 2L, 3L, 3L, 3L, 3L, 1L, 
3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 3L, 1L, 1L, 1L, 1L, 1L, 2L, 3L, 
2L, 1L, 1L, 3L, 3L, 2L, 1L, 1L, 1L, 2L, 1L, 3L, 1L, 3L, 1L, 1L, 
1L, 2L, 1L, 3L, 2L, 1L, 1L, 2L, 1L, 3L, 1L, 1L, 1L, 3L, 1L, 3L, 
3L, 3L, 2L, 3L, 1L, 3L, 3L, 3L, 2L, 2L, 1L, 2L, 2L, 1L, 3L, 1L, 
1L, 1L, 2L, 2L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 2L, 3L, 1L, 2L, 1L, 
2L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 1L, 2L, 2L, 2L, 1L, 3L, 
3L, 3L, 3L, 3L, 2L, 3L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 
1L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 3L, 1L, 1L, 1L, 1L, 2L, 3L, 2L, 
2L, 1L, 1L, 1L, 3L, 2L, 1L, 3L, 2L, 2L, 2L, 2L, 1L, 3L, 1L, 3L, 
1L, 1L, 1L, 3L, 1L, 1L, 1L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 3L, 
1L, 2L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 1L, 3L, 2L, 1L, 1L, 
1L, 3L, 1L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 
1L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 3L, 2L, 1L, 3L, 3L, 
1L, 2L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 3L, 1L, 1L, 3L, 1L, 1L, 1L, 
1L, 1L, 1L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 3L, 2L, 3L, 2L, 1L, 1L, 
3L, 3L, 2L, 1L, 3L, 2L, 3L, 3L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 1L, 
3L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 
3L, 3L, 1L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 3L, 1L, 3L, 3L, 
2L, 3L, 2L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 2L, 3L, 3L, 3L, 1L, 3L, 
1L, 1L, 1L, 3L, 1L, 2L, 3L, 1L, 1L, 3L, 2L, 1L, 3L, 3L, 2L, 2L, 
1L, 1L, 3L, 2L, 3L, 3L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 3L, 
3L, 3L, 2L, 1L, 1L, 3L, 3L, 1L, 2L, 3L, 3L, 1L, 3L, 3L, 1L, 1L, 
1L, 3L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 3L, 2L, 1L, 3L, 1L, 1L, 1L, 
3L, 2L, 2L, 2L, 1L, 3L, 1L, 3L, 1L, 3L, 2L, 1L, 2L, 3L, 1L, 3L, 
1L, 1L, 1L, 1L, 2L, 1L, 3L, 1L, 1L, 1L, 3L, 2L, 2L, 2L, 1L, 3L, 
1L, 1L, 3L), .Label = c("Normal", "Overweight", "Obesity"), class = "factor"), 
    Leptin = c(47710.88, 200022.04, 161067.35, 55561.76, 100728.06, 
    69783.61, 54981.01, 58801.34, 128313.05, 157378.46, 292366.57, 
    121608.04, 206046.88, 54981.01, 154969.33, 516791.75, 104766.73, 
    440134.48, 286576.47, 343513.87, 40020.2, 30077.63, 359266.48, 
    290381.41, 23005.7, 48080.73, 134741.37, 114631.03, 49644.25, 
    139956.69, 138242.54, 19862, 64541.08, 57119.32, 115382.48, 
    7238.99, 154969.33, 82321.93, 85406.54, 19170.47, 57208.08, 
    277488.74, 290791.3, 206703.97, 25333.82, 20134.62, 32823.3, 
    231036.03, 111986.18, 352190.59, 128041.35, 185025.96, 63451.72, 
    143404.56, 71163.46, 252067.35, 46223.39, 185077.75, 172339.07, 
    41381.36, 91498.49, 233969.82, 24245.94, 248133.29, 145890.48, 
    196431.01, 146690.84, 218617.65, 151333.68, 245695.08, 336242.88, 
    266936.45, 64105.63, 301181.31, 150192.02, 253863.48, 314169.03, 
    406059.04, 68228.37, 335171.04, 37547.56, 123713.8, 75034, 
    45708.91, 67449.43, 15920.57, 38444.37, 19170.47, 174853.97, 
    236689.18, 22879.68, 34599.46, 57562.83, 177486.58, 244481.84, 
    122637.48, 58094.2, 82921.65, 382788.21, 119733.17, 64192.75, 
    8787.33, 17146.98, 21986.45, 13077.71, 18320.19, 119777.74, 
    61615.67, 5708.97, 24307.05, 244118.62, 10780.13, 12158.23, 
    80265.64, 70215.06, 122189.66, 48219.23, 156702.5, 128313.05, 
    115072.95, 152956.29, 107776.73, 108914.21, 85835.09, 13608.28, 
    24853.42, 58359.56, 29967.69, 168944.14, 22435.55, 67709.18, 
    17444.89, 51058.87, 21072.27, 34702.75, 9711.01, 43870.71, 
    113571.74, 26863.91, 294914.16, 15920.57, 23381.51, 309409.6, 
    19587.14, 99905.3, 79494.37, 90768.21, 131129.25, 411527.63, 
    132269.4, 83735.58, 92014.19, 57030.54, 62578.38, 131676.19, 
    238711.8, 48080.73, 429691.15, 88750.76, 32770.45, 163022.26, 
    98045.93, 8421.27, 113659.95, 27210.74, 421265.4, 225005.8, 
    39431.91, 18748.27, 224660.83, 13695.33, 11186.36, 42727.62, 
    863581.67, 18031.36, 250895.16, 326547.74, 69351.93, 34288.82, 
    64932.66, 23381.51, 392858.01, 32399.47, 176370.64, 31651.9, 
    17592.65, 93304.24, 71938.68, 297130.98, 58624.7, 311565.88, 
    143685.29, 204518.07, 28689.43, 612308, 119688.61, 116888.21, 
    60738.48, 274462.8, 307122.48, 202886.86, 119777.74, 194409.2, 
    259555.37, 479766.12, 97527.66, 177029.67, 17146.98, 70560.06, 
    50922.4, 213003.8, 142470.09, 26747.8, 235563.59, 49460.99, 
    185181.36, 27210.74, 156220.34, 284284.42, 254982.61, 67059.61, 
    46736.22, 97657.21, 399497.2, 13433.03, 385197.12, 143685.29, 
    46503.31, 333111.93, 228589.14, 40117.95, 86563.73, 459114.82, 
    334559.84, 39824.45, 90295.84, 19309.96, 25333.82, 15604.37, 
    548683.37, 13954.22, 63974.92, 283344.56, 47061.73, 14794.69, 
    56852.91, 63320.83, 21335.74, 18176.13, 44060.31, 31436.88, 
    779337.47, 177842.32, 15683.81, 1804.18, 18031.36, 150572.24, 
    69956.22, 353788.11, 42823.25, 25927.76, 23131.34, 351871.83, 
    130355.47, 48034.54, 9711.01, 296020.99, 77994.24, 106641.08, 
    NA, 68876.79, 64323.41, 37947.12, 166071.05, 239189.29, 376318.03, 
    132041.15, 48818.15, 209454.17, 25572.25, 232324.09, 142750.23, 
    34185.02, 21204.24, 6040.1, 5708.97, 252190.95, 129219.75, 
    50922.4, 97786.76, 117464.95, 84978.04, 15122, 6356.95, NA, 
    299220.74, 28801.64, 535105.27, 421922.32, 9486.52, 159801.65, 
    139492.77, 40410.71, 28011.68, 67189.58, 10780.13, 173997.11, 
    15283.91, 192081.41, 169590.94, 29747.24, 57961.45, 55606.38, 
    351712.55, 157233.52, 117553.73, 201046.58, NA, 204409.11, 
    468179.87, 201640.99, 374968.45, 330911.94, 153817.84, 45098.7, 
    83050.16, NA, 20134.62, 20606.55, 328498.24, 22115.29, 40313.21, 
    196751.22, 6356.95, 8042.41, 252005.56, 124522.47, 9711.01, 
    168745.34, 110580.08, 78722.96, 104897.35, 43728.34, 20270.11, 
    339321.01, 170488.25, 55829.38, 173292.85, 29967.69, 5708.97, 
    30132.53, 12715.53, 180648.71, 146219.86, 33716.28, 85835.09, 
    110404.53, 327146.88, 259303.38, 164396.3, 206156.31, 21204.24, 
    105158.65, 152478.41, 327897.07, 29025.44, 36237.65, 426358.52, 
    265525.58, 52464.02, 287117.75, 658217.42, 67709.18, 107645.6, 
    46829.29, 186790.78, 68920, 363915.23, 269385.74, 126324.01, 
    146361.1, 153243.28, 101161.4, 318839.47, 132223.74, 96190, 
    143966.19, 162141.4, 63495.34, 35371.14, 261070.81, 197071.7, 
    240146.08, 73100.38, 63713.39, 248622.82, 92616.07, 163120.25, 
    95026.25, 266807.98, 153434.72, 145937.52, 127950.82, 376487.04, 
    81208.15, 311998.55, 41767.47, 59595.08, 13256.19, 35011.88, 
    99083.27, 47571.98, 174450.51, 8296.48, 35524.66, 68747.15, 
    214064.04, 127272.35, 70603.17, 99256.27, 19862, 145373.38, 
    184560.15, 57828.63, 115426.71)), row.names = c(NA, -425L
), class = c("tbl_df", "tbl", "data.frame"))

user_10944942 · Answer

It is an issue of lep$Hessian having NA values. If you do this:

lep <- polr(bmicat2 ~ Leptin, data = a,Hess = TRUE)
lep$Hessian[1,1]<-0
lep$Hessian[1,2]<-0
lep$Hessian[1,3]<-0
lep$Hessian[2,1]<-0
lep$Hessian[3,1]<-0
summary(lep)

You do not have any problems but the output from lep and summary(lep) are pretty much the same, I think. Is it the imputation of 0 to missing values in the Hessian that disturbing?

getting Error in svd(X) : infinite or missing values in 'x' when using summary of regression model

1 Answers