Issue with metalonda() command: Error: $ operator is invalid for atomic vectors

[jlucore]

Hello, I am having issues running the metalonda() command because I keep producing the error: $ operator is invalid for atomic vectors. This error seems strange because I have ensured all of my vectors are numeric. I am also confused as to what the "points" vector is and how to create it appropriately. For now, my points vector is a list 1:49 since my samples are from days 1:49. Thank you for your assistance. A reproducible answer is below:

otu <- structure(c(2547, 0, 600, 3, 17, 0, 372, 202, 0, 339, 10491,
0, 1417, 2083, 0, 325, 4521, 0, 12366, 6, 5891, 0, 0, 0, 643,
399, 0, 301, 343, 0, 1194, 9, 15835, 0, 56, 0, 20554, 0, 11336,
2, 0, 0, 538, 1104, 0, 2736, 3430, 0, 1347, 1249, 0, 977, 6455,
0, 80, 39, 0, 429, 341, 0, 156, 70, 0, 382, 186, 0, 1751, 925,
0, 0, 7634, 0, 561, 99, 0, 1067, 655, 0, 160, 654, 0, 0, 2009,
0, 139, 0, 5433, 0, 0, 0, 169, 85, 0, 406, 206, 0, 374, 236,
4, 459, 718, 51, 123, 81, 0, 623, 1992, 0, 0, 0, 344, 0, 40,
0, 304, 88, 0, 284, 1372, 0, 79, 96, 0, 130, 403, 0, 144, 61,
0, 357, 731, 40, 95, 504, 0, 2912, 9435, 0, 323, 15, 0, 485,
340, 0, 254, 100, 4, 863, 2210, 0, 32, 21, 0, 219, 443, 0, 1925,
103, 0, 327, 1420, 0, 457, 23, 0, 95, 370, 0, 68, 399, 0, 159,
932, 0, 82, 13, 0, 105, 225, 0, 244, 46, 0, 153, 786, 0, 3105,
1114, 0, 0, 1011, 0, 276, 364, 0, 604, 2936, 0, 417, 154, 0,
224, 710, 0, 55, 26, 0, 198, 254, 0, 92, 8, 0, 236, 37, 0, 243,
123, 0, 195, 161, 0, 115, 123, 0, 869, 577, 0, 1272, 730, 0,
520, 844, 0, 50, 368, 8, 5, 902, 0, 602, 52, 0, 828, 2176, 0,
338, 143, 3, 416, 1341, 31, 1032, 12727, 25637, 0, 5566, 0, 41,
11, 0, 309, 205, 0, 70, 4, 0, 359, 198, 0, 154, 60, 0, 51, 1221,
0, 3, 4, 0, 77, 85, 0, 65, 152, 0, 257, 917, 0, 136, 60, 0, 78,
746, 0), .Dim = c(6L, 49L), .Dimnames = list(c("taxa 1", "taxa 2",
"taxa 3", "taxa 4", "taxa 5", "taxa 6"), c("LID_100039", "LID_100080",
"LID_100105", "LID_100125", "LID_100194", "LID_100225", "LID_100229",
"LID_100551", "LID_101556", "LID_101558", "LID_101560", "LID_101562",
"LID_101564", "LID_101566", "LID_101569", "LID_101570", "LID_101571",
"LID_101573", "LID_101575", "LID_101577", "LID_101581", "LID_101584",
"LID_101587", "LID_101590", "LID_101591", "LID_101592", "LID_101593",
"LID_101594", "LID_101596", "LID_101597", "LID_101601", "LID_101602",
"LID_101604", "LID_101606", "LID_101608", "LID_101610", "LID_101612",
"LID_101613", "LID_101616", "LID_101617", "LID_101618", "LID_101619",
"LID_101620", "LID_101621", "LID_101622", "LID_101623", "LID_101624",
"LID_101630", "LID_101632")))

Group <- structure(c(2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L,
1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L), .Label = c("Female", "Male"))

Individual <- structure(c(64L, 34L, 5L, 23L, 53L, 4L, 47L, 80L, 71L, 43L, 1L,
87L, 48L, 45L, 55L, 18L, 11L, 47L, 75L, 44L, 47L, 10L, 86L, 44L,
28L, 61L, 21L, 73L, 70L, 86L, 45L, 1L, 43L, 47L, 48L, 11L, 16L,
60L, 58L, 40L, 30L, 31L, 50L, 17L, 5L, 86L, 76L, 60L, 69L), .Label = c("F100",
"F101", "F102", "F103", "F104", "F105", "F106", "F107", "F108",
"F109", "F110", "F111", "F112", "F113", "F114", "F115", "F116",
"F117", "F118", "F119", "F120", "F121", "F122", "F123", "F124",
"F125", "F126", "F127", "F128", "F129", "F130", "F131", "F132",
"F32", "F74", "F84", "F85", "F86", "F87", "F88", "F89", "F90",
"F91", "F92", "F93", "F94", "F95", "F96", "F97", "F98", "F99",
"M49", "M50", "M51", "M52", "M53", "M54", "M55", "M56", "M57",
"M58", "M59", "M60", "M61", "M62", "M63", "M64", "M65", "M66",
"M67", "M68", "M69", "M70", "M71", "M72", "M73", "M74", "M75",
"M76", "M77", "M78", "M79", "M80", "M81", "M82", "M83", "M84",
"M85", "M86"))

Time <- structure(c(13L, 5L, 2L, 6L, 4L, 1L, 12L, 3L, 44L, 45L, 44L,
43L, 42L, 42L, 40L, 41L, 39L, 38L, 36L, 37L, 34L, 35L, 33L, 32L,
8L, 9L, 7L, 7L, 26L, 27L, 23L, 22L, 24L, 21L, 28L, 29L, 25L,
19L, 20L, 14L, 15L, 16L, 17L, 18L, 18L, 11L, 10L, 30L, 31L), .Label = c("2015-02-20",
"2015-04-01", "2015-04-03", "2015-05-13", "2015-05-14", "2015-05-18",
"2015-11-25", "2016-01-09", "2016-01-12", "2016-02-02", "2016-02-13",
"2016-02-22", "2016-04-06", "2016-04-15", "2016-04-18", "2016-05-19",
"2016-05-23", "2016-07-02", "2017-06-02", "2017-06-06", "2017-06-16",
"2017-06-23", "2017-06-29", "2017-08-03", "2017-08-12", "2017-08-15",
"2017-08-21", "2017-10-03", "2017-10-06", "2017-12-02", "2017-12-21",
"2018-02-16", "2018-03-02", "2018-05-01", "2018-05-02", "2018-05-24",
"2018-06-01", "2018-06-02", "2018-06-05", "2018-06-11", "2018-06-16",
"2018-07-03", "2018-07-14", "2018-08-01", "2018-08-02"))

points = as.numeric(seq(1, 49, length.out = 49))

output2.metalonda.f5 = metalonda(Count = otu[5,], Time = Time, Group = Group,
ID = Individual, n.perm = 100, fit.method = "nbinomial", points = points,
text = rownames(subset_otu)[5], parall = FALSE, pvalue.threshold = 0.05,
adjust.method = "BH", time.unit = "days", ylabel = "Normalized Count",
col = c("black", "green"), prefix = "Test2_F5")

[Swindle98]

Hi I'm also getting this issue but when calling the metalondaAll function.

Traceback:

Feature  =  
Start MetaLonDA 
Visualizing Feature =  
Start Curve Fitting 
Fitting: NB SS 
[1] "ERROR in gss = Error in qr.default(s): NA/NaN/Inf in foreign function call (arg 1)\n"
Visualizing Splines of Feature =  
Error in model$dd.null : $ operator is invalid for atomic vectors
3.
visualizeFeatureSpline(aggregate.df, model, fit.method, text,
group.levels, unit = time.unit, ylabel = ylabel, col = col,
prefix = prefix) at Metalonda.R#114
2.
metalonda(Count = data.count.filt[i, ], Time = Time, Group = Group,
ID = ID, fit.method = fit.method, n.perm = n.perm, points = points,
text = rownames(data.count.filt)[i], parall = parall, pvalue.threshold,
adjust.method, time.unit, ylabel = ylabel, col = col, prefix = prefix) at Metalonda.R#320
1.
metalondaAll(Count = count, Group = group, Time = time, ID = ID,
n.perm = 1000, fit.method = "nbinomial", pvalue.threshold = 0.05,
adjust.method = "BH", time.unit = "days", norm.method = "none",
prefix = "Output", ylabel = "Normalized Count", col = c("blue", ...

Looks like its having an error with the gss package?

Edit:
Looks like it was an issue with my data input. I only had one time point for one of the groups.