我已经建立了一个效果很好的线性混合效果模型：
MDA_counts_lme <- lme(fixed = counts ~ treatment, data = dt_meta,
random = ~ 1 | participant)
MDA_counts_lme
new.dat <- data.frame(treatment = c("treatmentnat", "treatmentnatH2", "treatmentRNAlat", "treatmentOmni"))
当我尝试提取predict值时出现问题。
new.dat$pred_nat <- predict(MDA_counts_lme, newdata=new.dat, level=0)
我收到错误消息：
Error in sprintf(ngettext(sum(wch), "level %s not allowed for %s", "levels %s not allowed for %s"), :
too few arguments
即使我将级别变量设置为level=1或level=1，错误仍然存在。谁可以请详细说明这个选项
以下是我的数据
df_nat <- structure(list(name_to_use = structure(c(1L, 5L, 41L, 73L, 14L,
73L, 10L, 18L, 21L, 29L, 39L, 57L, 59L, 65L, 25L, 34L, 44L, 50L,
69L, 48L), .Label = c("S1", "S10", "S11", "S12", "S13", "S17",
"S18", "S19", "S2", "S20", "S21", "S22", "S23", "S24", "S25",
"S26", "S27", "S28", "S29", "S3", "S30", "S31", "S32", "S33",
"S34", "S35", "S36", "S37", "S38", "S39", "S4", "S40", "S41",
"S42", "S43", "S44", "S45", "S47", "S48", "S49", "S5", "S50",
"S51", "S52", "S53", "S54", "S55", "S56", "S57", "S58", "S59",
"S6", "S60", "S61", "S62", "S63", "S64", "S65", "S66", "S67",
"S68", "S69", "S7", "S70", "S71", "S72", "S73", "S74", "S75",
"S76", "S77", "S8", "S9"), class = "factor"), technology = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = "MDA", class = "factor"), taxon = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = "strain", class = "factor"), sample_name = structure(c(1L,
9L, 14L, 22L, 30L, 38L, 46L, 54L, 61L, 69L, 77L, 85L, 93L, 101L,
109L, 117L, 125L, 133L, 142L, 147L), .Label = c("01_00H_NA_DNA",
"01_00H_NA_S", "01_00H_NW_DNA", "01_00H_NW_S", "01_00H_OM_DNA",
"01_00H_OM_S", "01_00H_RL_DNA", "01_00H_RL_S", "01_24H_NA_DNA",
"01_24H_NA_S", "01_24H_NW_DNA", "01_24H_NW_S", "01_24H_RL_S",
"02_00H_NA_DNA", "02_00H_NA_S", "02_00H_NW_DNA", "02_00H_NW_S",
"02_00H_OM_DNA", "02_00H_OM_S", "02_00H_RL_DNA", "02_00H_RL_S",
"02_24H_NA_DNA", "02_24H_NA_S", "02_24H_NW_DNA", "02_24H_NW_S",
"02_24H_OM_DNA", "02_24H_OM_S", "02_24H_RL_DNA", "02_24H_RL_S",
"02_48H_NA_DNA", "02_48H_NA_S", "02_48H_NW_DNA", "02_48H_NW_S",
"02_48H_OM_DNA", "02_48H_OM_S", "02_48H_RL_DNA", "02_48H_RL_S",
"03_00H_NA_DNA", "03_00H_NA_S", "03_00H_NW_DNA", "03_00H_NW_S",
"03_00H_OM_DNA", "03_00H_OM_S", "03_00H_RL_DNA", "03_00H_RL_S",
"03_24H_NA_DNA", "03_24H_NA_S", "03_24H_NW_DNA", "03_24H_NW_S",
"03_24H_OM_DNA", "03_24H_OM_S", "03_24H_RL_DNA", "03_24H_RL_S",
"03_48H_NA_DNA", "03_48H_NA_S", "03_48H_NW_DNA", "03_48H_NW_S",
"03_48H_OM_S", "03_48H_RL_DNA", "03_48H_RL_S", "04_00H_NA_DNA",
"04_00H_NA_S", "04_00H_NW_DNA", "04_00H_NW_S", "04_00H_OM_DNA",
"04_00H_OM_S", "04_00H_RL_DNA", "04_00H_RL_S", "04_24H_NA_DNA",
"04_24H_NA_S", "04_24H_NW_DNA", "04_24H_NW_S", "04_24H_OM_DNA",
"04_24H_OM_S", "04_24H_RL_DNA", "04_24H_RL_S", "04_48H_NA_DNA",
"04_48H_NA_S", "04_48H_NW_DNA", "04_48H_NW_S", "04_48H_OM_DNA",
"04_48H_OM_S", "04_48H_RL_DNA", "04_48H_RL_S", "05_00H_NA_DNA",
"05_00H_NA_S", "05_00H_NW_DNA", "05_00H_NW_S", "05_00H_OM_DNA",
"05_00H_OM_S", "05_00H_RL_DNA", "05_00H_RL_S", "05_24H_NA_DNA",
"05_24H_NA_S", "05_24H_NW_DNA", "05_24H_NW_S", "05_24H_OM_DNA",
"05_24H_OM_S", "05_24H_RL_DNA", "05_24H_RL_S", "05_48H_NA_DNA",
"05_48H_NA_S", "05_48H_NW_DNA", "05_48H_NW_S", "05_48H_OM_DNA",
"05_48H_OM_S", "05_48H_RL_DNA", "05_48H_RL_S", "06_00H_NA_DNA",
"06_00H_NA_S", "06_00H_NW_DNA", "06_00H_NW_S", "06_00H_OM_DNA",
"06_00H_OM_S", "06_00H_RL_DNA", "06_00H_RL_S", "06_24H_NA_DNA",
"06_24H_NA_S", "06_24H_NW_DNA", "06_24H_NW_S", "06_24H_OM_DNA",
"06_24H_OM_S", "06_24H_RL_DNA", "06_24H_RL_S", "06_48H_NA_DNA",
"06_48H_NA_S", "06_48H_NW_DNA", "06_48H_NW_S", "06_48H_OM_DNA",
"06_48H_OM_S", "06_48H_RL_DNA", "06_48H_RL_S", "07_00H_NA_DNA",
"07_00H_NA_S", "07_00H_NW_DNA", "07_00H_NW_S", "07_00H_OM_DNA",
"07_00H_OM_S", "07_00H_RL_DNA", "07_00H_RL_S", "07_24H_NA_ S",
"07_24H_NA_DNA", "07_24H_NW_DNA", "07_24H_NW_S", "07_24H_OM_DNA",
"07_24H_RL_DNA", "07_48H_NA_DNA", "07_48H_NA_S", "07_48H_NW_DNA",
"07_48H_NW_S", "07_48H_OM_DNA", "07_48H_OM_S", "07_48H_RL_DNA",
"07_48H_RL_S"), class = "factor"), DV = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L), .Label = "1", class = "factor"), material = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = "fecal", class = "factor"), time_post_collection = c(1L,
2L, 1L, 2L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 3L, 1L, 2L, 3L,
1L, 2L, 3L), timePoint = structure(c(3L, 1L, 3L, 1L, 2L, 3L,
3L, 1L, 3L, 3L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L), .Label = c("1D",
"2D", "Baseline"), class = "factor"), treatment_long = c("native",
"native", "native", "native", "native", "native", "native", "native",
"native", "native", "native", "native", "native", "native", "native",
"native", "native", "native", "native", "native"), treatment = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = c("nat", "natH2", "Om", "RNALat"), class = "factor"),
tech_trt_pair = structure(c(1L, 5L, 8L, 12L, 16L, 20L, 24L,
28L, 32L, 36L, 40L, 44L, 48L, 52L, 56L, 61L, 65L, 69L, 73L,
77L), .Label = c(" 1", " 2", " 3", " 4", " 5", " 6", " 7",
" 8", " 9", "10", "11", "12", "13", "14", "15", "16", "17",
"18", "19", "20", "21", "22", "23", "24", "25", "26", "27",
"28", "29", "30", "31", "32", "33", "34", "35", "36", "37",
"38", "39", "40", "41", "42", "43", "44", "45", "46", "47",
"48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67",
"68", "69", "70", "71", "72", "73", "74", "75", "76", "77",
"78", "79", "80"), class = "factor"), participant = structure(c(1L,
1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L,
6L, 7L, 7L, 7L), .Label = c("P1", "P2", "P3", "P4", "P5",
"P6", "P7"), class = "factor"), antibiotics = structure(c(2L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
replicate = structure(c(1L, 5L, 44L, 76L, 16L, 76L, 12L,
20L, 23L, 31L, 42L, 60L, 62L, 68L, 27L, 36L, 47L, 53L, 72L,
51L), .Label = c("S1", "S10", "S11", "S12", "S13", "S14",
"S15", "S17", "S18", "S19", "S2", "S20", "S21", "S22", "S23",
"S24", "S25", "S26", "S27", "S28", "S29", "S3", "S30", "S31",
"S32", "S33", "S34", "S35", "S36", "S37", "S38", "S39", "S4",
"S40", "S41", "S42", "S43", "S44", "S45", "S46", "S47", "S48",
"S49", "S5", "S50", "S51", "S52", "S53", "S54", "S55", "S56",
"S57", "S58", "S59", "S6", "S60", "S61", "S62", "S63", "S64",
"S65", "S66", "S67", "S68", "S69", "S7", "S70", "S71", "S72",
"S73", "S74", "S75", "S76", "S77", "S8", "S9"), class = "factor"),
type = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "DNA", class = "factor"),
ID1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0), ID2 = c(0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0), ID3 = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID4 = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID5 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0),
ID6 = c(1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1,
0, 0, 0), ID7 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 1, 0, 0, 0), ID8 = c(1, 1, 0, 0, 0, 1, 1, 1, 1,
1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1), ID9 = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID10 = c(1,
1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1),
ID12 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1), ID13 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID15 = c(1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID16 = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1), ID17 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID18 = c(0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0), ID19 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID20 = c(1, 1, 0, 0, 0, 1, 1, 1,
0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1), ID21 = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID22 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID23 = c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1), ID24 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID25 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0), ID26 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0), ID27 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID28 = c(0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
1, 0, 0, 0), ID29 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID30 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID31 = c(1, 1, 0, 0,
0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1), ID32 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0),
ID33 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID34 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID35 = c(1, 1, 1, 1, 1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID36 = c(1, 1, 0, 0,
0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0), ID37 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0),
ID38 = c(0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1,
1, 0, 0, 0), ID39 = c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID40 = c(1, 1, 1, 1, 1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID41 = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID42 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID43 = c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID44 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0), ID45 = c(1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID46 = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID47 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
ID48 = c(1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1,
0, 0, 0, 0), ID50 = c(1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1,
1, 1, 1, 1, 0, 1, 1, 1), ID51 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID52 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID53 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID55 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID56 = c(0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1), ID57 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID58 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID59 = c(0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0),
ID60 = c(0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID61 = c(1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0,
0, 0, 0, 0, 0, 1, 0, 1), ID62 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1), ID63 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1), ID64 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
ID65 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID67 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID68 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID69 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID70 = c(1,
1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
ID71 = c(0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID72 = c(0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0), ID73 = c(1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID74 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID75 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID77 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID78 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 1, 1, 0, 0, 0), ID79 = c(1, 1, 1, 1, 1, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1), ID80 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0), ID81 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0),
ID82 = c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0,
0, 1, 1, 1), ID83 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1), ID84 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID85 = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0), ID86 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID87 = c(0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1,
1, 0, 0, 0), ID88 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID89 = c(1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID90 = c(1, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0), ID91 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID92 = c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
1, 0, 0, 0), ID93 = c(0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0), ID94 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID95 = c(0, 0, 0, 0,
0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ID96 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
ID97 = c(1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0,
0, 0, 0, 0), ID98 = c(1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 0, 0, 0), ID99 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0), ID100 = c(0, 0, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ID101 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1),
ID102 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), ID103 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0), Sampleid = structure(c(1L, 9L, 14L,
22L, 30L, 38L, 46L, 54L, 61L, 69L, 77L, 85L, 93L, 101L, 109L,
117L, 125L, 133L, 142L, 147L), .Label = c("01_00H_NA_DNA",
"01_00H_NA_S", "01_00H_NW_DNA", "01_00H_NW_S", "01_00H_OM_DNA",
"01_00H_OM_S", "01_00H_RL_DNA", "01_00H_RL_S", "01_24H_NA_DNA",
"01_24H_NA_S", "01_24H_NW_DNA", "01_24H_NW_S", "01_24H_RL_S",
"02_00H_NA_DNA", "02_00H_NA_S", "02_00H_NW_DNA", "02_00H_NW_S",
"02_00H_OM_DNA", "02_00H_OM_S", "02_00H_RL_DNA", "02_00H_RL_S",
"02_24H_NA_DNA", "02_24H_NA_S", "02_24H_NW_DNA", "02_24H_NW_S",
"02_24H_OM_DNA", "02_24H_OM_S", "02_24H_RL_DNA", "02_24H_RL_S",
"02_48H_NA_DNA", "02_48H_NA_S", "02_48H_NW_DNA", "02_48H_NW_S",
"02_48H_OM_DNA", "02_48H_OM_S", "02_48H_RL_DNA", "02_48H_RL_S",
"03_00H_NA_DNA", "03_00H_NA_S", "03_00H_NW_DNA", "03_00H_NW_S",
"03_00H_OM_DNA", "03_00H_OM_S", "03_00H_RL_DNA", "03_00H_RL_S",
"03_24H_NA_DNA", "03_24H_NA_S", "03_24H_NW_DNA", "03_24H_NW_S",
"03_24H_OM_DNA", "03_24H_OM_S", "03_24H_RL_DNA", "03_24H_RL_S",
"03_48H_NA_DNA", "03_48H_NA_S", "03_48H_NW_DNA", "03_48H_NW_S",
"03_48H_OM_S", "03_48H_RL_DNA", "03_48H_RL_S", "04_00H_NA_DNA",
"04_00H_NA_S", "04_00H_NW_DNA", "04_00H_NW_S", "04_00H_OM_DNA",
"04_00H_OM_S", "04_00H_RL_DNA", "04_00H_RL_S", "04_24H_NA_DNA",
"04_24H_NA_S", "04_24H_NW_DNA", "04_24H_NW_S", "04_24H_OM_DNA",
"04_24H_OM_S", "04_24H_RL_DNA", "04_24H_RL_S", "04_48H_NA_DNA",
"04_48H_NA_S", "04_48H_NW_DNA", "04_48H_NW_S", "04_48H_OM_DNA",
"04_48H_OM_S", "04_48H_RL_DNA", "04_48H_RL_S", "05_00H_NA_DNA",
"05_00H_NA_S", "05_00H_NW_DNA", "05_00H_NW_S", "05_00H_OM_DNA",
"05_00H_OM_S", "05_00H_RL_DNA", "05_00H_RL_S", "05_24H_NA_DNA",
"05_24H_NA_S", "05_24H_NW_DNA", "05_24H_NW_S", "05_24H_OM_DNA",
"05_24H_OM_S", "05_24H_RL_DNA", "05_24H_RL_S", "05_48H_NA_DNA",
"05_48H_NA_S", "05_48H_NW_DNA", "05_48H_NW_S", "05_48H_OM_DNA",
"05_48H_OM_S", "05_48H_RL_DNA", "05_48H_RL_S", "06_00H_NA_DNA",
"06_00H_NA_S", "06_00H_NW_DNA", "06_00H_NW_S", "06_00H_OM_DNA",
"06_00H_OM_S", "06_00H_RL_DNA", "06_00H_RL_S", "06_24H_NA_DNA",
"06_24H_NA_S", "06_24H_NW_DNA", "06_24H_NW_S", "06_24H_OM_DNA",
"06_24H_OM_S", "06_24H_RL_DNA", "06_24H_RL_S", "06_48H_NA_DNA",
"06_48H_NA_S", "06_48H_NW_DNA", "06_48H_NW_S", "06_48H_OM_DNA",
"06_48H_OM_S", "06_48H_RL_DNA", "06_48H_RL_S", "07_00H_NA_DNA",
"07_00H_NA_S", "07_00H_NW_DNA", "07_00H_NW_S", "07_00H_OM_DNA",
"07_00H_OM_S", "07_00H_RL_DNA", "07_00H_RL_S", "07_24H_NA_ S",
"07_24H_NA_DNA", "07_24H_NW_DNA", "07_24H_NW_S", "07_24H_OM_DNA",
"07_24H_RL_DNA", "07_48H_NA_DNA", "07_48H_NA_S", "07_48H_NW_DNA",
"07_48H_NW_S", "07_48H_OM_DNA", "07_48H_OM_S", "07_48H_RL_DNA",
"07_48H_RL_S"), class = "factor"), counts = c(33, 33, 26,
31, 28, 27, 27, 28, 28, 27, 31, 37, 35, 33, 30, 32, 30, 25,
26, 29)), .Names = c("name_to_use", "technology", "taxon",
"sample_name", "DV", "material", "time_post_collection", "timePoint",
"treatment_long", "treatment", "tech_trt_pair", "participant",
"antibiotics", "replicate", "type", "ID1", "ID2", "ID3", "ID4",
"ID5", "ID6", "ID7", "ID8", "ID9", "ID10", "ID12", "ID13", "ID15",
"ID16", "ID17", "ID18", "ID19", "ID20", "ID21", "ID22", "ID23",
"ID24", "ID25", "ID26", "ID27", "ID28", "ID29", "ID30", "ID31",
"ID32", "ID33", "ID34", "ID35", "ID36", "ID37", "ID38", "ID39",
"ID40", "ID41", "ID42", "ID43", "ID44", "ID45", "ID46", "ID47",
"ID48", "ID50", "ID51", "ID52", "ID53", "ID55", "ID56", "ID57",
"ID58", "ID59", "ID60", "ID61", "ID62", "ID63", "ID64", "ID65",
"ID67", "ID68", "ID69", "ID70", "ID71", "ID72", "ID73", "ID74",
"ID75", "ID77", "ID78", "ID79", "ID80", "ID81", "ID82", "ID83",
"ID84", "ID85", "ID86", "ID87", "ID88", "ID89", "ID90", "ID91",
"ID92", "ID93", "ID94", "ID95", "ID96", "ID97", "ID98", "ID99",
"ID100", "ID101", "ID102", "ID103", "Sampleid", "counts"), row.names = c(NA,
-20L), class = "data.frame")