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aodom@bu.edu + + +
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+
+Introduction to LegATo
+Aubrey R. +Odom
+ + Program in Bioinformatics, Boston University, Boston, +MAaodom@bu.edu + + +
January 25, 2024
+ + +LegATo_vignette.Rmd
+
+Introduction to LegATo: Longitudinal mEtaGenomic Analysis +TOolkit +
+
+
+Streamlining longitudinal microbiome profiling in Bioconductor +
+LegATo is a suite of open-source software tools for longitudinal +microbiome analysis that is extendable to several different study forms +with optimal ease-of-use for researchers. Microbiome time-series data +presents distinct challenges including complex covariate dependencies +and variety of longitudinal study designs. This toolkit will allow +researchers to determine which microbial taxa are affected over time by +perturbations such as onset of disease or lifestyle choices, and to +predict the effects of these perturbations over time, including changes +in composition or stability of commensal bacteria.
+LegATo integrates visualization, modeling and testing procedures. It +will be supplemented by hierarchical clustering tools and multivariate +generalized estimating equations (JGEEs) to adjust for the compositional +nature of microbiome data.
+
+
+Setup +
+ +## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
+## ✔ dplyr 1.1.4 ✔ readr 2.1.5
+## ✔ forcats 1.0.0 ✔ stringr 1.5.1
+## ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
+## ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
+## ✔ purrr 1.0.2
+## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
+## ✖ dplyr::filter() masks stats::filter()
+## ✖ dplyr::lag() masks stats::lag()
+## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
+
+
+
+
+
+
+
+
+
+Data +
+We will be utilizing nasopharyngeal microbiome data from Zambian +Infants from Odom et al.:
+
+dat <- system.file("extdata", "MAE.RDS", package = "LegATo") %>%
+ readRDS()
+
+dat_0.05 <- filter_animalcules_MAE(dat, 0.05)
+
+parsed <- parse_MAE_SE(dat, which_assay = "MicrobeGenetics", type = "MAE")
+parsed$sam## Sample Subject HIVStatus MothChild timepoint Age pairing
+## X1754 X1754 0469-0 Control Mother 0 9999 NA
+## X1755 X1755 0469-1 Control Infant 0 7 1
+## X2214 X2214 0507-0 Control Mother 0 9999 NA
+## X2216 X2216 0507-1 Control Infant 0 6 2
+## X2429 X2429 0539-0 Control Mother 0 9999 NA
+## X2431 X2431 0539-1 Control Infant 0 9 3
+## X2561 X2561 0554-1 HIV Infant 0 6 1
+## X2562 X2562 0554-0 HIV Mother 0 9999 NA
+## X2697 X2697 0620-0 HIV Mother 0 9999 NA
+## X2699 X2699 0620-1 HIV Infant 0 4 2
+## X2927 X2927 0469-1 Control Infant 1 21 1
+## X3042 X3042 0645-0 HIV Mother 0 9999 NA
+## X3043 X3043 0645-1 HIV Infant 0 7 3
+## X3266 X3266 0507-1 Control Infant 1 20 2
+## X3306 X3306 0718-1 Control Infant 0 6 4
+## X3308 X3308 0718-0 Control Mother 0 9999 NA
+## X3646 X3646 0539-1 Control Infant 1 25 3
+## X3847 X3847 0749-1 HIV Infant 0 6 4
+## X3848 X3848 0749-0 HIV Mother 0 9999 NA
+## X3897 X3897 0620-1 HIV Infant 1 21 2
+## X3928 X3928 0554-1 HIV Infant 1 24 1
+## X4212 X4212 0645-1 HIV Infant 1 23 3
+## X4247 X4247 0801-1 Control Infant 0 6 5
+## X4249 X4249 0801-0 Control Mother 0 9999 NA
+## X4335 X4335 0798-0 HIV Mother 0 9999 NA
+## X4336 X4336 0798-1 HIV Infant 0 9 5
+## X4632 X4632 0718-1 Control Infant 1 24 4
+## X4753 X4753 0839-0 Control Mother 0 9999 NA
+## X4755 X4755 0839-1 Control Infant 0 6 6
+## X4756 X4756 0469-1 Control Infant 2 44 1
+## X4927 X4927 0850-1 HIV Infant 0 5 6
+## X4928 X4928 0850-0 HIV Mother 0 9999 NA
+## X5031 X5031 0749-1 HIV Infant 1 25 4
+## X5035 X5035 0554-1 HIV Infant 2 42 1
+## X5036 X5036 0890-0 Control Mother 0 9999 NA
+## X5037 X5037 0890-1 Control Infant 0 10 8
+## X5042 X5042 0507-1 Control Infant 2 42 2
+## X5116 X5116 0539-1 Control Infant 2 44 3
+## X5186 X5186 0645-1 HIV Infant 2 35 3
+## X5218 X5218 0878-0 Control Mother 0 9999 NA
+## X5220 X5220 0878-1 Control Infant 0 7 7
+## X5382 X5382 0895-1 HIV Infant 0 7 7
+## X5383 X5383 0895-0 HIV Mother 0 9999 NA
+## X5449 X5449 0620-1 HIV Infant 2 36 2
+## X5650 X5650 0801-1 Control Infant 1 20 5
+## X5659 X5659 0915-0 HIV Mother 0 9999 NA
+## X5660 X5660 0915-1 HIV Infant 0 6 8
+## X5806 X5806 0798-1 HIV Infant 1 24 5
+## X6202 X6202 0469-1 Control Infant 3 58 1
+## X6214 X6214 0839-1 Control Infant 1 20 6
+## X6280 X6280 0890-1 Control Infant 1 20 8
+## X6354 X6354 0507-1 Control Infant 3 56 2
+## X6474 X6474 0850-1 HIV Infant 1 24 6
+## X6534 X6534 0878-1 Control Infant 1 22 7
+## X6541 X6541 0718-1 Control Infant 2 44 4
+## X6644 X6644 0539-1 Control Infant 3 59 3
+## X6822 X6822 0554-1 HIV Infant 3 57 1
+## X6863 X6863 0895-0 HIV Mother 6 9999 NA
+## X6864 X6864 0895-1 HIV Infant 1 23 7
+## X6870 X6870 0749-1 HIV Infant 2 42 4
+## X7031 X7031 0987-1 HIV Infant 0 8 9
+## X7090 X7090 0915-1 HIV Infant 1 25 8
+## X7223 X7223 0620-1 HIV Infant 3 58 2
+## X7272 X7272 0801-1 Control Infant 2 42 5
+## X7274 X7274 0507-1 Control Infant 4 70 2
+## X7288 X7288 0798-1 HIV Infant 2 44 5
+## X7426 X7426 0645-1 HIV Infant 3 60 3
+## X7448 X7448 0469-1 Control Infant 4 74 1
+## X7695 X7695 0718-1 Control Infant 3 59 4
+## X7746 X7746 0539-1 Control Infant 4 74 3
+## X7958 X7958 0554-1 HIV Infant 4 72 1
+## X8066 X8066 0839-1 Control Infant 2 42 6
+## X8180 X8180 0987-1 HIV Infant 1 22 9
+## X8261 X8261 1049-0 Control Mother 0 9999 NA
+## X8262 X8262 1049-1 Control Infant 0 6 10
+## X8268 X8268 0890-1 Control Infant 2 45 8
+## X8285 X8285 1040-0 Control Mother 0 9999 NA
+## X8287 X8287 1040-1 Control Infant 0 7 9
+## X8288 X8288 0850-1 HIV Infant 2 44 6
+## X8312 X8312 0878-1 Control Infant 2 42 7
+## X8332 X8332 0749-1 HIV Infant 3 60 4
+## X8500 X8500 0620-1 HIV Infant 4 72 2
+## X8550 X8550 0801-1 Control Infant 3 56 5
+## X8607 X8607 1095-0 HIV Mother 0 9999 NA
+## X8608 X8608 1095-1 HIV Infant 0 6 10
+## X8686 X8686 0915-0 HIV Mother 6 9999 NA
+## X8688 X8688 0915-1 HIV Infant 2 41 8
+## X8726 X8726 0645-1 HIV Infant 4 73 3
+## X8736 X8736 0507-1 Control Infant 5 84 2
+## X8742 X8742 0798-1 HIV Infant 3 59 5
+## X8789 X8789 0469-1 Control Infant 5 92 1
+## X9000 X9000 0718-1 Control Infant 4 74 4
+## X9080 X9080 0539-1 Control Infant 5 88 3
+## X9376 X9376 0839-1 Control Infant 3 56 6
+## X9384 X9384 1040-1 Control Infant 1 21 9
+## X9424 X9424 1049-1 Control Infant 1 22 10
+## X9518 X9518 0850-1 HIV Infant 3 60 6
+## X9555 X9555 0620-1 HIV Infant 5 86 2
+## X9572 X9572 0554-1 HIV Infant 5 91 1
+## X9603 X9603 0749-1 HIV Infant 4 74 4
+## X9632 X9632 0878-1 Control Infant 3 58 7
+## X9684 X9684 0890-1 Control Infant 3 60 8
+## X9708 X9708 1095-1 HIV Infant 1 20 10
+## X9714 X9714 0645-1 HIV Infant 5 87 3
+## X9922 X9922 0987-1 HIV Infant 2 42 9
+## X9956 X9956 0798-1 HIV Infant 4 76 5
+## X9983 X9983 0469-0 Control Mother 6 9999 NA
+## X9984 X9984 0469-1 Control Infant 6 105 1
+## X10062 X10062 0507-0 Control Mother 6 9999 NA
+## X10064 X10064 0507-1 Control Infant 6 101 2
+## X10255 X10255 0718-1 Control Infant 5 88 4
+## X10401 X10401 0539-0 Control Mother 6 9999 NA
+## X10402 X10402 0539-1 Control Infant 6 104 3
+## X10590 X10590 0554-0 HIV Mother 6 9999 NA
+## X10592 X10592 0554-1 HIV Infant 6 104 1
+## X10724 X10724 0749-1 HIV Infant 5 88 4
+## X10754 X10754 0850-1 HIV Infant 4 75 6
+## X10892 X10892 0987-1 HIV Infant 3 56 9
+## X10907 X10907 0890-1 Control Infant 4 75 8
+## X10973 X10973 0878-1 Control Infant 4 73 7
+## X10986 X10986 1040-1 Control Infant 2 42 9
+## X11041 X11041 0620-0 HIV Mother 6 9999 NA
+## X11043 X11043 0620-1 HIV Infant 6 102 2
+## X11120 X11120 1049-1 Control Infant 2 42 10
+## X11170 X11170 0801-1 Control Infant 5 87 5
+## X11220 X11220 0839-1 Control Infant 4 80 6
+## X11244 X11244 0798-1 HIV Infant 5 90 5
+## X11269 X11269 0645-0 HIV Mother 6 9999 NA
+## X11270 X11270 0645-1 HIV Infant 6 106 3
+## X11373 X11373 0718-0 Control Mother 6 9999 NA
+## X11374 X11374 0718-1 Control Infant 6 104 4
+## X11376 X11376 1095-1 HIV Infant 2 42 10
+## X11822 X11822 0850-1 HIV Infant 5 89 6
+## X11916 X11916 0878-1 Control Infant 5 88 7
+## X12080 X12080 0987-1 HIV Infant 4 74 9
+## X12115 X12115 0839-1 Control Infant 5 95 6
+## X12136 X12136 0890-1 Control Infant 5 88 8
+## X12185 X12185 0749-0 HIV Mother 6 9999 NA
+## X12187 X12187 0749-1 HIV Infant 6 105 4
+## X12327 X12327 1049-1 Control Infant 3 56 10
+## X12342 X12342 0798-0 HIV Mother 6 9999 NA
+## X12344 X12344 0798-1 HIV Infant 6 107 5
+## X12455 X12455 0801-0 Control Mother 6 9999 NA
+## X12456 X12456 0801-1 Control Infant 6 104 5
+## X12504 X12504 1095-1 HIV Infant 3 56 10
+## X12838 X12838 0850-0 HIV Mother 6 9999 NA
+## X12840 X12840 0850-1 HIV Infant 6 104 6
+## X13074 X13074 1095-1 HIV Infant 4 73 10
+## X13183 X13183 0878-0 Control Mother 6 9999 NA
+## X13184 X13184 0878-1 Control Infant 6 105 7
+## X13219 X13219 1040-1 Control Infant 4 73 9
+## X13281 X13281 0890-0 Control Mother 6 9999 NA
+## X13283 X13283 0890-1 Control Infant 6 107 8
+## X13354 X13354 0987-1 HIV Infant 5 90 9
+## X13473 X13473 0839-0 Control Mother 6 9999 NA
+## X13474 X13474 0839-1 Control Infant 6 111 6
+## X13530 X13530 1049-1 Control Infant 4 73 10
+## X14194 X14194 1040-1 Control Infant 5 87 9
+## X14385 X14385 0987-0 HIV Mother 0 9999 NA
+## X14387 X14387 0987-1 HIV Infant 6 104 9
+## X14502 X14502 1049-1 Control Infant 5 87 10
+## X14800 X14800 1095-1 HIV Infant 5 87 10
+## X15367 X15367 1040-0 Control Mother 6 9999 NA
+## X15368 X15368 1040-1 Control Infant 6 103 9
+## X15601 X15601 1049-1 Control Infant 6 104 10
+## X15925 X15925 1095-1 HIV Infant 6 103 10
+## X15926 X15926 1095-0 HIV Mother 6 9999 NA
+alluvial_df <- get_long_data(dat_0.05, "genus")## Registered S3 method overwritten by 'httr':
+## method from
+## print.response rmutil
+group_vars <- c("HIVStatus", "MothChild")
+get_summary_table(dat_0.05, group_vars)## HIVStatus MothChild mean_reads sd_reads min_reads max_reads num_total
+## 1 Control Infant 156209.16 408000.52 24176 3016276 68
+## 2 Control Mother 68648.79 50526.74 14339 168157 19
+## 3 HIV Infant 90008.20 51395.08 13218 202079 61
+## 4 HIV Mother 72277.53 48180.28 20118 208029 19
+best_genus <- get_top_taxa(dat_0.05, "genus")
+best_species <- get_top_taxa(dat_0.05, "species")
+this_palette <- paletteer::palettes_d[["ggsci"]]["category20_d3"] |>
+ unlist() |> unname()
+
+plot_stacked_area(dat_0.05, "genus",
+ "HIVStatus",
+ "timepoint",
+ palette_input = this_palette)
+plot_stacked_bar(dat_0.05, "genus",
+ "HIVStatus",
+ "timepoint",
+ palette_input = this_palette)
+plot_alluvial(dat = dat_0.05,
+ taxon_level = "genus",
+ covariate_1 = "HIVStatus",
+ covariate_time = "timepoint",
+ palette_input = this_palette,
+ subtitle = "Alluvial plot")
+plot_spaghetti(dat = dat_0.05,
+ covariate_time = "timepoint",
+ covariate_1 = "HIVStatus",
+ unit_var = "Subject",
+ taxon_level = "genus",
+ which_taxon = "Corynebacterium",
+ palette_input= this_palette,
+ title = "Spaghetti Plot",
+ subtitle = NULL) +
+ ggplot2::xlab("Infant Age (Days)") +
+ ggplot2::ylab("Relative Abundance (log CPM)")
+
+
+
+GEE Modeling +
+
+run_gee_model(dat, unit_var = "Subject",
+ fixed_cov = c("HIVStatus", "MothChild", "Age"),
+ corstr = "ar1",
+ plot_out = FALSE,
+ plotsave_loc = ".",
+ plot_terms = NULL)## Coefficient Coefficient Estimate Standard Error Statistic
+## 1 (Intercept) 4.702448e+04 3.979432e+04 1.396387e+00
+## 2 (Intercept) 2.070172e+03 3.238258e+03 4.086862e-01
+## 3 (Intercept) 9.530864e+03 5.106186e+03 3.483945e+00
+## 4 (Intercept) 6.120925e+04 2.592733e+04 5.573378e+00
+## 5 (Intercept) 4.741639e+04 2.051563e+04 5.341797e+00
+## 6 (Intercept) -7.011414e+02 1.529727e+03 2.100794e-01
+## 7 (Intercept) 1.134651e+03 5.499470e+02 4.256798e+00
+## 8 (Intercept) 2.076618e+03 1.219839e+03 2.898065e+00
+## 9 (Intercept) 2.054780e+03 9.842547e+02 4.358285e+00
+## 10 (Intercept) 4.195871e+03 3.007082e+03 1.946945e+00
+## 11 (Intercept) 5.014573e+02 2.760020e+02 3.300985e+00
+## 12 (Intercept) 2.959834e+02 1.259813e+02 5.519786e+00
+## 13 (Intercept) 1.281196e+02 1.274034e+02 1.011273e+00
+## 14 (Intercept) -9.488892e+02 9.262133e+02 1.049564e+00
+## 15 (Intercept) 7.089552e+02 3.755248e+02 3.564185e+00
+## 16 (Intercept) 1.526145e+02 5.257275e+01 8.426950e+00
+## 17 (Intercept) 2.063306e+02 1.062556e+02 3.770717e+00
+## 18 (Intercept) 8.101896e+01 7.929888e+01 1.043853e+00
+## 19 (Intercept) 9.430793e+01 5.240601e+01 3.238428e+00
+## 20 (Intercept) 6.308457e+02 4.130694e+02 2.332385e+00
+## 21 (Intercept) 9.930723e+01 4.060469e+01 5.981489e+00
+## 22 (Intercept) 1.053014e+03 1.026625e+03 1.052069e+00
+## 23 (Intercept) 5.994022e+01 5.712665e+01 1.100929e+00
+## 24 (Intercept) 4.534493e+01 1.834481e+01 6.109856e+00
+## 25 (Intercept) 1.062805e+01 3.764940e+01 7.968771e-02
+## 26 (Intercept) 6.342971e+01 4.223319e+01 2.255682e+00
+## 27 (Intercept) 5.549567e+01 3.041488e+01 3.329246e+00
+## 28 (Intercept) -2.081198e+01 2.518016e+01 6.831396e-01
+## 29 (Intercept) -3.351121e+00 1.594618e+01 4.416383e-02
+## 30 (Intercept) 6.842275e+01 3.907756e+01 3.065816e+00
+## 31 (Intercept) -8.542355e+00 4.939945e+01 2.990274e-02
+## 32 (Intercept) 9.639983e+01 4.651837e+01 4.294410e+00
+## 33 (Intercept) 7.738408e+01 4.553870e+01 2.887633e+00
+## 34 (Intercept) 2.303199e+01 1.765742e+01 1.701407e+00
+## 35 (Intercept) 4.166442e+01 2.137829e+01 3.798261e+00
+## 36 (Intercept) 3.552748e+02 3.130368e+02 1.288065e+00
+## 37 (Intercept) -1.512589e+00 1.912379e+01 6.255965e-03
+## 38 (Intercept) -2.227466e+00 2.902759e+01 5.888438e-03
+## 39 (Intercept) 5.701181e+01 4.849190e+01 1.382264e+00
+## 40 (Intercept) 5.348917e+01 4.274545e+01 1.565856e+00
+## 41 (Intercept) 9.075834e+01 5.902282e+01 2.364467e+00
+## 42 (Intercept) 4.329713e+01 2.060413e+01 4.415801e+00
+## 43 (Intercept) 3.358584e+01 3.241233e+01 1.073722e+00
+## 44 (Intercept) -1.286103e+00 8.452930e+00 2.314924e-02
+## 45 (Intercept) 6.159703e+01 3.617142e+01 2.899937e+00
+## 46 (Intercept) 7.605558e+00 3.006248e+01 6.400479e-02
+## 47 (Intercept) 6.443894e+01 3.079589e+01 4.378357e+00
+## 48 (Intercept) 1.277925e+01 2.037126e+01 3.935277e-01
+## 49 (Intercept) 1.425788e+01 9.919692e+00 2.065921e+00
+## 50 (Intercept) 4.074046e+01 2.753721e+01 2.188830e+00
+## 51 (Intercept) 2.272532e+01 1.558961e+01 2.124955e+00
+## 52 (Intercept) 6.454419e+00 1.348331e+01 2.291508e-01
+## 53 (Intercept) 7.543769e+00 7.934460e+00 9.039449e-01
+## 54 (Intercept) 1.985378e+01 1.624549e+01 1.493553e+00
+## 55 (Intercept) 5.863766e+01 3.339047e+01 3.083956e+00
+## 56 (Intercept) 3.604530e+01 1.767795e+01 4.157511e+00
+## 57 (Intercept) -4.052184e-01 1.122229e+01 1.303812e-03
+## 58 (Intercept) 8.018781e+00 8.656160e+00 8.581557e-01
+## 59 (Intercept) 1.676624e+01 1.050890e+01 2.545407e+00
+## 60 (Intercept) 1.023403e+01 8.501561e+00 1.449092e+00
+## 61 (Intercept) 8.486455e+01 6.536480e+01 1.685640e+00
+## 62 (Intercept) 8.308952e+01 5.277141e+01 2.479106e+00
+## 63 (Intercept) 6.770671e+01 3.371497e+01 4.032905e+00
+## 64 (Intercept) 1.539512e+01 2.920865e+01 2.778071e-01
+## 65 (Intercept) 1.539590e+01 8.506559e+00 3.275686e+00
+## 66 (Intercept) -4.472032e+00 4.812331e+00 8.635724e-01
+## 67 (Intercept) 1.852459e+01 1.255395e+01 2.177391e+00
+## 68 (Intercept) 1.504187e+01 6.047327e+00 6.186955e+00
+## 69 (Intercept) 9.284554e+00 1.077920e+01 7.419067e-01
+## 70 (Intercept) 1.438389e+01 9.335799e+00 2.373829e+00
+## 71 (Intercept) -7.131572e+00 5.477546e+00 1.695112e+00
+## 72 (Intercept) 1.023608e+02 8.244052e+01 1.541652e+00
+## 73 (Intercept) -1.232703e+01 1.318638e+01 8.739074e-01
+## 74 (Intercept) 2.971374e+01 1.778998e+01 2.789739e+00
+## 75 (Intercept) -1.628307e+00 7.822308e+00 4.333142e-02
+## 76 (Intercept) 6.629574e+00 8.935556e+00 5.504630e-01
+## 77 (Intercept) 1.543420e+01 8.814437e+00 3.066047e+00
+## 78 (Intercept) 2.365216e+01 1.032264e+01 5.250007e+00
+## 79 (Intercept) -5.121470e-01 2.874809e+00 3.173740e-02
+## 80 (Intercept) 5.382371e-01 3.252847e+00 2.737916e-02
+## 81 (Intercept) 1.224725e+01 7.297333e+00 2.816754e+00
+## 82 (Intercept) 2.886423e+01 1.872218e+01 2.376878e+00
+## 83 (Intercept) 9.190484e+00 4.445900e+00 4.273242e+00
+## 84 (Intercept) 9.492862e+00 7.003668e+00 1.837144e+00
+## 85 (Intercept) 3.614868e+01 2.886017e+01 1.568871e+00
+## 86 (Intercept) -3.539824e+00 7.982123e+00 1.966647e-01
+## 87 (Intercept) 9.446837e+00 6.479941e+00 2.125352e+00
+## 88 (Intercept) -5.655511e+00 1.013204e+01 3.115662e-01
+## 89 (Intercept) -1.189325e-01 3.201013e+00 1.380468e-03
+## 90 (Intercept) 2.125350e+00 2.343013e+00 8.228329e-01
+## 91 (Intercept) -3.670697e-02 1.549623e+00 5.611060e-04
+## 92 (Intercept) 4.817714e+00 1.042632e+01 2.135109e-01
+## 93 (Intercept) -4.471902e+01 4.523907e+01 9.771408e-01
+## 94 (Intercept) 5.085840e+00 5.860439e+00 7.531215e-01
+## 95 (Intercept) 1.945372e+01 1.790447e+01 1.180544e+00
+## 96 (Intercept) 1.380070e+01 6.031061e+00 5.236182e+00
+## 97 (Intercept) 2.183605e+01 1.151965e+01 3.593099e+00
+## 98 (Intercept) 8.216747e+00 5.234313e+00 2.464225e+00
+## 99 (Intercept) -1.641367e+01 1.951238e+01 7.076054e-01
+## 100 (Intercept) -7.042350e+00 5.512644e+00 1.631982e+00
+## 101 (Intercept) 6.830413e+00 6.638050e+00 1.058797e+00
+## 102 (Intercept) 1.195322e+01 1.020503e+01 1.371960e+00
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+## 1395 HIVStatusHIV 5.593879e+00 5.257848e+00 1.131905e+00
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+## 1641 HIVStatusHIV 3.547330e-01 2.685569e-01 1.744739e+00
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+## 1643 HIVStatusHIV -4.457351e-01 4.247800e-01 1.101097e+00
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+## 1648 HIVStatusHIV -3.697707e-01 2.760344e-01 1.794481e+00
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+## 1895 HIVStatusHIV -6.337990e-02 6.028787e-02 1.105206e+00
+## 1896 HIVStatusHIV 2.621310e-02 2.463630e-02 1.132103e+00
+## 1897 HIVStatusHIV 2.621310e-02 2.463630e-02 1.132103e+00
+## 1898 HIVStatusHIV 2.356800e-02 2.560989e-02 8.468962e-01
+## 1899 HIVStatusHIV 1.189083e-02 1.162946e-02 1.045455e+00
+## 1900 HIVStatusHIV 2.568400e-02 2.416381e-02 1.129781e+00
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+## 1903 HIVStatusHIV -4.183634e-02 3.959740e-02 1.116283e+00
+## 1904 HIVStatusHIV -1.821186e-02 3.231834e-02 3.175489e-01
+## 1905 HIVStatusHIV 3.567249e-02 3.488838e-02 1.045455e+00
+## 1906 HIVStatusHIV -2.402212e-02 2.285310e-02 1.104924e+00
+## 1907 HIVStatusHIV 1.345738e-02 1.261722e-02 1.137612e+00
+## 1908 HIVStatusHIV 1.345738e-02 1.261722e-02 1.137612e+00
+## 1909 HIVStatusHIV -4.213989e-02 3.993121e-02 1.113684e+00
+## 1910 HIVStatusHIV 2.378166e-02 2.325892e-02 1.045455e+00
+## 1911 HIVStatusHIV -1.030536e-01 9.916696e-02 1.079922e+00
+## 1912 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1913 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1914 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1915 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1916 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1917 HIVStatusHIV -1.169607e-02 1.107591e-02 1.115117e+00
+## 1918 HIVStatusHIV -1.207921e-02 1.148593e-02 1.105974e+00
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+## 1920 HIVStatusHIV -1.189083e-02 1.162946e-02 1.045455e+00
+## 1921 HIVStatusHIV -1.189083e-02 1.162946e-02 1.045455e+00
+## 1922 HIVStatusHIV -1.165674e-02 1.107147e-02 1.108521e+00
+## 1923 HIVStatusHIV -1.208225e-02 1.153177e-02 1.097750e+00
+## 1924 HIVStatusHIV -3.168995e-02 3.014393e-02 1.105206e+00
+## 1925 HIVStatusHIV 1.336531e-02 1.262769e-02 1.120238e+00
+## 1926 HIVStatusHIV 1.310655e-02 1.231815e-02 1.132103e+00
+## 1927 HIVStatusHIV 3.946604e-02 3.705050e-02 1.134642e+00
+## 1928 HIVStatusHIV -1.209442e-02 1.151014e-02 1.104100e+00
+## 1929 HIVStatusHIV -5.725201e-02 5.509276e-02 1.079922e+00
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+## 1932 HIVStatusHIV 1.189083e-02 1.162946e-02 1.045455e+00
+## 1933 HIVStatusHIV -1.102694e-02 1.045101e-02 1.113253e+00
+## 1934 HIVStatusHIV -2.284845e-02 2.168049e-02 1.110645e+00
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+## 1937 HIVStatusHIV -2.338807e-02 2.217847e-02 1.112053e+00
+## 1938 HIVStatusHIV 1.337917e-02 1.260365e-02 1.126849e+00
+## 1939 HIVStatusHIV 1.242471e-02 1.221920e-02 1.033921e+00
+## 1940 HIVStatusHIV -3.027605e-01 2.875803e-01 1.108358e+00
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+## 1943 MothChildMother -1.884367e+06 4.657222e+05 1.637107e+01
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+## 1945 MothChildMother 6.081656e+06 2.170732e+06 7.849302e+00
+## 1946 MothChildMother 3.537821e+06 1.691472e+06 4.374637e+00
+## 1947 MothChildMother -1.417844e+06 3.856761e+05 1.351485e+01
+## 1948 MothChildMother -1.127497e+05 1.295451e+05 7.575109e-01
+## 1949 MothChildMother 9.338708e+04 8.614884e+04 1.175100e+00
+## 1950 MothChildMother 6.371588e+04 9.196123e+04 4.800493e-01
+## 1951 MothChildMother 6.269315e+05 4.837589e+05 1.679508e+00
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+## 1953 MothChildMother -1.486818e+04 2.183899e+04 4.635005e-01
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+## 1955 MothChildMother -1.861381e+05 1.811074e+05 1.056325e+00
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+## 1959 MothChildMother 9.684195e+03 9.569952e+03 1.024018e+00
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+## 1979 MothChildMother -1.295684e+03 2.246386e+03 3.326822e-01
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+## 1981 MothChildMother 1.138283e+03 2.897735e+03 1.543060e-01
+## 1982 MothChildMother 4.931563e+03 5.004530e+03 9.710520e-01
+## 1983 MothChildMother 1.335885e+03 1.602256e+03 6.951439e-01
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+## 1986 MothChildMother -1.104230e+03 9.909517e+02 1.241693e+00
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+## 1989 MothChildMother 4.173224e+02 1.384304e+03 9.088255e-02
+## 1990 MothChildMother 2.532507e+02 5.554646e+02 2.078684e-01
+## 1991 MothChildMother -4.402697e+03 5.034859e+03 7.646504e-01
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+## 1997 MothChildMother -2.403196e+03 4.538350e+03 2.804027e-01
+## 1998 MothChildMother 3.828057e+02 3.330689e+02 1.320957e+00
+## 1999 MothChildMother 6.024198e+02 6.093111e+02 9.775079e-01
+## 2000 MothChildMother -1.413500e+03 2.573279e+03 3.017295e-01
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+## 2014 MothChildMother 3.412602e+01 2.762009e+02 1.526585e-02
+## 2015 MothChildMother 2.418606e+03 1.584301e+03 2.330531e+00
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+## 2395 MothChildMother 6.187947e-01 7.044411e-01 7.716205e-01
+## 2396 MothChildMother 1.515521e+01 1.731745e+01 7.658721e-01
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+## 2398 MothChildMother 3.092522e+01 2.077281e+01 2.216333e+00
+## 2399 MothChildMother 9.182390e+00 9.276553e+00 9.798016e-01
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+## 2401 MothChildMother -8.870352e+01 8.655968e+01 1.050148e+00
+## 2402 MothChildMother 1.778712e+01 1.786881e+01 9.908784e-01
+## 2403 MothChildMother 2.205385e+01 1.598004e+01 1.904641e+00
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+## 2406 MothChildMother -1.946447e+00 8.571571e+00 5.156610e-02
+## 2407 MothChildMother -4.050186e+01 3.912140e+01 1.071818e+00
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+## 2409 MothChildMother 2.578309e+00 2.935171e+00 7.716198e-01
+## 2410 MothChildMother -9.584091e-01 1.537746e+00 3.884479e-01
+## 2411 MothChildMother -2.396468e+01 2.321446e+01 1.065679e+00
+## 2412 MothChildMother 1.705361e+01 1.658838e+01 1.056878e+00
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+## 2414 MothChildMother -8.065938e+01 7.719471e+01 1.091779e+00
+## 2415 MothChildMother 2.333080e+02 2.515326e+02 8.603408e-01
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+## 2417 MothChildMother -3.019579e+01 2.962291e+01 1.039052e+00
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+## 2420 MothChildMother -4.575298e+00 3.965413e+00 1.331257e+00
+## 2421 MothChildMother -2.344903e+00 2.532814e+00 8.571236e-01
+## 2422 MothChildMother -1.242426e+01 1.202781e+01 1.067008e+00
+## 2423 MothChildMother 1.959515e+00 2.230730e+00 7.716198e-01
+## 2424 MothChildMother -2.054116e+01 1.989811e+01 1.065679e+00
+## 2425 MothChildMother -2.054116e+01 1.989811e+01 1.065679e+00
+## 2426 MothChildMother -6.030223e-01 5.774953e-01 1.090360e+00
+## 2427 MothChildMother 1.745706e+01 1.699559e+01 1.055042e+00
+## 2428 MothChildMother 2.006330e+01 1.962119e+01 1.045572e+00
+## 2429 MothChildMother -5.516068e+00 5.207207e+00 1.122146e+00
+## 2430 MothChildMother -2.388107e+01 1.529992e+01 2.436292e+00
+## 2431 MothChildMother -5.233389e+01 5.065105e+01 1.067552e+00
+## 2432 MothChildMother -7.061962e-01 1.133076e+00 3.884478e-01
+## 2433 MothChildMother -1.583791e+01 1.540254e+01 1.057331e+00
+## 2434 MothChildMother -2.601910e+01 2.509101e+01 1.075346e+00
+## 2435 MothChildMother -6.764257e+00 1.012250e+01 4.465441e-01
+## 2436 MothChildMother -2.592403e+01 2.845140e+01 8.302285e-01
+## 2437 MothChildMother -1.611274e+01 1.906961e+01 7.139287e-01
+## 2438 MothChildMother 7.162556e+01 6.970143e+01 1.055973e+00
+## 2439 MothChildMother 7.030701e+01 6.677526e+01 1.108577e+00
+## 2440 MothChildMother -3.673578e+00 7.788607e+00 2.224636e-01
+## 2441 MothChildMother -2.312401e-02 1.637713e-01 1.993660e-02
+## 2442 MothChildMother 3.018963e+01 3.484129e+01 7.508048e-01
+## 2443 MothChildMother -1.711763e+01 1.658176e+01 1.065679e+00
+## 2444 MothChildMother -4.423019e+00 7.332170e+00 3.638920e-01
+## 2445 MothChildMother -3.091210e+00 3.010407e+00 1.054402e+00
+## 2446 MothChildMother -2.025931e+01 1.983023e+01 1.043743e+00
+## 2447 MothChildMother -1.184378e+01 6.382823e+00 3.443142e+00
+## 2448 MothChildMother 3.093973e-01 3.522206e-01 7.716205e-01
+## 2449 MothChildMother -3.867435e+01 3.817052e+01 1.026573e+00
+## 2450 MothChildMother -4.522667e-01 4.331215e-01 1.090360e+00
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+## 2452 MothChildMother -1.031264e+01 1.026840e+01 1.008636e+00
+## 2453 MothChildMother -1.348572e+01 1.393544e+01 9.364988e-01
+## 2454 MothChildMother 7.684812e+01 7.499708e+01 1.049972e+00
+## 2455 MothChildMother 3.642614e+01 3.819086e+01 9.097194e-01
+## 2456 MothChildMother 1.246933e+01 1.213971e+01 1.055042e+00
+## 2457 MothChildMother -2.146895e+01 2.077926e+01 1.067484e+00
+## 2458 MothChildMother -3.026560e-01 4.856042e-01 3.884487e-01
+## 2459 MothChildMother -1.610790e+01 1.373024e+01 1.376327e+00
+## 2460 MothChildMother -8.282840e+00 8.018542e+00 1.067008e+00
+## 2461 MothChildMother 3.428040e+00 3.363097e+00 1.038993e+00
+## 2462 MothChildMother 2.078633e+01 2.021498e+01 1.057326e+00
+## 2463 MothChildMother -1.734683e-02 1.228275e-01 1.994568e-02
+## 2464 MothChildMother -3.782721e+01 3.676204e+01 1.058789e+00
+## 2465 MothChildMother 7.710625e+00 7.486883e+00 1.060662e+00
+## 2466 MothChildMother 1.201754e+01 1.782258e+01 4.546634e-01
+## 2467 MothChildMother 1.490127e+01 1.472053e+01 1.024706e+00
+## 2468 MothChildMother -3.485830e+00 3.265643e+00 1.139397e+00
+## 2469 MothChildMother -3.459409e+01 3.100874e+01 1.244617e+00
+## 2470 MothChildMother -1.091816e+01 1.313400e+01 6.910426e-01
+## 2471 MothChildMother 1.443853e+00 1.643695e+00 7.716198e-01
+## 2472 MothChildMother -1.825546e+01 1.754948e+01 1.082074e+00
+## 2473 MothChildMother -3.761063e+01 4.030493e+01 8.707730e-01
+## 2474 MothChildMother 1.221772e+01 9.727349e+00 1.577580e+00
+## 2475 MothChildMother 2.275863e+00 2.183110e+00 1.086779e+00
+## 2476 MothChildMother 4.022602e+00 3.874036e+00 1.078169e+00
+## 2477 MothChildMother 4.022602e+00 3.874036e+00 1.078169e+00
+## 2478 MothChildMother 5.116405e+01 4.980409e+01 1.055358e+00
+## 2479 MothChildMother -2.208007e+00 2.150291e+00 1.054402e+00
+## 2480 MothChildMother 8.592163e+00 7.364933e+00 1.361029e+00
+## 2481 MothChildMother 5.606614e+00 6.896507e+00 6.609110e-01
+## 2482 MothChildMother -6.902367e+00 6.682118e+00 1.067008e+00
+## 2483 MothChildMother 4.125298e-01 4.696274e-01 7.716205e-01
+## 2484 MothChildMother -9.595311e-01 4.514420e+00 4.517667e-02
+## 2485 MothChildMother -1.612065e+01 1.577634e+01 1.044125e+00
+## 2486 MothChildMother 1.712076e+01 1.685074e+01 1.032305e+00
+## 2487 MothChildMother -1.490519e-01 2.190134e-01 4.631627e-01
+## 2488 MothChildMother 1.727336e+00 1.692349e+00 1.041775e+00
+## 2489 MothChildMother 1.727336e+00 1.692349e+00 1.041775e+00
+## 2490 MothChildMother 2.044163e+01 1.899670e+01 1.157910e+00
+## 2491 MothChildMother -3.015111e-01 2.887476e-01 1.090360e+00
+## 2492 MothChildMother -1.342035e+01 1.316574e+01 1.039052e+00
+## 2493 MothChildMother -5.037742e+00 6.841743e+00 5.421736e-01
+## 2494 MothChildMother 3.361795e+00 3.373830e+00 9.928781e-01
+## 2495 MothChildMother -1.916923e+01 1.832405e+01 1.094376e+00
+## 2496 MothChildMother 2.750241e+01 2.675220e+01 1.056872e+00
+## 2497 MothChildMother 2.750241e+01 2.675220e+01 1.056872e+00
+## 2498 MothChildMother 1.031324e+00 1.174069e+00 7.716205e-01
+## 2499 MothChildMother 1.994942e+01 1.946861e+01 1.050003e+00
+## 2500 MothChildMother -1.509908e+01 1.469179e+01 1.056213e+00
+## 2501 MothChildMother -7.251138e+00 7.020677e+00 1.066730e+00
+## 2502 MothChildMother -7.251138e+00 7.020677e+00 1.066730e+00
+## 2503 MothChildMother -1.156455e-02 8.188500e-02 1.994568e-02
+## 2504 MothChildMother -1.156455e-02 8.188500e-02 1.994568e-02
+## 2505 MothChildMother 5.140417e+00 4.991256e+00 1.060662e+00
+## 2506 MothChildMother 5.140417e+00 4.991256e+00 1.060662e+00
+## 2507 MothChildMother 3.410741e+01 3.319116e+01 1.055973e+00
+## 2508 MothChildMother 7.481596e+00 7.283823e+00 1.055042e+00
+## 2509 MothChildMother -3.035948e+00 2.904883e+00 1.092273e+00
+## 2510 MothChildMother -1.115104e+01 1.075329e+01 1.075346e+00
+## 2511 MothChildMother -3.828847e+00 1.152952e+01 1.102843e-01
+## 2512 MothChildMother -1.006526e+01 9.874304e+00 1.039052e+00
+## 2513 MothChildMother -1.006526e+01 9.874304e+00 1.039052e+00
+## 2514 MothChildMother 7.155065e+00 6.469721e+00 1.223083e+00
+## 2515 MothChildMother 7.155065e+00 6.469721e+00 1.223083e+00
+## 2516 MothChildMother -2.407390e+01 2.339571e+01 1.058816e+00
+## 2517 MothChildMother -1.746173e+00 3.103344e+00 3.166027e-01
+## 2518 MothChildMother -2.656455e+00 2.541773e+00 1.092273e+00
+## 2519 MothChildMother -4.215892e+00 4.424623e+00 9.078755e-01
+## 2520 MothChildMother -6.847052e+00 6.632703e+00 1.065679e+00
+## 2521 MothChildMother -7.558712e+00 6.503102e+00 1.350997e+00
+## 2522 MothChildMother -3.194879e+00 2.921192e+00 1.196158e+00
+## 2523 MothChildMother 7.219271e-01 8.218480e-01 7.716205e-01
+## 2524 MothChildMother -5.044267e-02 8.093404e-02 3.884487e-01
+## 2525 MothChildMother -2.397291e+01 2.331871e+01 1.056897e+00
+## 2526 MothChildMother 2.548703e+01 2.494557e+01 1.043883e+00
+## 2527 MothChildMother -1.719419e+01 1.671002e+01 1.058789e+00
+## 2528 MothChildMother -9.378862e+00 1.090928e+01 7.391082e-01
+## 2529 MothChildMother 2.011301e+00 1.937018e+00 1.078169e+00
+## 2530 MothChildMother -3.177036e+00 3.037921e+00 1.093683e+00
+## 2531 MothChildMother 1.460888e+01 1.420163e+01 1.058175e+00
+## 2532 MothChildMother 4.987731e+00 4.855882e+00 1.055042e+00
+## 2533 MothChildMother -3.026560e-01 4.856042e-01 3.884486e-01
+## 2534 MothChildMother 3.093973e-01 3.522206e-01 7.716205e-01
+## 2535 MothChildMother 6.187947e-01 7.044411e-01 7.716205e-01
+## 2536 MothChildMother 1.616251e+01 1.109990e+01 2.120213e+00
+## 2537 MothChildMother -2.333257e+00 2.274144e+00 1.052662e+00
+## 2538 MothChildMother 6.960422e+00 6.740913e+00 1.066188e+00
+## 2539 MothChildMother 8.636719e-01 8.461742e-01 1.041785e+00
+## 2540 MothChildMother 8.636719e-01 8.461742e-01 1.041785e+00
+## 2541 MothChildMother 8.636719e-01 8.461742e-01 1.041785e+00
+## 2542 MothChildMother -2.054821e+01 1.998746e+01 1.056897e+00
+## 2543 MothChildMother -2.628670e+00 2.537286e+00 1.073330e+00
+## 2544 MothChildMother -2.628670e+00 2.537286e+00 1.073330e+00
+## 2545 MothChildMother -1.804175e+00 5.576677e+00 1.046662e-01
+## 2546 MothChildMother -5.044267e-02 8.093404e-02 3.884487e-01
+## 2547 MothChildMother -4.676951e-01 4.993972e-01 8.770683e-01
+## 2548 MothChildMother -6.709657e+00 6.535406e+00 1.054036e+00
+## 2549 MothChildMother -5.782276e-03 4.094250e-02 1.994568e-02
+## 2550 MothChildMother -1.536369e+01 1.470376e+01 1.091779e+00
+## 2551 MothChildMother -1.265216e+01 1.008604e+01 1.573577e+00
+## 2552 MothChildMother -1.513280e-01 2.428021e-01 3.884486e-01
+## 2553 MothChildMother 4.434506e+00 4.349372e+00 1.039531e+00
+## 2554 MothChildMother -2.552323e+00 2.462376e+00 1.074392e+00
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+## 2556 MothChildMother -1.425857e+01 1.382515e+01 1.063683e+00
+## 2557 MothChildMother -1.008853e-01 1.618681e-01 3.884487e-01
+## 2558 MothChildMother -2.594128e-01 5.330842e-01 2.368052e-01
+## 2559 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2560 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2561 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2562 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2563 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2564 MothChildMother 1.005655e+00 9.685087e-01 1.078180e+00
+## 2565 MothChildMother 2.493865e+00 2.427941e+00 1.055042e+00
+## 2566 MothChildMother 2.493865e+00 2.427941e+00 1.055042e+00
+## 2567 MothChildMother 1.031324e-01 1.174069e-01 7.716205e-01
+## 2568 MothChildMother 1.031324e-01 1.174069e-01 7.716205e-01
+## 2569 MothChildMother 8.554035e-01 8.451423e-01 1.024430e+00
+## 2570 MothChildMother 3.480212e+00 3.370456e+00 1.066188e+00
+## 2571 MothChildMother -1.027411e+01 9.993731e+00 1.056897e+00
+## 2572 MothChildMother -3.369349e+00 3.279866e+00 1.055309e+00
+## 2573 MothChildMother -1.314335e+00 1.268643e+00 1.073330e+00
+## 2574 MothChildMother -4.561624e+00 4.386462e+00 1.081460e+00
+## 2575 MothChildMother 3.481373e+00 3.396171e+00 1.050805e+00
+## 2576 MothChildMother -1.441182e-01 2.961579e-01 2.368052e-01
+## 2577 MothChildMother -7.129283e+00 6.912573e+00 1.063683e+00
+## 2578 MothChildMother 6.821482e+00 6.638232e+00 1.055973e+00
+## 2579 MothChildMother -5.044267e-02 8.093404e-02 3.884487e-01
+## 2580 MothChildMother -2.315068e+00 2.252116e+00 1.056686e+00
+## 2581 MothChildMother -2.933509e-01 2.932920e-01 1.000402e+00
+## 2582 MothChildMother 2.150318e-01 2.506225e-01 7.361479e-01
+## 2583 MothChildMother 2.150318e-01 2.506225e-01 7.361479e-01
+## 2584 MothChildMother 2.004335e+00 1.945544e+00 1.061350e+00
+## 2585 MothChildMother -3.438837e+00 3.342004e+00 1.058789e+00
+## 2586 MothChildMother 2.080698e+00 1.992931e+00 1.090018e+00
+## 2587 MothChildMother 2.063294e+01 2.036972e+01 1.026011e+00
+## 2588 MothChildMother -4.461865e-01 4.327966e-01 1.062833e+00
+## Unadj p-value Lower 95% CI Upper 95% CI
+## 1 2.373294e-01 -3.097095e+04 1.250199e+05
+## 2 5.226371e-01 -4.276698e+03 8.417042e+03
+## 3 6.196683e-02 -4.770759e+02 1.953880e+04
+## 4 1.823554e-02 1.039262e+04 1.120259e+05
+## 5 2.082000e-02 7.206499e+03 8.762628e+04
+## 6 6.467052e-01 -3.699351e+03 2.297068e+03
+## 7 3.909353e-02 5.677489e+01 2.212527e+03
+## 8 8.868597e-02 -3.142228e+02 4.467458e+03
+## 9 3.682936e-02 1.256762e+02 3.983884e+03
+## 10 1.629165e-01 -1.697902e+03 1.008964e+04
+## 11 6.923834e-02 -3.949660e+01 1.042411e+03
+## 12 1.880255e-02 4.906451e+01 5.429022e+02
+## 13 3.145980e-01 -1.215866e+02 3.778257e+02
+## 14 3.056075e-01 -2.764234e+03 8.664555e+02
+## 15 5.903872e-02 -2.705998e+01 1.444970e+03
+## 16 3.697000e-03 4.957384e+01 2.556552e+02
+## 17 5.215727e-02 -1.926472e+00 4.145877e+02
+## 18 3.069271e-01 -7.440399e+01 2.364419e+02
+## 19 7.192961e-02 -8.405956e+00 1.970218e+02
+## 20 1.267076e-01 -1.787554e+02 1.440447e+03
+## 21 1.445679e-02 1.972350e+01 1.788910e+02
+## 22 3.050310e-01 -9.591346e+02 3.065162e+03
+## 23 2.940624e-01 -5.202595e+01 1.719064e+02
+## 24 1.344301e-02 9.389761e+00 8.130010e+01
+## 25 7.777211e-01 -6.316341e+01 8.441952e+01
+## 26 1.331248e-01 -1.934581e+01 1.462052e+02
+## 27 6.805805e-02 -4.116401e+00 1.151077e+02
+## 28 4.085077e-01 -7.016419e+01 2.854024e+01
+## 29 8.335491e-01 -3.460506e+01 2.790282e+01
+## 30 7.995502e-02 -8.167871e+00 1.450134e+02
+## 31 8.627111e-01 -1.053635e+02 8.827879e+01
+## 32 3.823786e-02 5.225495e+00 1.875742e+02
+## 33 8.926197e-02 -1.187013e+01 1.666383e+02
+## 34 1.921040e-01 -1.157592e+01 5.763989e+01
+## 35 5.130584e-02 -2.362562e-01 8.356509e+01
+## 36 2.564048e-01 -2.582661e+02 9.688157e+02
+## 37 9.369573e-01 -3.899453e+01 3.596935e+01
+## 38 9.388334e-01 -5.912050e+01 5.466557e+01
+## 39 2.397158e-01 -3.803058e+01 1.520542e+02
+## 40 2.108098e-01 -3.029038e+01 1.372687e+02
+## 41 1.241263e-01 -2.492426e+01 2.064409e+02
+## 42 3.560756e-02 2.913769e+00 8.368049e+01
+## 43 3.001062e-01 -2.994116e+01 9.711284e+01
+## 44 8.790696e-01 -1.785354e+01 1.528134e+01
+## 45 8.858301e-02 -9.297639e+00 1.324917e+02
+## 46 8.002746e-01 -5.131582e+01 6.652694e+01
+## 47 3.639807e-02 4.080098e+00 1.247978e+02
+## 48 5.304509e-01 -2.714767e+01 5.270618e+01
+## 49 1.506239e-01 -5.184358e+00 3.370012e+01
+## 50 1.390149e-01 -1.323147e+01 9.471239e+01
+## 51 1.449171e-01 -7.829748e+00 5.328039e+01
+## 52 6.321542e-01 -1.997238e+01 3.288122e+01
+## 53 3.417261e-01 -8.007487e+00 2.309502e+01
+## 54 2.216660e-01 -1.198680e+01 5.169435e+01
+## 55 7.906798e-02 -6.806458e+00 1.240818e+02
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+## 1712 3.065567e-01 -2.071476e-01 6.589987e-01
+## 1713 1.569752e-01 -2.544415e-01 1.576827e+00
+## 1714 2.887952e-01 -2.101802e-01 7.060732e-01
+## 1715 2.921657e-01 -4.335253e-01 1.304284e-01
+## 1716 3.065567e-01 -8.324194e-01 2.616601e-01
+## 1717 2.848625e-01 -2.309030e-01 6.787432e-02
+## 1718 4.641225e-01 -3.461398e-01 1.578807e-01
+## 1719 2.927620e-01 -3.348596e-01 1.009324e-01
+## 1720 2.927620e-01 -3.348596e-01 1.009324e-01
+## 1721 3.117907e-01 -4.740949e-01 1.513327e-01
+## 1722 3.003557e-01 -5.613362e-01 1.819291e+00
+## 1723 2.234529e-01 -1.447583e+00 3.383079e-01
+## 1724 3.065562e-01 -1.090249e-01 3.468415e-01
+## 1725 1.204518e-01 -4.992008e-01 5.784959e-02
+## 1726 6.794029e-01 -2.370689e-01 3.637596e-01
+## 1727 5.997718e-01 -1.353074e-01 2.342454e-01
+## 1728 2.993488e-01 -1.475269e+01 4.537982e+00
+## 1729 2.842625e-01 -2.528408e-01 8.618129e-01
+## 1730 6.009818e-01 -1.203240e-01 6.963584e-02
+## 1731 3.873530e-01 -2.464981e-01 6.354944e-01
+## 1732 2.861574e-01 -1.127190e-01 3.818667e-01
+## 1733 2.925519e-01 -2.101539e-01 6.330238e-02
+## 1734 1.446240e-01 -1.932774e-01 2.833385e-02
+## 1735 3.065562e-01 -2.427891e-01 7.631745e-02
+## 1736 6.851948e-01 -2.929849e-01 1.925586e-01
+## 1737 2.917678e-01 -4.480417e-01 1.346277e-01
+## 1738 2.939405e-01 -2.416552e+01 7.310710e+00
+## 1739 2.502564e-01 -7.634847e-01 1.989277e-01
+## 1740 3.065567e-01 -2.725626e-01 8.671035e-01
+## 1741 2.921657e-01 -3.334810e-01 1.003296e-01
+## 1742 3.065562e-01 -3.468415e-01 1.090249e-01
+## 1743 2.995323e-01 -1.100122e+00 3.385907e-01
+## 1744 5.326453e-01 -5.166788e-01 9.993071e-01
+## 1745 7.544418e-01 -3.726738e-01 5.142104e-01
+## 1746 2.884912e-01 -3.318440e-01 1.115864e+00
+## 1747 4.248311e-01 -2.251991e-01 5.345627e-01
+## 1748 3.065562e-01 -2.081049e-01 6.541496e-02
+## 1749 9.967193e-01 -3.292699e-01 3.306543e-01
+## 1750 2.920837e-01 -2.716647e-01 8.171079e-02
+## 1751 8.791881e-01 -1.299754e-01 1.518299e-01
+## 1752 2.885675e-01 -1.175205e-01 3.950806e-01
+## 1753 6.446628e-01 -5.552271e-01 3.437041e-01
+## 1754 3.014078e-01 -8.285626e-01 2.564658e-01
+## 1755 2.884247e-01 -2.242509e-01 7.542293e-01
+## 1756 6.485183e-01 -1.885626e-01 1.174049e-01
+## 1757 2.917691e-01 -1.965130e-01 5.904854e-02
+## 1758 2.840352e-01 -1.114660e-01 3.802136e-01
+## 1759 9.348337e-01 -6.392130e-02 6.948676e-02
+## 1760 2.872866e-01 -3.096391e-01 1.045202e+00
+## 1761 3.065562e-01 -3.121574e-01 9.812244e-02
+## 1762 3.065567e-01 -8.671035e-01 2.725626e-01
+## 1763 3.065567e-01 -2.071476e-01 6.589987e-01
+## 1764 2.920837e-01 -2.112948e-01 6.355283e-02
+## 1765 2.935775e-01 -1.729478e-01 5.226222e-02
+## 1766 3.065567e-01 -9.017877e-01 2.834651e-01
+## 1767 2.907203e-01 -6.270906e-01 1.878089e-01
+## 1768 2.912925e-01 -1.062622e+01 3.188210e+00
+## 1769 7.831644e-01 -4.308510e-01 5.716055e-01
+## 1770 3.046438e-01 -2.770176e-01 8.658285e-02
+## 1771 9.550404e-01 -6.973538e-02 7.386607e-02
+## 1772 2.949605e-01 -3.469346e-01 1.052897e-01
+## 1773 3.369840e-01 -1.749479e-01 5.109570e-01
+## 1774 2.882191e-01 -8.694090e-02 2.926021e-01
+## 1775 2.877085e-01 -9.961210e-02 3.357931e-01
+## 1776 3.065567e-01 -6.589987e-01 2.071476e-01
+## 1777 2.920837e-01 -1.811098e-01 5.447386e-02
+## 1778 2.920837e-01 -1.811098e-01 5.447386e-02
+## 1779 2.919483e-01 -1.306792e-01 3.928875e-02
+## 1780 2.929588e-01 -2.421385e-01 7.302955e-02
+## 1781 2.887952e-01 -9.458108e-02 3.177329e-01
+## 1782 2.918902e-01 -6.190374e-01 1.860800e-01
+## 1783 4.791781e-01 -1.760422e-01 8.264558e-02
+## 1784 2.868928e-01 -2.264331e-01 7.652989e-01
+## 1785 3.065567e-01 -1.526351e-01 4.855780e-01
+## 1786 2.920865e-01 -4.166878e-01 1.253317e-01
+## 1787 2.840352e-01 -7.802619e-02 2.661495e-01
+## 1788 7.941884e-01 -2.295459e-01 1.756177e-01
+## 1789 2.399980e-01 -7.970575e-02 3.183221e-01
+## 1790 4.976873e-01 -1.357421e-01 2.793667e-01
+## 1791 2.980489e-01 -7.307854e-01 2.239021e-01
+## 1792 2.892785e-01 -2.222475e-01 7.454683e-01
+## 1793 6.002577e-02 -6.362430e-03 3.079062e-01
+## 1794 2.917691e-01 -1.310087e-01 3.936569e-02
+## 1795 1.860402e-01 -9.857020e-02 5.074531e-01
+## 1796 2.920837e-01 -1.509248e-01 4.539488e-02
+## 1797 2.446079e-02 -1.266786e-01 -8.722009e-03
+## 1798 2.876021e-01 -7.606327e-02 2.564969e-01
+## 1799 2.995323e-01 -5.500608e-01 1.692953e-01
+## 1800 7.221131e-02 -1.354086e-02 3.137440e-01
+## 1801 3.065562e-01 -1.040525e-01 3.270748e-02
+## 1802 1.463944e-01 -4.728771e-01 7.033926e-02
+## 1803 2.919483e-01 -9.800937e-02 2.946656e-02
+## 1804 2.919483e-01 -9.800937e-02 2.946656e-02
+## 1805 2.878867e-01 -2.610259e-01 8.794206e-01
+## 1806 4.126004e-01 -5.864466e-02 1.428942e-01
+## 1807 2.941845e-01 -8.272366e-01 2.504509e-01
+## 1808 2.365712e-01 -1.104874e-01 4.473734e-01
+## 1809 2.929588e-01 -1.729560e-01 5.216397e-02
+## 1810 2.859496e-01 -6.732931e-02 2.282488e-01
+## 1811 3.065562e-01 -6.541496e-02 2.081049e-01
+## 1812 1.668416e-01 -2.159867e-01 3.732092e-02
+## 1813 2.877085e-01 -6.640807e-02 2.238621e-01
+## 1814 2.921657e-01 -1.333924e-01 4.013183e-02
+## 1815 2.873961e-01 -5.984973e-02 2.019551e-01
+## 1816 2.917780e-01 -9.825596e-02 2.952493e-02
+## 1817 2.884485e-01 -1.245588e-01 4.189005e-01
+## 1818 2.900406e-01 -1.035606e-01 3.094918e-02
+## 1819 1.393469e-01 -2.792066e-02 1.992720e-01
+## 1820 2.907285e-01 -7.420378e-02 2.477587e-01
+## 1821 4.903494e-01 -4.643560e-02 9.686677e-02
+## 1822 4.597195e-01 -2.506005e-01 1.133256e-01
+## 1823 3.522826e-01 -3.444861e-01 1.227449e-01
+## 1824 3.065567e-01 -4.855780e-01 1.526351e-01
+## 1825 3.244649e-01 -1.448021e-01 4.375811e-01
+## 1826 2.464139e-01 -3.736095e-01 9.592899e-02
+## 1827 1.699155e-01 -1.161319e-01 2.047335e-02
+## 1828 5.367122e-01 -5.019346e-02 2.613445e-02
+## 1829 2.909730e-01 -1.336178e-01 4.004938e-02
+## 1830 2.909730e-01 -1.336178e-01 4.004938e-02
+## 1831 2.925625e-01 -5.182650e-01 1.561166e-01
+## 1832 2.876021e-01 -5.433090e-02 1.832121e-01
+## 1833 1.700192e-01 -1.173057e-01 2.069407e-02
+## 1834 7.343808e-01 -6.951596e-02 9.862390e-02
+## 1835 2.877085e-01 -5.534006e-02 1.865517e-01
+## 1836 3.065562e-01 -1.387366e-01 4.360997e-02
+## 1837 2.948017e-01 -2.930305e-01 8.888683e-02
+## 1838 2.289438e-01 -2.340681e-01 5.600972e-02
+## 1839 2.898730e-01 -8.451258e-02 2.829414e-01
+## 1840 1.624140e-01 -1.424292e-02 8.493053e-02
+## 1841 2.922463e-01 -6.672515e-02 2.007969e-02
+## 1842 2.922463e-01 -6.672515e-02 2.007969e-02
+## 1843 2.340876e-01 -2.874210e-01 7.026788e-02
+## 1844 2.919483e-01 -6.533958e-02 1.964438e-02
+## 1845 3.046438e-01 -1.231189e-01 3.848126e-02
+## 1846 9.166660e-01 -6.175818e-02 6.872408e-02
+## 1847 6.514202e-01 -3.945568e-02 6.309446e-02
+## 1848 1.984263e-01 -1.604702e-01 3.331577e-02
+## 1849 2.981290e-01 -3.833718e-01 1.174883e-01
+## 1850 2.981290e-01 -3.833718e-01 1.174883e-01
+## 1851 3.065562e-01 -3.468415e-01 1.090249e-01
+## 1852 2.888427e-01 -6.037384e-02 2.027876e-01
+## 1853 2.880556e-01 -1.218824e-01 4.104123e-01
+## 1854 2.876010e-01 -3.395447e-02 1.145000e-01
+## 1855 2.876010e-01 -3.395447e-02 1.145000e-01
+## 1856 2.917780e-01 -6.550397e-02 1.968329e-02
+## 1857 2.917780e-01 -6.550397e-02 1.968329e-02
+## 1858 2.900406e-01 -6.904038e-02 2.063279e-02
+## 1859 2.900406e-01 -6.904038e-02 2.063279e-02
+## 1860 2.980489e-01 -3.479931e-01 1.066200e-01
+## 1861 2.929588e-01 -1.037736e-01 3.129838e-02
+## 1862 2.873620e-01 -8.675231e-02 2.927662e-01
+## 1863 2.840352e-01 -3.343979e-02 1.140641e-01
+## 1864 5.202235e-01 -1.159377e-01 2.291497e-01
+## 1865 3.046438e-01 -9.233919e-02 2.886095e-02
+## 1866 3.046438e-01 -9.233919e-02 2.886095e-02
+## 1867 3.144110e-01 -9.416647e-02 2.927763e-01
+## 1868 3.144110e-01 -9.416647e-02 2.927763e-01
+## 1869 2.881640e-01 -1.134089e-01 3.817477e-01
+## 1870 1.378016e-01 -1.637307e-02 1.184795e-01
+## 1871 2.873620e-01 -7.590827e-02 2.561704e-01
+## 1872 7.932529e-02 -1.215641e-01 6.720314e-03
+## 1873 2.920837e-01 -6.036994e-02 1.815795e-02
+## 1874 1.070372e-01 -1.129641e-02 1.158350e-01
+## 1875 5.810301e-01 -3.790070e-02 6.761012e-02
+## 1876 3.065562e-01 -2.427891e-01 7.631745e-02
+## 1877 3.065562e-01 -1.090249e-02 3.468415e-02
+## 1878 2.931264e-01 -2.117989e-01 6.391251e-02
+## 1879 2.903642e-01 -8.128550e-02 2.717157e-01
+## 1880 2.884485e-01 -5.661764e-02 1.904093e-01
+## 1881 6.960445e-01 -1.145017e-01 7.644223e-02
+## 1882 2.909730e-01 -6.680889e-02 2.002469e-02
+## 1883 2.860028e-01 -2.204826e-02 7.473160e-02
+## 1884 2.915169e-01 -2.069839e-01 6.214563e-02
+## 1885 2.929588e-01 -6.918242e-02 2.086559e-02
+## 1886 3.065562e-01 -6.541496e-02 2.081049e-01
+## 1887 3.065562e-01 -1.040525e-01 3.270748e-02
+## 1888 3.065562e-01 -2.081049e-01 6.541496e-02
+## 1889 1.194579e-01 -1.533008e-02 1.338164e-01
+## 1890 2.891739e-01 -1.137410e-02 3.816397e-02
+## 1891 2.947605e-01 -6.936820e-02 2.103922e-02
+## 1892 2.922456e-01 -3.336259e-02 1.003983e-02
+## 1893 2.922456e-01 -3.336259e-02 1.003983e-02
+## 1894 2.922456e-01 -3.336259e-02 1.003983e-02
+## 1895 2.931264e-01 -1.815419e-01 5.478215e-02
+## 1896 2.873273e-01 -2.207316e-02 7.449936e-02
+## 1897 2.873273e-01 -2.207316e-02 7.449936e-02
+## 1898 3.574319e-01 -2.662646e-02 7.376246e-02
+## 1899 3.065562e-01 -1.090249e-02 3.468415e-02
+## 1900 2.878221e-01 -2.167621e-02 7.304420e-02
+## 1901 2.914809e-01 -6.046161e-02 1.815117e-02
+## 1902 2.917780e-01 -3.275199e-02 9.841645e-03
+## 1903 2.907203e-01 -1.194458e-01 3.577313e-02
+## 1904 5.730844e-01 -8.155464e-02 4.513092e-02
+## 1905 3.065562e-01 -3.270748e-02 1.040525e-01
+## 1906 2.931880e-01 -6.881337e-02 2.076913e-02
+## 1907 2.861574e-01 -1.127190e-02 3.818667e-02
+## 1908 2.861574e-01 -1.127190e-02 3.818667e-02
+## 1909 2.912825e-01 -1.204036e-01 3.612384e-02
+## 1910 3.065562e-01 -2.180499e-02 6.936831e-02
+## 1911 2.987150e-01 -2.974173e-01 9.131006e-02
+## 1912 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1913 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1914 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1915 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1916 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1917 2.909722e-01 -3.340446e-02 1.001233e-02
+## 1918 2.929588e-01 -3.459121e-02 1.043279e-02
+## 1919 2.929588e-01 -3.459121e-02 1.043279e-02
+## 1920 3.065562e-01 -3.468415e-02 1.090249e-02
+## 1921 3.065562e-01 -3.468415e-02 1.090249e-02
+## 1922 2.924037e-01 -3.335641e-02 1.004294e-02
+## 1923 2.947604e-01 -3.468411e-02 1.051961e-02
+## 1924 2.931264e-01 -9.077097e-02 2.739108e-02
+## 1925 2.898672e-01 -1.138451e-02 3.811512e-02
+## 1926 2.873273e-01 -1.103658e-02 3.724968e-02
+## 1927 2.867873e-01 -3.315160e-02 1.120837e-01
+## 1928 2.933680e-01 -3.465389e-02 1.046505e-02
+## 1929 2.987150e-01 -1.652318e-01 5.072781e-02
+## 1930 2.912825e-01 -6.020181e-02 1.806192e-02
+## 1931 2.980489e-01 -6.959861e-02 2.132401e-02
+## 1932 3.065562e-01 -1.090249e-02 3.468415e-02
+## 1933 2.913759e-01 -3.151055e-02 9.456657e-03
+## 1934 2.919417e-01 -6.534143e-02 1.964453e-02
+## 1935 3.218275e-01 -7.431796e-02 2.441240e-02
+## 1936 3.218275e-01 -7.431796e-02 2.441240e-02
+## 1937 2.916360e-01 -6.685707e-02 2.008093e-02
+## 1938 2.884485e-01 -1.132353e-02 3.808186e-02
+## 1939 3.092395e-01 -1.152447e-02 3.637390e-02
+## 1940 2.924391e-01 -8.664076e-01 2.608866e-01
+## 1941 2.875464e-01 -1.086544e-02 3.664642e-02
+## 1942 9.765692e-01 -3.644586e+06 3.755477e+06
+## 1943 5.207389e-05 -2.797166e+06 -9.715685e+05
+## 1944 3.916445e-02 -2.341973e+06 -5.967330e+04
+## 1945 5.084033e-03 1.827098e+06 1.033621e+07
+## 1946 3.647760e-02 2.225966e+05 6.853046e+06
+## 1947 2.366835e-04 -2.173755e+06 -6.619322e+05
+## 1948 3.841086e-01 -3.666534e+05 1.411540e+05
+## 1949 2.783559e-01 -7.546155e+04 2.622357e+05
+## 1950 4.884000e-01 -1.165248e+05 2.439566e+05
+## 1951 1.949898e-01 -3.212186e+05 1.575082e+06
+## 1952 7.900100e-01 -5.642372e+04 4.292530e+04
+## 1953 4.959926e-01 -5.767182e+04 2.793546e+04
+## 1954 3.726929e-01 -2.645872e+03 7.060634e+03
+## 1955 3.040548e-01 -5.411021e+05 1.688260e+05
+## 1956 5.314263e-02 -1.157338e+03 1.719730e+05
+## 1957 9.236906e-01 -2.540801e+04 2.304028e+04
+## 1958 1.816588e-01 -4.272321e+03 2.255327e+04
+## 1959 3.115679e-01 -9.072567e+03 2.844096e+04
+## 1960 5.696093e-01 -6.968803e+03 3.834528e+03
+## 1961 1.551429e-01 -3.581412e+04 2.249543e+05
+## 1962 9.889712e-02 -8.523224e+02 9.934283e+03
+## 1963 3.082336e-01 -1.566118e+05 4.957668e+05
+## 1964 5.694521e-01 -5.835504e+03 1.060808e+04
+## 1965 3.781748e-02 1.596771e+02 5.515689e+03
+## 1966 2.889204e-01 -2.354882e+03 7.907780e+03
+## 1967 3.644554e-01 -1.037478e+03 2.824461e+03
+## 1968 4.722862e-01 -1.029845e+03 2.222588e+03
+## 1969 3.546039e-01 -5.032669e+03 1.803791e+03
+## 1970 8.926165e-01 -1.746238e+03 1.521191e+03
+## 1971 1.362950e-01 -6.017019e+03 8.201887e+02
+## 1972 9.493297e-01 -3.376417e+03 3.164344e+03
+## 1973 7.362065e-01 -6.339136e+03 8.970591e+03
+## 1974 7.167151e-01 -6.407373e+03 9.318793e+03
+## 1975 2.855241e-01 -1.372219e+04 4.042268e+03
+## 1976 7.311700e-01 -1.980706e+03 1.389865e+03
+## 1977 3.127365e-01 -2.931981e+04 9.160130e+04
+## 1978 7.933767e-02 -1.461260e+04 8.081152e+02
+## 1979 5.640840e-01 -5.698521e+03 3.107152e+03
+## 1980 3.289897e-01 -2.501415e+03 7.465282e+03
+## 1981 6.944539e-01 -4.541174e+03 6.817740e+03
+## 1982 3.244179e-01 -4.877136e+03 1.474026e+04
+## 1983 4.044203e-01 -1.804478e+03 4.476248e+03
+## 1984 8.387525e-01 -2.130475e+03 1.729700e+03
+## 1985 3.181673e-01 -2.655564e+03 8.633453e+02
+## 1986 2.651449e-01 -3.046460e+03 8.379993e+02
+## 1987 7.748537e-01 -7.055544e+03 5.258470e+03
+## 1988 3.909326e-02 1.704270e+02 6.641392e+03
+## 1989 7.630582e-01 -2.295863e+03 3.130508e+03
+## 1990 6.484433e-01 -8.354400e+02 1.341941e+03
+## 1991 3.818771e-01 -1.427084e+04 5.465446e+03
+## 1992 2.819052e-01 -1.046364e+03 3.593985e+03
+## 1993 3.868115e-01 -9.395117e+03 3.639663e+03
+## 1994 3.095446e-01 -1.128932e+04 3.580037e+03
+## 1995 2.890084e-01 -2.284014e+03 7.667663e+03
+## 1996 1.040263e-01 -9.955969e+02 1.067771e+04
+## 1997 5.964374e-01 -1.129820e+04 6.491807e+03
+## 1998 2.504204e-01 -2.699974e+02 1.035609e+03
+## 1999 3.228148e-01 -5.918080e+02 1.796648e+03
+## 2000 5.828002e-01 -6.457035e+03 3.630035e+03
+## 2001 8.495713e-01 -8.670177e+02 7.140209e+02
+## 2002 2.665002e-01 -2.262192e+03 8.184993e+03
+## 2003 1.346548e-01 -2.396710e+03 1.785236e+04
+## 2004 5.172353e-02 -4.088820e+01 1.098519e+04
+## 2005 2.548243e-01 -7.170481e+04 1.900422e+04
+## 2006 9.205679e-02 -9.088367e+01 1.203104e+03
+## 2007 3.177582e-01 -2.204401e+03 7.158348e+02
+## 2008 2.084910e-01 -6.208866e+03 1.355042e+03
+## 2009 1.005320e-01 -8.239558e+01 9.342892e+02
+## 2010 5.257857e-01 -2.103775e+03 1.074838e+03
+## 2011 6.881615e-01 -7.995960e+02 1.211397e+03
+## 2012 1.824945e-01 -2.758831e+03 5.251542e+02
+## 2013 2.753033e-01 -1.132830e+04 3.977001e+04
+## 2014 9.016676e-01 -5.072179e+02 5.754699e+02
+## 2015 1.268586e-01 -6.865670e+02 5.523779e+03
+## 2016 8.930167e-02 -6.465380e+01 9.068542e+02
+## 2017 1.527593e-01 -1.309351e+03 2.047609e+02
+## 2018 2.042484e-01 -6.027901e+02 2.819593e+03
+## 2019 5.136293e-01 -8.102723e+02 1.620313e+03
+## 2020 2.255138e-01 -1.450708e+03 3.420858e+02
+## 2021 8.737346e-01 -9.386681e+01 1.104316e+02
+## 2022 1.235176e-01 -2.139949e+02 1.784260e+03
+## 2023 1.588164e-01 -7.113285e+02 4.350123e+03
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+## 2028 1.558231e-01 -6.016027e+03 9.626134e+02
+## 2029 5.307125e-01 -4.040427e+02 7.840778e+02
+## 2030 1.317452e-01 -7.188066e+02 9.385327e+01
+## 2031 7.865765e-01 -1.236027e+02 1.632267e+02
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+## 2533 5.331160e-01 -1.254423e+00 6.491108e-01
+## 2534 3.797162e-01 -3.809423e-01 9.997369e-01
+## 2535 3.797162e-01 -7.618846e-01 1.999474e+00
+## 2536 1.453663e-01 -5.592896e+00 3.791792e+01
+## 2537 3.048948e-01 -6.790498e+00 2.123984e+00
+## 2538 3.018081e-01 -6.251525e+00 2.017237e+01
+## 2539 3.074068e-01 -7.947992e-01 2.522143e+00
+## 2540 3.074068e-01 -7.947992e-01 2.522143e+00
+## 2541 3.074068e-01 -7.947992e-01 2.522143e+00
+## 2542 3.039239e-01 -5.972292e+01 1.862649e+01
+## 2543 3.001945e-01 -7.601658e+00 2.344319e+00
+## 2544 3.001945e-01 -7.601658e+00 2.344319e+00
+## 2545 7.463003e-01 -1.273426e+01 9.125910e+00
+## 2546 5.331160e-01 -2.090705e-01 1.081851e-01
+## 2547 3.490059e-01 -1.446496e+00 5.111055e-01
+## 2548 3.045793e-01 -1.951882e+01 6.099503e+00
+## 2549 8.876889e-01 -8.602810e-02 7.446355e-02
+## 2550 2.960774e-01 -4.418252e+01 1.345514e+01
+## 2551 2.096883e-01 -3.242044e+01 7.116115e+00
+## 2552 5.331160e-01 -6.272114e-01 3.245554e-01
+## 2553 3.079307e-01 -4.090107e+00 1.295912e+01
+## 2554 2.999555e-01 -7.378491e+00 2.273844e+00
+## 2555 2.999555e-01 -7.378491e+00 2.273844e+00
+## 2556 3.023767e-01 -4.135536e+01 1.283822e+01
+## 2557 5.331160e-01 -4.181409e-01 2.163703e-01
+## 2558 6.265232e-01 -1.304239e+00 7.854131e-01
+## 2559 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2560 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2561 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2562 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2563 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2564 2.991051e-01 -8.925870e-01 2.903897e+00
+## 2565 3.043487e-01 -2.264811e+00 7.252542e+00
+## 2566 3.043487e-01 -2.264811e+00 7.252542e+00
+## 2567 3.797162e-01 -1.269808e-01 3.332456e-01
+## 2568 3.797162e-01 -1.269808e-01 3.332456e-01
+## 2569 3.114705e-01 -8.010450e-01 2.511852e+00
+## 2570 3.018080e-01 -3.125762e+00 1.008618e+01
+## 2571 3.039239e-01 -2.986146e+01 9.313246e+00
+## 2572 3.042875e-01 -9.797769e+00 3.059071e+00
+## 2573 3.001945e-01 -3.800829e+00 1.172160e+00
+## 2574 2.983713e-01 -1.315893e+01 4.035683e+00
+## 2575 3.053218e-01 -3.174999e+00 1.013774e+01
+## 2576 6.265232e-01 -7.245771e-01 4.363406e-01
+## 2577 3.023767e-01 -2.067768e+01 6.419112e+00
+## 2578 3.041356e-01 -6.189213e+00 1.983218e+01
+## 2579 5.331160e-01 -2.090705e-01 1.081851e-01
+## 2580 3.039722e-01 -6.729133e+00 2.098997e+00
+## 2581 3.172133e-01 -8.681926e-01 2.814908e-01
+## 2582 3.908976e-01 -2.761793e-01 7.062429e-01
+## 2583 3.908976e-01 -2.761793e-01 7.062429e-01
+## 2584 3.029075e-01 -1.808861e+00 5.817530e+00
+## 2585 3.034915e-01 -9.989044e+00 3.111370e+00
+## 2586 2.964672e-01 -1.825374e+00 5.986770e+00
+## 2587 3.110974e-01 -1.929098e+01 6.055685e+01
+## 2588 3.025699e-01 -1.294452e+00 4.020794e-01
+## Taxon Adj p-value
+## 1 Dolosigranulum 1.00000000
+## 2 Streptococcus 1.00000000
+## 3 Moraxella 1.00000000
+## 4 Staphylococcus 1.00000000
+## 5 Corynebacterium 1.00000000
+## 6 Haemophilus 1.00000000
+## 7 Anaerobacillus 1.00000000
+## 8 Paracoccus 1.00000000
+## 9 Acinetobacter 1.00000000
+## 10 Pseudomonas 1.00000000
+## 11 Alkalihalophilus 1.00000000
+## 12 Delftia 1.00000000
+## 13 Noviherbaspirillum 1.00000000
+## 14 Weissella 1.00000000
+## 15 Escherichia 1.00000000
+## 16 Brucella 1.00000000
+## 17 Aeromonas 1.00000000
+## 18 Mycoplasma 1.00000000
+## 19 Kocuria 1.00000000
+## 20 Enterobacter 1.00000000
+## 21 Cutibacterium 1.00000000
+## 22 Listeria 1.00000000
+## 23 Micrococcus 1.00000000
+## 24 Sphingomonas 1.00000000
+## 25 Knoellia 1.00000000
+## 26 Finegoldia 1.00000000
+## 27 Peptoniphilus 1.00000000
+## 28 Ornithinimicrobium 1.00000000
+## 29 Nocardioides 1.00000000
+## 30 Agrobacterium 1.00000000
+## 31 Neisseria 1.00000000
+## 32 Janibacter 1.00000000
+## 33 Alkalihalobacillus 1.00000000
+## 34 Halolactibacillus 1.00000000
+## 35 Anaerococcus 1.00000000
+## 36 Bifidobacterium 1.00000000
+## 37 Bacillus 1.00000000
+## 38 Exiguobacterium 1.00000000
+## 39 Marmoricola 1.00000000
+## 40 Brachybacterium 1.00000000
+## 41 Salinicoccus 1.00000000
+## 42 Halomonas 1.00000000
+## 43 Suttonella 1.00000000
+## 44 Microvirga 1.00000000
+## 45 Rothia 1.00000000
+## 46 Planococcus 1.00000000
+## 47 Herbaspirillum 1.00000000
+## 48 Psychrobacter 1.00000000
+## 49 Dietzia 1.00000000
+## 50 Veillonella 1.00000000
+## 51 Alishewanella 1.00000000
+## 52 Glaesserella 1.00000000
+## 53 Helcococcus 1.00000000
+## 54 Paenisporosarcina 1.00000000
+## 55 Serinicoccus 1.00000000
+## 56 Gemella 1.00000000
+## 57 Rubellimicrobium 1.00000000
+## 58 Lysobacter 1.00000000
+## 59 Variovorax 1.00000000
+## 60 Tessaracoccus 1.00000000
+## 61 Stenotrophomonas 1.00000000
+## 62 Ligilactobacillus 1.00000000
+## 63 Klebsiella 1.00000000
+## 64 Fusobacterium 1.00000000
+## 65 Campylobacter 1.00000000
+## 66 Gordonia 1.00000000
+## 67 Alkalihalobacterium 1.00000000
+## 68 Brevibacterium 1.00000000
+## 69 Pseudarthrobacter 1.00000000
+## 70 Jeotgalicoccus 1.00000000
+## 71 Neobacillus 1.00000000
+## 72 Enterococcus 1.00000000
+## 73 Haematobacter 1.00000000
+## 74 Comamonas 1.00000000
+## 75 Kaistella 1.00000000
+## 76 Aeribacillus 1.00000000
+## 77 Bradyrhizobium 1.00000000
+## 78 Shewanella 1.00000000
+## 79 Domibacillus 1.00000000
+## 80 Aquimonas 1.00000000
+## 81 Cytobacillus 1.00000000
+## 82 Thalassospira 1.00000000
+## 83 Citrobacter 1.00000000
+## 84 Rhodococcus 1.00000000
+## 85 Pantoea 1.00000000
+## 86 Arthrobacter 1.00000000
+## 87 Granulicatella 1.00000000
+## 88 Piscicoccus 1.00000000
+## 89 Aerococcus 1.00000000
+## 90 Actinotalea 1.00000000
+## 91 Priestia 1.00000000
+## 92 Metabacillus 1.00000000
+## 93 Pluralibacter 1.00000000
+## 94 Negativicoccus 1.00000000
+## 95 Proteus 1.00000000
+## 96 Flavisolibacter 1.00000000
+## 97 Halopseudomonas 1.00000000
+## 98 Nosocomiicoccus 1.00000000
+## 99 Streptomyces 1.00000000
+## 100 Planomicrobium 1.00000000
+## 101 Pusillimonas_(ex_Stolz_et_al._2005) 1.00000000
+## 102 Pedococcus 1.00000000
+## 103 Eremococcus 1.00000000
+## 104 Massilia 1.00000000
+## 105 Novosphingobium 1.00000000
+## 106 Ruminococcus 1.00000000
+## 107 Blastococcus 1.00000000
+## 108 Cellulomonas 1.00000000
+## 109 Pontibacter 1.00000000
+## 110 Gardnerella 1.00000000
+## 111 Anoxybacillus 1.00000000
+## 112 Lawsonella 1.00000000
+## 113 Obesumbacterium 1.00000000
+## 114 Epilithonimonas 1.00000000
+## 115 Tepidimonas 1.00000000
+## 116 Flavobacterium 1.00000000
+## 117 Glutamicibacter 1.00000000
+## 118 Prevotella 1.00000000
+## 119 Phycicoccus 1.00000000
+## 120 Geodermatophilus 1.00000000
+## 121 Limosilactobacillus 1.00000000
+## 122 Sphaerobacter 1.00000000
+## 123 Schinkia 1.00000000
+## 124 Mediterraneibacter 1.00000000
+## 125 Alkalibacterium 1.00000000
+## 126 Fenollaria 1.00000000
+## 127 Bosea 1.00000000
+## 128 Lautropia 1.00000000
+## 129 Pseudostreptobacillus 1.00000000
+## 130 Nissabacter 1.00000000
+## 131 Luteimonas 1.00000000
+## 132 Globicatella 1.00000000
+## 133 Thauera 1.00000000
+## 134 Microbacterium 1.00000000
+## 135 Archangium 1.00000000
+## 136 Enterocloster 1.00000000
+## 137 Leptothrix 1.00000000
+## 138 Dyadobacter 1.00000000
+## 139 Lactobacillus 1.00000000
+## 140 Rhizorhabdus 1.00000000
+## 141 Azospirillum 1.00000000
+## 142 Acidovorax 1.00000000
+## 143 Aeromicrobium 1.00000000
+## 144 Paenarthrobacter 1.00000000
+## 145 Deinococcus 1.00000000
+## 146 Burkholderia 1.00000000
+## 147 Clostridium 1.00000000
+## 148 Aquabacterium 1.00000000
+## 149 Aquincola 1.00000000
+## 150 Macrococcus 1.00000000
+## 151 Rheinheimera 1.00000000
+## 152 Aliarcobacter 1.00000000
+## 153 Collinsella 1.00000000
+## 154 Brochothrix 1.00000000
+## 155 Caulobacter 1.00000000
+## 156 Niallia 1.00000000
+## 157 Brevundimonas 1.00000000
+## 158 Desnuesiella 1.00000000
+## 159 Rubrobacter 1.00000000
+## 160 Pediococcus 1.00000000
+## 161 Mycolicibacterium 1.00000000
+## 162 Fimbriimonas 1.00000000
+## 163 Tsuneonella 1.00000000
+## 164 Methylobacterium 1.00000000
+## 165 Lactococcus 1.00000000
+## 166 Devosia 1.00000000
+## 167 Leptotrichia 1.00000000
+## 168 Chishuiella 1.00000000
+## 169 Pseudorhizobium 1.00000000
+## 170 Cloacibacterium 1.00000000
+## 171 Abyssicoccus 1.00000000
+## 172 Pseudoxanthomonas 1.00000000
+## 173 Thermoactinomyces 1.00000000
+## 174 Megamonas 1.00000000
+## 175 Methylibium 1.00000000
+## 176 Beutenbergia 1.00000000
+## 177 Vibrio 1.00000000
+## 178 Schaalia 1.00000000
+## 179 Jeotgalibacillus 1.00000000
+## 180 Afipia 1.00000000
+## 181 Bryobacter 1.00000000
+## 182 Bacteroides 1.00000000
+## 183 Qipengyuania 1.00000000
+## 184 Mesobacillus 1.00000000
+## 185 Capnocytophaga 1.00000000
+## 186 Gemmatimonas 1.00000000
+## 187 Mesorhizobium 1.00000000
+## 188 Kallipyga 1.00000000
+## 189 Arenimonas 1.00000000
+## 190 Sphingobium 1.00000000
+## 191 Megasphaera 1.00000000
+## 192 Erythrobacter 1.00000000
+## 193 Youngiibacter 1.00000000
+## 194 Mucilaginibacter 1.00000000
+## 195 Rufibacter 1.00000000
+## 196 Methylorubrum 1.00000000
+## 197 Sphingobacterium 1.00000000
+## 198 Ferrimicrobium 1.00000000
+## 199 Flaviflexus 1.00000000
+## 200 Solibacillus 1.00000000
+## 201 Phocaeicola 1.00000000
+## 202 Paeniglutamicibacter 1.00000000
+## 203 Achromobacter 1.00000000
+## 204 Latilactobacillus 1.00000000
+## 205 Nakamurella 1.00000000
+## 206 Legionella 1.00000000
+## 207 Cellvibrio 1.00000000
+## 208 Leuconostoc 1.00000000
+## 209 Viridibacillus 1.00000000
+## 210 Leucobacter 1.00000000
+## 211 Propionicicella 1.00000000
+## 212 Oerskovia 1.00000000
+## 213 Catenibacterium 1.00000000
+## 214 Saccharopolyspora 1.00000000
+## 215 Paramesorhizobium 1.00000000
+## 216 Silanimonas 1.00000000
+## 217 Blautia 1.00000000
+## 218 Lancefieldella 1.00000000
+## 219 Mageeibacillus 1.00000000
+## 220 Fimbriiglobus 1.00000000
+## 221 Croceibacterium 1.00000000
+## 222 Gemmobacter 1.00000000
+## 223 Curvibacter 1.00000000
+## 224 Ensifer 1.00000000
+## 225 Mammaliicoccus 1.00000000
+## 226 Halarcobacter 1.00000000
+## 227 Janthinobacterium 1.00000000
+## 228 Belnapia 1.00000000
+## 229 Pseudidiomarina 1.00000000
+## 230 Nitratireductor 1.00000000
+## 231 Schlegelella 1.00000000
+## 232 Erysipelatoclostridium 1.00000000
+## 233 Phenylobacterium 1.00000000
+## 234 Luteipulveratus 1.00000000
+## 235 Daejeonella 1.00000000
+## 236 Ezakiella 1.00000000
+## 237 Nigerium 1.00000000
+## 238 Peribacillus 1.00000000
+## 239 Alloiococcus 1.00000000
+## 240 Trichococcus 1.00000000
+## 241 Buttiauxella 1.00000000
+## 242 Saccharothrix 1.00000000
+## 243 Intestinibacter 1.00000000
+## 244 Rodentibacter 1.00000000
+## 245 Brevibacillus 1.00000000
+## 246 Liquorilactobacillus 1.00000000
+## 247 Nonomuraea 1.00000000
+## 248 Thioclava 1.00000000
+## 249 Pimelobacter 1.00000000
+## 250 Scytonema 1.00000000
+## 251 Geosporobacter 1.00000000
+## 252 Kushneria 1.00000000
+## 253 Eubacterium 1.00000000
+## 254 Catonella 1.00000000
+## 255 Roseomonas 1.00000000
+## 256 Aggregatibacter 1.00000000
+## 257 Geobacter 1.00000000
+## 258 Xenophilus 1.00000000
+## 259 Flavihumibacter 1.00000000
+## 260 Akkermansia 1.00000000
+## 261 Acetobacter 1.00000000
+## 262 Altererythrobacter 1.00000000
+## 263 Pseudonocardia 1.00000000
+## 264 Fructobacillus 1.00000000
+## 265 Peptostreptococcus 1.00000000
+## 266 Rubrivivax 1.00000000
+## 267 Ciceribacter 1.00000000
+## 268 Desulfuromonas 1.00000000
+## 269 Pseudoglutamicibacter 1.00000000
+## 270 Fictibacillus 1.00000000
+## 271 Porphyromonas 1.00000000
+## 272 Caldilinea 1.00000000
+## 273 Stomatobaculum 1.00000000
+## 274 Pelagerythrobacter 1.00000000
+## 275 Marinilactibacillus 1.00000000
+## 276 Kluyvera 1.00000000
+## 277 Abiotrophia 1.00000000
+## 278 Acidisphaera 1.00000000
+## 279 Pelomonas 1.00000000
+## 280 Kytococcus 1.00000000
+## 281 Actinomyces 1.00000000
+## 282 Carnobacterium 1.00000000
+## 283 Robertmurraya 1.00000000
+## 284 Micromonospora 1.00000000
+## 285 Paucilactobacillus 1.00000000
+## 286 Agrococcus 1.00000000
+## 287 Chryseobacterium 1.00000000
+## 288 Lysinibacillus 1.00000000
+## 289 Demequina 1.00000000
+## 290 Sphaerochaeta 1.00000000
+## 291 Riemerella 1.00000000
+## 292 Amphibacillus 1.00000000
+## 293 Nesterenkonia 1.00000000
+## 294 Tenacibaculum 1.00000000
+## 295 Wenxinia 1.00000000
+## 296 Pyrinomonas 1.00000000
+## 297 Asanoa 1.00000000
+## 298 Sandaracinus 1.00000000
+## 299 Nocardia 1.00000000
+## 300 Dermabacter 1.00000000
+## 301 Cronobacter 1.00000000
+## 302 Ornatilinea 1.00000000
+## 303 Solirubrum 1.00000000
+## 304 Cereibacter 1.00000000
+## 305 Rossellomorea 1.00000000
+## 306 Thermanaerothrix 1.00000000
+## 307 Solirubrobacter 1.00000000
+## 308 Raineyella 1.00000000
+## 309 Azotobacter 1.00000000
+## 310 Ramlibacter 1.00000000
+## 311 Aquamicrobium 1.00000000
+## 312 Faecalibacterium 1.00000000
+## 313 Pararheinheimera 1.00000000
+## 314 Chondromyces 1.00000000
+## 315 Marinobacter 1.00000000
+## 316 Ralstonia 1.00000000
+## 317 Sphingopyxis 1.00000000
+## 318 Halalkalibacterium_(ex_Joshi_et_al._2022) 1.00000000
+## 319 Salinimicrobium 1.00000000
+## 320 Gillisia 1.00000000
+## 321 Hyphomicrobium 1.00000000
+## 322 Immundisolibacter 1.00000000
+## 323 Methylovorus 1.00000000
+## 324 Pedobacter 1.00000000
+## 325 Aequorivita 1.00000000
+## 326 Aureimonas 1.00000000
+## 327 Kurthia 1.00000000
+## 328 Methylocystis 1.00000000
+## 329 Snodgrassella 1.00000000
+## 330 Hymenobacter 1.00000000
+## 331 Bergeyella 1.00000000
+## 332 Paenibacillus 1.00000000
+## 333 Alkanindiges 1.00000000
+## 334 Aromatoleum 1.00000000
+## 335 Pseudoalteromonas 1.00000000
+## 336 Auraticoccus 1.00000000
+## 337 Dorea 1.00000000
+## 338 Facklamia 1.00000000
+## 339 Tolumonas 1.00000000
+## 340 Geobacillus 1.00000000
+## 341 Ilumatobacter 1.00000000
+## 342 Palleronia 1.00000000
+## 343 Lachnoclostridium 1.00000000
+## 344 Trueperella 1.00000000
+## 345 Rhodopseudomonas 1.00000000
+## 346 Kingella 1.00000000
+## 347 Terribacillus 1.00000000
+## 348 Fannyhessea 1.00000000
+## 349 Rudanella 1.00000000
+## 350 Lactiplantibacillus 1.00000000
+## 351 Rickettsia 1.00000000
+## 352 Methylophilus 1.00000000
+## 353 Algoriphagus 1.00000000
+## 354 Sanguibacteroides 1.00000000
+## 355 Ureaplasma 1.00000000
+## 356 Rubritepida 1.00000000
+## 357 Azoarcus 1.00000000
+## 358 Pseudooctadecabacter 1.00000000
+## 359 Cupriavidus 1.00000000
+## 360 Oceanospirillum 1.00000000
+## 361 Anaeromyxobacter 1.00000000
+## 362 Oscillatoria 1.00000000
+## 363 Salmonella 1.00000000
+## 364 Cellulosimicrobium 1.00000000
+## 365 Jannaschia 1.00000000
+## 366 Curtobacterium 1.00000000
+## 367 Alcanivorax 1.00000000
+## 368 Conexibacter 1.00000000
+## 369 Atopostipes 1.00000000
+## 370 Salegentibacter 1.00000000
+## 371 Acetivibrio 1.00000000
+## 372 Leifsonia 1.00000000
+## 373 Pseudorhodoplanes 1.00000000
+## 374 Agarivorans 1.00000000
+## 375 Hydrogenophaga 1.00000000
+## 376 Krasilnikoviella 1.00000000
+## 377 Rickettsiella 1.00000000
+## 378 Bellilinea 1.00000000
+## 379 Romboutsia 1.00000000
+## 380 Skermanella 1.00000000
+## 381 Morganella 1.00000000
+## 382 Nioella 1.00000000
+## 383 Simiduia 1.00000000
+## 384 Frankia 1.00000000
+## 385 Myxococcus 1.00000000
+## 386 Serratia 1.00000000
+## 387 Virgibacillus 1.00000000
+## 388 Avibacterium 1.00000000
+## 389 Marinomonas 1.00000000
+## 390 Turicibacter 1.00000000
+## 391 Merdimonas 1.00000000
+## 392 Diaphorobacter 1.00000000
+## 393 Acidithrix 1.00000000
+## 394 Tolypothrix 1.00000000
+## 395 Buchnera 1.00000000
+## 396 Margalitia 1.00000000
+## 397 Sarcina 1.00000000
+## 398 Lacticaseibacillus 1.00000000
+## 399 Pedosphaera 1.00000000
+## 400 Allgaiera 1.00000000
+## 401 Lacrimispora 1.00000000
+## 402 Erwinia 1.00000000
+## 403 Gulosibacter 1.00000000
+## 404 Parabacteroides 1.00000000
+## 405 Castellaniella 1.00000000
+## 406 Sutcliffiella 1.00000000
+## 407 Ruminobacter 1.00000000
+## 408 Vagococcus 1.00000000
+## 409 Ketogulonicigenium 1.00000000
+## 410 Aestuariimicrobium 1.00000000
+## 411 Nitriliruptor 1.00000000
+## 412 Dokdonella 1.00000000
+## 413 Williamsia 1.00000000
+## 414 Rhizobium 1.00000000
+## 415 Modestobacter 1.00000000
+## 416 Colwellia 1.00000000
+## 417 Holdemanella 1.00000000
+## 418 Caldimonas 1.00000000
+## 419 Phascolarctobacterium 1.00000000
+## 420 Neomicrococcus 1.00000000
+## 421 Hyalangium 1.00000000
+## 422 Brevefilum 1.00000000
+## 423 Sporosarcina 1.00000000
+## 424 Geminicoccus 1.00000000
+## 425 Falsiruegeria 1.00000000
+## 426 Oceanibacterium 1.00000000
+## 427 Allorhizobium 1.00000000
+## 428 Pseudoclavibacter 1.00000000
+## 429 Rhizobacter 1.00000000
+## 430 Patulibacter 1.00000000
+## 431 Roseburia 1.00000000
+## 432 Herbiconiux 1.00000000
+## 433 Nitrospira 1.00000000
+## 434 Cryobacterium 1.00000000
+## 435 Oceanobacillus 1.00000000
+## 436 Gemmata 1.00000000
+## 437 Rhodoferax 1.00000000
+## 438 Chromohalobacter 1.00000000
+## 439 Kitasatospora 1.00000000
+## 440 Verrucomicrobium 1.00000000
+## 441 Aphanizomenon 1.00000000
+## 442 Senegalimassilia 1.00000000
+## 443 Tepidibacter 1.00000000
+## 444 Plesiocystis 1.00000000
+## 445 Nitrosospira 1.00000000
+## 446 Yaniella 1.00000000
+## 447 Subdoligranulum 1.00000000
+## 448 Spirosoma 1.00000000
+## 449 Pseudoflavonifractor 1.00000000
+## 450 Metaplanococcus 1.00000000
+## 451 Sinorhizobium 1.00000000
+## 452 Fredinandcohnia 1.00000000
+## 453 Alcaligenes 1.00000000
+## 454 Thermoleophilum 1.00000000
+## 455 Oceanicella 1.00000000
+## 456 Thiolapillus 1.00000000
+## 457 Pseudobdellovibrio 1.00000000
+## 458 Plantibacter 1.00000000
+## 459 Thermus 1.00000000
+## 460 Quasibacillus 1.00000000
+## 461 Cesiribacter 1.00000000
+## 462 Sulfitobacter 1.00000000
+## 463 Plesiomonas 1.00000000
+## 464 Promicromonospora 1.00000000
+## 465 Streptacidiphilus 1.00000000
+## 466 Perlucidibaca 1.00000000
+## 467 Kutzneria 1.00000000
+## 468 Sanguibacter 1.00000000
+## 469 Oceaniovalibus 1.00000000
+## 470 Neosynechococcus 1.00000000
+## 471 Selenomonas 1.00000000
+## 472 Alloprevotella 1.00000000
+## 473 Providencia 1.00000000
+## 474 Dialister 1.00000000
+## 475 Siminovitchia 1.00000000
+## 476 Aliivibrio 1.00000000
+## 477 Aquimixticola 1.00000000
+## 478 Chitinimonas 1.00000000
+## 479 Pleomorphomonas 1.00000000
+## 480 Hyphomonas 1.00000000
+## 481 Caenibius 1.00000000
+## 482 Spirillospora 1.00000000
+## 483 Edaphobacter 1.00000000
+## 484 Geminisphaera 1.00000000
+## 485 Chloroflexus 1.00000000
+## 486 Fervidicola 1.00000000
+## 487 Cloacibacillus 1.00000000
+## 488 Desulfovibrio 1.00000000
+## 489 Oligella 1.00000000
+## 490 Adhaeribacter 1.00000000
+## 491 Lentzea 1.00000000
+## 492 Chthoniobacter 1.00000000
+## 493 Rhodoluna 1.00000000
+## 494 Kineococcus 1.00000000
+## 495 Mobilicoccus 1.00000000
+## 496 Oceanisphaera 1.00000000
+## 497 Lentilactobacillus 1.00000000
+## 498 Methylomonas 1.00000000
+## 499 Halobacillus 1.00000000
+## 500 Rhodovibrio 1.00000000
+## 501 Pelagibacterium 1.00000000
+## 502 Gottschalkia 1.00000000
+## 503 Actinokineospora 1.00000000
+## 504 Thalassobacillus 1.00000000
+## 505 Stigmatella 1.00000000
+## 506 Steroidobacter 1.00000000
+## 507 Pirellula 1.00000000
+## 508 Canicola 1.00000000
+## 509 Desulfonatronum 1.00000000
+## 510 Thermosinus 1.00000000
+## 511 Blastochloris 1.00000000
+## 512 Thermomonas 1.00000000
+## 513 Kerstersia 1.00000000
+## 514 Intrasporangium 1.00000000
+## 515 Flexilinea 1.00000000
+## 516 Clostridioides 1.00000000
+## 517 Pelosinus 1.00000000
+## 518 Cardiobacterium 1.00000000
+## 519 Albimonas 1.00000000
+## 520 Thermostaphylospora 1.00000000
+## 521 Falseniella 1.00000000
+## 522 Acidiferrobacter 1.00000000
+## 523 Catellicoccus 1.00000000
+## 524 Acidobacterium 1.00000000
+## 525 Methylocella 1.00000000
+## 526 Isoptericola 1.00000000
+## 527 Tepidiphilus 1.00000000
+## 528 Kribbella 1.00000000
+## 529 Kosakonia 1.00000000
+## 530 Nocardiopsis 1.00000000
+## 531 Weizmannia 1.00000000
+## 532 Mannheimia 1.00000000
+## 533 Niastella 1.00000000
+## 534 Nitrobacter 1.00000000
+## 535 Limimonas 1.00000000
+## 536 Wolinella 1.00000000
+## 537 Mycobacteroides 1.00000000
+## 538 Negativibacillus 1.00000000
+## 539 Rhodomicrobium 1.00000000
+## 540 Caloramator 1.00000000
+## 541 Pandoraea 1.00000000
+## 542 Cnuella 1.00000000
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+## 1843 Soonwooa 1.00000000
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+## 1850 Chroococcidiopsis 1.00000000
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+## 1863 Coprococcus 1.00000000
+## 1864 Roseateles 1.00000000
+## 1865 Dactylosporangium 1.00000000
+## 1866 Jonesia 1.00000000
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+## 1869 Tissierella 1.00000000
+## 1870 Microlunatus 1.00000000
+## 1871 Mariniphaga 1.00000000
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+## 1877 Roseivivax 1.00000000
+## 1878 Dolosicoccus 1.00000000
+## 1879 Yokenella 1.00000000
+## 1880 Melissococcus 1.00000000
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+## 1882 Xanthomonas 1.00000000
+## 1883 Lampropedia 1.00000000
+## 1884 Mycobacterium 1.00000000
+## 1885 Maricaulis 1.00000000
+## 1886 Oribacterium 1.00000000
+## 1887 Planctopirus 1.00000000
+## 1888 Ruania 1.00000000
+## 1889 Cedecea 1.00000000
+## 1890 Rahnella 1.00000000
+## 1891 Jeotgalibaca 1.00000000
+## 1892 Edwardsiella 1.00000000
+## 1893 Mycoplasmopsis 1.00000000
+## 1894 Pseudaminobacter 1.00000000
+## 1895 Bibersteinia 1.00000000
+## 1896 Kribbia 1.00000000
+## 1897 Salinarimonas 1.00000000
+## 1898 Shimwellia 1.00000000
+## 1899 Bordetella 1.00000000
+## 1900 Neofamilia 1.00000000
+## 1901 Lentibacillus 1.00000000
+## 1902 Thiohalomonas 1.00000000
+## 1903 Paeniclostridium 1.00000000
+## 1904 Actinobacillus 1.00000000
+## 1905 Salinibacillus 1.00000000
+## 1906 Terrisporobacter 1.00000000
+## 1907 Heyndrickxia 1.00000000
+## 1908 Lederbergia 1.00000000
+## 1909 Caldalkalibacillus 1.00000000
+## 1910 Beijerinckia 1.00000000
+## 1911 Agromyces 1.00000000
+## 1912 Hydrogenoanaerobacterium 1.00000000
+## 1913 Massilioclostridium 1.00000000
+## 1914 Pasteurella 1.00000000
+## 1915 Rhodopirellula 1.00000000
+## 1916 Saccharomonospora 1.00000000
+## 1917 Wolbachia 1.00000000
+## 1918 Afifella 1.00000000
+## 1919 Ardenticatena 1.00000000
+## 1920 Companilactobacillus 1.00000000
+## 1921 Paraburkholderia 1.00000000
+## 1922 Azospira 1.00000000
+## 1923 Barnesiella 1.00000000
+## 1924 Marivita 1.00000000
+## 1925 Altibacter 1.00000000
+## 1926 Dysgonomonas 1.00000000
+## 1927 Neorhizobium 1.00000000
+## 1928 Tumebacillus 1.00000000
+## 1929 Nitrosovibrio 1.00000000
+## 1930 Glycomyces 1.00000000
+## 1931 Salinicola 1.00000000
+## 1932 Methylosinus 1.00000000
+## 1933 Xylophilus 1.00000000
+## 1934 Fusicatenibacter 1.00000000
+## 1935 Azovibrio 1.00000000
+## 1936 Geotalea 1.00000000
+## 1937 Microbulbifer 1.00000000
+## 1938 Algoriella 1.00000000
+## 1939 Shigella 1.00000000
+## 1940 Mycetocola 1.00000000
+## 1941 Urmitella 1.00000000
+## 1942 Dolosigranulum 1.00000000
+## 1943 Streptococcus 0.03369181
+## 1944 Moraxella 1.00000000
+## 1945 Staphylococcus 1.00000000
+## 1946 Corynebacterium 1.00000000
+## 1947 Haemophilus 0.15313421
+## 1948 Anaerobacillus 1.00000000
+## 1949 Paracoccus 1.00000000
+## 1950 Acinetobacter 1.00000000
+## 1951 Pseudomonas 1.00000000
+## 1952 Alkalihalophilus 1.00000000
+## 1953 Delftia 1.00000000
+## 1954 Noviherbaspirillum 1.00000000
+## 1955 Weissella 1.00000000
+## 1956 Escherichia 1.00000000
+## 1957 Brucella 1.00000000
+## 1958 Aeromonas 1.00000000
+## 1959 Mycoplasma 1.00000000
+## 1960 Kocuria 1.00000000
+## 1961 Enterobacter 1.00000000
+## 1962 Cutibacterium 1.00000000
+## 1963 Listeria 1.00000000
+## 1964 Micrococcus 1.00000000
+## 1965 Sphingomonas 1.00000000
+## 1966 Knoellia 1.00000000
+## 1967 Finegoldia 1.00000000
+## 1968 Peptoniphilus 1.00000000
+## 1969 Ornithinimicrobium 1.00000000
+## 1970 Nocardioides 1.00000000
+## 1971 Agrobacterium 1.00000000
+## 1972 Neisseria 1.00000000
+## 1973 Janibacter 1.00000000
+## 1974 Alkalihalobacillus 1.00000000
+## 1975 Halolactibacillus 1.00000000
+## 1976 Anaerococcus 1.00000000
+## 1977 Bifidobacterium 1.00000000
+## 1978 Bacillus 1.00000000
+## 1979 Exiguobacterium 1.00000000
+## 1980 Marmoricola 1.00000000
+## 1981 Brachybacterium 1.00000000
+## 1982 Salinicoccus 1.00000000
+## 1983 Halomonas 1.00000000
+## 1984 Suttonella 1.00000000
+## 1985 Microvirga 1.00000000
+## 1986 Rothia 1.00000000
+## 1987 Planococcus 1.00000000
+## 1988 Herbaspirillum 1.00000000
+## 1989 Psychrobacter 1.00000000
+## 1990 Dietzia 1.00000000
+## 1991 Veillonella 1.00000000
+## 1992 Alishewanella 1.00000000
+## 1993 Glaesserella 1.00000000
+## 1994 Helcococcus 1.00000000
+## 1995 Paenisporosarcina 1.00000000
+## 1996 Serinicoccus 1.00000000
+## 1997 Gemella 1.00000000
+## 1998 Rubellimicrobium 1.00000000
+## 1999 Lysobacter 1.00000000
+## 2000 Variovorax 1.00000000
+## 2001 Tessaracoccus 1.00000000
+## 2002 Stenotrophomonas 1.00000000
+## 2003 Ligilactobacillus 1.00000000
+## 2004 Klebsiella 1.00000000
+## 2005 Fusobacterium 1.00000000
+## 2006 Campylobacter 1.00000000
+## 2007 Gordonia 1.00000000
+## 2008 Alkalihalobacterium 1.00000000
+## 2009 Brevibacterium 1.00000000
+## 2010 Pseudarthrobacter 1.00000000
+## 2011 Jeotgalicoccus 1.00000000
+## 2012 Neobacillus 1.00000000
+## 2013 Enterococcus 1.00000000
+## 2014 Haematobacter 1.00000000
+## 2015 Comamonas 1.00000000
+## 2016 Kaistella 1.00000000
+## 2017 Aeribacillus 1.00000000
+## 2018 Bradyrhizobium 1.00000000
+## 2019 Shewanella 1.00000000
+## 2020 Domibacillus 1.00000000
+## 2021 Aquimonas 1.00000000
+## 2022 Cytobacillus 1.00000000
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+## 2024 Citrobacter 1.00000000
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+## 2443 Gottschalkia 1.00000000
+## 2444 Actinokineospora 1.00000000
+## 2445 Thalassobacillus 1.00000000
+## 2446 Stigmatella 1.00000000
+## 2447 Steroidobacter 1.00000000
+## 2448 Pirellula 1.00000000
+## 2449 Canicola 1.00000000
+## 2450 Desulfonatronum 1.00000000
+## 2451 Thermosinus 1.00000000
+## 2452 Blastochloris 1.00000000
+## 2453 Thermomonas 1.00000000
+## 2454 Kerstersia 1.00000000
+## 2455 Intrasporangium 1.00000000
+## 2456 Flexilinea 1.00000000
+## 2457 Clostridioides 1.00000000
+## 2458 Pelosinus 1.00000000
+## 2459 Cardiobacterium 1.00000000
+## 2460 Albimonas 1.00000000
+## 2461 Thermostaphylospora 1.00000000
+## 2462 Falseniella 1.00000000
+## 2463 Acidiferrobacter 1.00000000
+## 2464 Catellicoccus 1.00000000
+## 2465 Acidobacterium 1.00000000
+## 2466 Methylocella 1.00000000
+## 2467 Isoptericola 1.00000000
+## 2468 Tepidiphilus 1.00000000
+## 2469 Kribbella 1.00000000
+## 2470 Kosakonia 1.00000000
+## 2471 Nocardiopsis 1.00000000
+## 2472 Weizmannia 1.00000000
+## 2473 Mannheimia 1.00000000
+## 2474 Niastella 1.00000000
+## 2475 Nitrobacter 1.00000000
+## 2476 Limimonas 1.00000000
+## 2477 Wolinella 1.00000000
+## 2478 Mycobacteroides 1.00000000
+## 2479 Negativibacillus 1.00000000
+## 2480 Rhodomicrobium 1.00000000
+## 2481 Caloramator 1.00000000
+## 2482 Pandoraea 1.00000000
+## 2483 Cnuella 1.00000000
+## 2484 Aurantiacibacter 1.00000000
+## 2485 Bavariicoccus 1.00000000
+## 2486 Rugamonas 1.00000000
+## 2487 Klenkia 1.00000000
+## 2488 Colibacter 1.00000000
+## 2489 Nitratifractor 1.00000000
+## 2490 Soonwooa 1.00000000
+## 2491 Tetrasphaera 1.00000000
+## 2492 Actinophytocola 1.00000000
+## 2493 Lactonifactor 1.00000000
+## 2494 Azohydromonas 1.00000000
+## 2495 Methylobacter 1.00000000
+## 2496 Actinomycetospora 1.00000000
+## 2497 Chroococcidiopsis 1.00000000
+## 2498 Arsenicicoccus 1.00000000
+## 2499 Pseudescherichia 1.00000000
+## 2500 Methylocapsa 1.00000000
+## 2501 Alteromonas 1.00000000
+## 2502 Psychromonas 1.00000000
+## 2503 Cryptosporangium 1.00000000
+## 2504 Marinospirillum 1.00000000
+## 2505 Kangiella 1.00000000
+## 2506 Zavarzinella 1.00000000
+## 2507 Sneathia 1.00000000
+## 2508 Niameybacter 1.00000000
+## 2509 Nostoc 1.00000000
+## 2510 Coprococcus 1.00000000
+## 2511 Roseateles 1.00000000
+## 2512 Dactylosporangium 1.00000000
+## 2513 Jonesia 1.00000000
+## 2514 Ornithinibacillus 1.00000000
+## 2515 Ruminiclostridium 1.00000000
+## 2516 Tissierella 1.00000000
+## 2517 Microlunatus 1.00000000
+## 2518 Mariniphaga 1.00000000
+## 2519 Caballeronia 1.00000000
+## 2520 Merdibacter 1.00000000
+## 2521 Salipiger 1.00000000
+## 2522 Pontibacillus 1.00000000
+## 2523 Croceicoccus 1.00000000
+## 2524 Roseivivax 1.00000000
+## 2525 Dolosicoccus 1.00000000
+## 2526 Yokenella 1.00000000
+## 2527 Melissococcus 1.00000000
+## 2528 Sutterella 1.00000000
+## 2529 Xanthomonas 1.00000000
+## 2530 Lampropedia 1.00000000
+## 2531 Mycobacterium 1.00000000
+## 2532 Maricaulis 1.00000000
+## 2533 Oribacterium 1.00000000
+## 2534 Planctopirus 1.00000000
+## 2535 Ruania 1.00000000
+## 2536 Cedecea 1.00000000
+## 2537 Rahnella 1.00000000
+## 2538 Jeotgalibaca 1.00000000
+## 2539 Edwardsiella 1.00000000
+## 2540 Mycoplasmopsis 1.00000000
+## 2541 Pseudaminobacter 1.00000000
+## 2542 Bibersteinia 1.00000000
+## 2543 Kribbia 1.00000000
+## 2544 Salinarimonas 1.00000000
+## 2545 Shimwellia 1.00000000
+## 2546 Bordetella 1.00000000
+## 2547 Neofamilia 1.00000000
+## 2548 Lentibacillus 1.00000000
+## 2549 Thiohalomonas 1.00000000
+## 2550 Paeniclostridium 1.00000000
+## 2551 Actinobacillus 1.00000000
+## 2552 Salinibacillus 1.00000000
+## 2553 Terrisporobacter 1.00000000
+## 2554 Heyndrickxia 1.00000000
+## 2555 Lederbergia 1.00000000
+## 2556 Caldalkalibacillus 1.00000000
+## 2557 Beijerinckia 1.00000000
+## 2558 Agromyces 1.00000000
+## 2559 Hydrogenoanaerobacterium 1.00000000
+## 2560 Massilioclostridium 1.00000000
+## 2561 Pasteurella 1.00000000
+## 2562 Rhodopirellula 1.00000000
+## 2563 Saccharomonospora 1.00000000
+## 2564 Wolbachia 1.00000000
+## 2565 Afifella 1.00000000
+## 2566 Ardenticatena 1.00000000
+## 2567 Companilactobacillus 1.00000000
+## 2568 Paraburkholderia 1.00000000
+## 2569 Azospira 1.00000000
+## 2570 Barnesiella 1.00000000
+## 2571 Marivita 1.00000000
+## 2572 Altibacter 1.00000000
+## 2573 Dysgonomonas 1.00000000
+## 2574 Neorhizobium 1.00000000
+## 2575 Tumebacillus 1.00000000
+## 2576 Nitrosovibrio 1.00000000
+## 2577 Glycomyces 1.00000000
+## 2578 Salinicola 1.00000000
+## 2579 Methylosinus 1.00000000
+## 2580 Xylophilus 1.00000000
+## 2581 Fusicatenibacter 1.00000000
+## 2582 Azovibrio 1.00000000
+## 2583 Geotalea 1.00000000
+## 2584 Microbulbifer 1.00000000
+## 2585 Algoriella 1.00000000
+## 2586 Shigella 1.00000000
+## 2587 Mycetocola 1.00000000
+## 2588 Urmitella 1.00000000
+# Trying out plotting
+#run_gee_model(dat, unit_var = "Subject",
+# taxon_level = "genus",
+# fixed_cov = c("MothChild", "HIVStatus", "Age"),
+# corstr = "ar1",
+# plot_out = TRUE,
+# plotsave_loc = #"/restricted/projectnb/infant-microbiome/work/aodom",
+# plot_terms = "MothChild",
+# width = 6, height = 4, units = "in", scale = 0.7)
+#
+
+
+
+
+ Add hotelling +
+
+test_hotelling_t2(dat = dat_0.05,
+ test_index = which(dat_0.05$MothChild == "Infant" &
+ dat_0.05$timepoint == 6),
+ taxon_level = "genus",
+ # To avoid n < p, use top 5-6 species
+ num_taxa = 6,
+ paired = TRUE,
+ grouping_var = "HIVStatus",
+ pairing_var = "pairing")## $df1
+## [1] 6
+##
+## $df2
+## [1] 2
+##
+## $crit_F
+## [1] 19.32953
+##
+## $F_stat
+## [1] 2.578132
+##
+## $pvalue
+## [1] 0.3056466
+test_hotelling_t2(dat = dat_0.05,
+ test_index = which(dat_0.05$MothChild == "Mother" &
+ dat_0.05$timepoint == 0),
+ taxon_level = "genus",
+ # To avoid n < p, use top 5-6 species
+ num_taxa = 12,
+ grouping_var = "HIVStatus",
+ unit_var = "Subject",
+ paired = FALSE)## $df1
+## [1] 12
+##
+## $df2
+## [1] 7
+##
+## $crit_F
+## [1] 3.574676
+##
+## $F_stat
+## [1] 0.4781539
+##
+## $pvalue
+## [1] 0.875078
+sessionInfo()## R version 4.3.1 (2023-06-16)
+## Platform: x86_64-pc-linux-gnu (64-bit)
+## Running under: AlmaLinux 8.9 (Midnight Oncilla)
+##
+## Matrix products: default
+## BLAS: /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRblas.so
+## LAPACK: /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0
+##
+## locale:
+## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
+## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
+## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
+## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
+## [9] LC_ADDRESS=C LC_TELEPHONE=C
+## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+##
+## time zone: America/New_York
+## tzcode source: system (glibc)
+##
+## attached base packages:
+## [1] stats graphics grDevices utils datasets methods base
+##
+## other attached packages:
+## [1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
+## [5] purrr_1.0.2 readr_2.1.5 tidyr_1.3.0 tibble_3.2.1
+## [9] ggplot2_3.4.4 tidyverse_2.0.0 LegATo_0.0.0.9000 BiocStyle_2.28.0
+##
+## loaded via a namespace (and not attached):
+## [1] rstudioapi_0.15.0 jsonlite_1.8.8
+## [3] umap_0.2.10.0 MultiAssayExperiment_1.28.0
+## [5] magrittr_2.0.3 farver_2.1.1
+## [7] rmarkdown_2.25 geepack_1.3.9
+## [9] fs_1.6.3 zlibbioc_1.48.0
+## [11] ragg_1.2.5 vctrs_0.6.5
+## [13] memoise_2.0.1 paletteer_1.5.0
+## [15] RCurl_1.98-1.14 askpass_1.2.0
+## [17] BiocBaseUtils_1.4.0 htmltools_0.5.7
+## [19] S4Arrays_1.2.0 broom_1.0.5
+## [21] SparseArray_1.2.3 sass_0.4.8
+## [23] TBSignatureProfiler_1.15.0 bslib_0.6.1
+## [25] htmlwidgets_1.6.4 desc_1.4.3
+## [27] plyr_1.8.9 covr_3.6.2
+## [29] plotly_4.10.2 cachem_1.0.8
+## [31] lifecycle_1.0.4 iterators_1.0.14
+## [33] pkgconfig_2.0.3 Matrix_1.6-5
+## [35] R6_2.5.1 fastmap_1.1.1
+## [37] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
+## [39] clue_0.3-65 digest_0.6.34
+## [41] colorspace_2.1-0 rematch2_2.1.2
+## [43] spatial_7.3-16 S4Vectors_0.40.2
+## [45] DESeq2_1.40.1 RSpectra_0.16-1
+## [47] textshaping_0.3.6 GenomicRanges_1.54.1
+## [49] vegan_2.6-4 labeling_0.4.3
+## [51] fansi_1.0.6 timechange_0.2.0
+## [53] httr_1.4.7 abind_1.4-5
+## [55] mgcv_1.8-42 compiler_4.3.1
+## [57] withr_3.0.0 backports_1.4.1
+## [59] inline_0.3.19 BiocParallel_1.36.0
+## [61] highr_0.10 MASS_7.3-60
+## [63] tsne_0.1-3.1 openssl_2.1.1
+## [65] DelayedArray_0.28.0 fBasics_4022.94.9000
+## [67] permute_0.9-7 tools_4.3.1
+## [69] ape_5.7-1 rentrez_1.2.3
+## [71] glue_1.7.0 stabledist_0.7-1
+## [73] nlme_3.1-162 grid_4.3.1
+## [75] cluster_2.1.4 reshape2_1.4.4
+## [77] generics_0.1.3 gtable_0.3.4
+## [79] tzdb_0.4.0 data.table_1.14.10
+## [81] hms_1.1.3 utf8_1.2.4
+## [83] XVector_0.42.0 rmutil_1.1.10
+## [85] BiocGenerics_0.48.1 ggrepel_0.9.3
+## [87] foreach_1.5.2 pillar_1.9.0
+## [89] limma_3.56.2 splines_4.3.1
+## [91] lattice_0.21-8 GUniFrac_1.8
+## [93] tidyselect_1.2.0 locfit_1.5-9.8
+## [95] knitr_1.45 bookdown_0.34
+## [97] IRanges_2.36.0 edgeR_3.42.4
+## [99] SummarizedExperiment_1.32.0 stats4_4.3.1
+## [101] xfun_0.41 Biobase_2.62.0
+## [103] statmod_1.5.0 timeDate_4032.109
+## [105] matrixStats_1.2.0 DT_0.28
+## [107] rex_1.2.1 stringi_1.8.3
+## [109] lazyeval_0.2.2 yaml_2.3.8
+## [111] evaluate_0.23 codetools_0.2-19
+## [113] timeSeries_4030.106.9000 BiocManager_1.30.22
+## [115] cli_3.6.2 rpart_4.1.19
+## [117] reticulate_1.30 systemfonts_1.0.4
+## [119] munsell_0.5.0 jquerylib_0.1.4
+## [121] Rcpp_1.0.12 GenomeInfoDb_1.38.5
+## [123] stable_1.1.6 png_0.1-8
+## [125] XML_3.99-0.16 parallel_4.3.1
+## [127] modeest_2.4.0 ellipsis_0.3.2
+## [129] pkgdown_2.0.7 assertthat_0.2.1
+## [131] animalcules_1.18.2 ggalluvial_0.12.5
+## [133] bitops_1.0-7 viridisLite_0.4.2
+## [135] scales_1.3.0 statip_0.2.3
+## [137] crayon_1.5.2 rlang_1.1.3
+## [139] shinyjs_2.1.0