DspikeIn v1

library(DspikeIn)

## Warning: replacing previous import 'ggplot2::alpha' by 'microbiome::alpha' when
## loading 'microbiomeutilities'

## Thank you for using the DspikeIn package.

## For support, please contact Mitra Ghotbi at mitra.ghotbi@gmail.com.

library(phyloseq)

setwd("C:/Users/mghotbi/Documents/ForGitHub/Version1/16SOTU")
physeq_16SOTU <- readRDS("physeq_16SOTU.rds")

# prerequisite
spiked_cells <-1847
species_name <- spiked_species <- merged_spiked_species<- c("Tetragenococcus_halophilus", "Tetragenococcus_sp")
Tetra <- subset_taxa(physeq_16SOTU,Species=="Tetragenococcus_halophilus" | Species=="Tetragenococcus_sp")

## Warning in prune_taxa(taxa, phy_tree(x)): prune_taxa attempted to reduce tree to 1 or fewer tips.
##  tree replaced with NULL.

hashcodes <- row.names(phyloseq::tax_table(Tetra))


physeq_16SOTU<-tidy_phyloseq(physeq_16SOTU)

# Subset spiked samples (264 samples are spiked)
spiked_16S_OTU <- subset_samples(physeq_16SOTU, spiked.volume %in% c("2", "1"))
spiked_16S_OTU <- tidy_phyloseq(spiked_16S_OTU)

# Preprocessing
Spiked_16S_sum_scaled <- Pre_processing_species(
  spiked_16S_OTU, 
  species_name, 
  merge_method = "sum", 
  output_file = "merged_physeq_sum.rds")

## Starting pre-processing...

## Processing species: Tetragenococcus_halophilus

## ASVs found for species Tetragenococcus_halophilus: 2ddb215ff668b6a24a9ccf2bb076a453

## No need to merge; only one ASV for species: Tetragenococcus_halophilus

## Processing species: Tetragenococcus_sp

## ASVs found for species Tetragenococcus_sp:

## No need to merge; only one ASV for species: Tetragenococcus_sp

## OTU table dimensions: 9212, 264

## Taxonomy table dimensions: 9212, 7

## OTU table row names: 020e00d90ba97c5898944ab6f7b1b7c9, b00466354053c9065c8aa3d6fbb33eaa, f872c4bf84bcf44434fa2023788f6517, df13f71584d4a579c81d909eaba11a74, ed285eb1aac505a1f062b482300b69f7, 63f5509575600a9e7afb6847d6296976

## Taxonomy table row names: 020e00d90ba97c5898944ab6f7b1b7c9, b00466354053c9065c8aa3d6fbb33eaa, f872c4bf84bcf44434fa2023788f6517, df13f71584d4a579c81d909eaba11a74, ed285eb1aac505a1f062b482300b69f7, 63f5509575600a9e7afb6847d6296976

## Pre-processing complete.

# Scaling factor
result <- calculate_spikeIn_factors(Spiked_16S_sum_scaled, 1847, merged_spiked_species)

## Identifying spiked species...
## Saved file: spikeIn_factors/Physeq_NO_Spiked_Species.rds
## Saved file: spikeIn_factors/Spiked_16S_Total_Reads.csv

## Warning in prune_taxa(taxa, phy_tree(x)): prune_taxa attempted to reduce tree to 1 or fewer tips.
##  tree replaced with NULL.

## Saved file: spikeIn_factors/Spiked_Species_MergedToOne.rds
## Saved file: spikeIn_factors/Spiked_Species_Reads.csv
## Negative values detected in spiked species reads. Converting to zero.
## Scaling factors saved as spikeIn_factors.csv.
## Process complete. Scaling factors for spiked species saved in the output directory.
## Table saved in docx format: spikeIn_factors/spikeIn_factors_summary.docx

scaling_factors<-result$scaling_factors

# Spiked species retrieval
# Calculate spike percentage for the defined spiked species within the range 0.1 to 12
calculate_spike_percentage(Spiked_16S_sum_scaled, 
                           merged_spiked_species = merged_spiked_species, 
                           passed_range = c(0.1, 12))

## Warning: package 'flextable' was built under R version 4.3.3

## Warning in prune_taxa(taxa, phy_tree(x)): prune_taxa attempted to reduce tree to 1 or fewer tips.
##  tree replaced with NULL.

## Table saved in docx format: merged_data.docx 
## Merged data saved as CSV: merged_data.csv

# Converting to absolute
absolute <- convert_to_absolute_counts(Spiked_16S_sum_scaled, scaling_factors)

## Absolute count data saved to: C:/Users/mghotbi/Documents/ForGitHub/Version1/16SOTU/physeq_adj_scaled_AbsoluteCount.csv

absolute_counts <- absolute$absolute_counts
physeq_absolute_abundance_16S_OTU <- absolute$physeq_obj

physeq_absolute16S_OTU<-tidy_phyloseq(physeq_absolute_abundance_16S_OTU)

# summary statistics # needs dataframe
post_eval_summary <- calculate_summary_stats_table(absolute_counts)

## Table saved in docx format: post_eval_summary.docx 
## Summary statistics saved as CSV: post_eval_summary.csv

print(post_eval_summary)

## a flextable object.
## col_keys: `spiked.blank.20433_S84_mean`, `spiked.blank.20817_S84_mean`, `Std2uL.20625_S84_mean`, `StdSwab1uL.20624_S72_mean`, `STP1719.20422_S47_mean`, `STP213.20423_S59_mean`, `STP268.20424_S71_mean`, `STP544.20419_S11_mean`, `STP570.20420_S23_mean`, `STP579.20421_S35_mean`, `STP614.20418_S94_mean`, `UHM1000.20604_S22_mean`, `UHM1001.20609_S82_mean`, `UHM1007.20622_S48_mean`, `UHM1009.20614_S47_mean`, `UHM1010.20621_S36_mean`, `UHM1011.20606_S46_mean`, `UHM1024.20620_S24_mean`, `UHM1026.20607_S58_mean`, `UHM1028.20613_S35_mean`, `UHM1032.20605_S34_mean`, `UHM1033.20619_S12_mean`, `UHM1034.20616_S71_mean`, `UHM1035.20611_S11_mean`, `UHM1036.20612_S23_mean`, `UHM1052.20615_S59_mean`, `UHM1060.20723_S1_mean`, `UHM1065.20724_S13_mean`, `UHM1068.20732_S14_mean`, `UHM1069.20742_S39_mean`, `UHM1070.20725_S25_mean`, `UHM1071.20733_S26_mean`, `UHM1072.20734_S38_mean`, `UHM1073.20735_S50_mean`, `UHM1075.20726_S37_mean`, `UHM1077.20736_S62_mean`, `UHM1078.20727_S49_mean`, `UHM1080.20737_S74_mean`, `UHM1081.20728_S61_mean`, `UHM1088.20738_S86_mean`, `UHM1090.20739_S3_mean`, `UHM1093.20729_S73_mean`, `UHM1095.20730_S85_mean`, `UHM1097.20623_S60_mean`, `UHM1099.20608_S70_mean`, `UHM1100.20788_S21_mean`, `UHM1102.20789_S33_mean`, `UHM1104.20790_S45_mean`, `UHM1105.20791_S57_mean`, `UHM1109.20531_S1_mean`, `UHM1110.20568_S65_mean`, `UHM1113.20792_S69_mean`, `UHM1114.20793_S81_mean`, `UHM1115.20794_S93_mean`, `UHM1117.20795_S10_mean`, `UHM1118.20796_S22_mean`, `UHM1120.20797_S34_mean`, `UHM1124.20798_S46_mean`, `UHM1126.20799_S58_mean`, `UHM1128.20800_S70_mean`, `UHM1140.20555_S4_mean`, `UHM1145.20801_S82_mean`, `UHM1163.20405_S33_mean`, `UHM1164.20402_S92_mean`, `UHM1169.20552_S63_mean`, `UHM1171.20579_S7_mean`, `UHM1176.20404_S21_mean`, `UHM1177.20546_S86_mean`, `UHM1182.20576_S66_mean`, `UHM1210.20802_S94_mean`, `UHM1212.20803_S11_mean`, `UHM1217.20804_S23_mean`, `UHM1218.20805_S35_mean`, `UHM1219.20806_S47_mean`, `UHM1220.20807_S59_mean`, `UHM1221.20808_S71_mean`, `UHM1222.20809_S83_mean`, `UHM1223.20810_S95_mean`, `UHM1225.20811_S12_mean`, `UHM1227.20812_S24_mean`, `UHM1228.20813_S36_mean`, `UHM1237.20814_S48_mean`, `UHM1240.20566_S41_mean`, `UHM1246.20815_S60_mean`, `UHM1247.20816_S72_mean`, `UHM1248.20575_S54_mean`, `UHM1256.20570_S89_mean`, `UHM1260.20596_S21_mean`, `UHM1270.20577_S78_mean`, `UHM1271.20397_S32_mean`, `UHM1272.20398_S44_mean`, `UHM1274.20554_S87_mean`, `UHM1275.20597_S33_mean`, `UHM1282.20599_S57_mean`, `UHM1287.20543_S50_mean`, `UHM1291.20416_S70_mean`, `UHM1296.20550_S39_mean`, `UHM1319.20561_S76_mean`, `UHM1324.20413_S34_mean`, `UHM1327.20545_S74_mean`, `UHM1328.20572_S18_mean`, `UHM1334.20417_S82_mean`, `UHM1338.20399_S56_mean`, `UHM1341.20602_S93_mean`, `UHM1356.20541_S26_mean`, `UHM1380.20580_S19_mean`, `UHM1383.20594_S92_mean`, `UHM1385.20563_S5_mean`, `UHM1399.20756_S17_mean`, `UHM1400.20757_S29_mean`, `UHM1401.20758_S41_mean`, `UHM1402.20759_S53_mean`, `UHM1403.20760_S65_mean`, `UHM1405.20761_S77_mean`, `UHM1406.20762_S89_mean`, `UHM1414.20763_S6_mean`, `UHM1419.20764_S18_mean`, `UHM1427.20389_S31_mean`, `UHM1428.20390_S43_mean`, `UHM1429.20391_S55_mean`, `UHM1430.20392_S67_mean`, `UHM1432.20393_S79_mean`, `UHM1435.20388_S19_mean`, `UHM162.20560_S64_mean`, `UHM198.20585_S79_mean`, `UHM20.3314_S52_mean`, `UHM20.3315_S64_mean`, `UHM204.20409_S81_mean`, `UHM206.20410_S93_mean`, `UHM207.20593_S80_mean`, `UHM208.20411_S10_mean`, `UHM211.20406_S45_mean`, `UHM215.20408_S69_mean`, `UHM216.20429_S36_mean`, `UHM219.20430_S48_mean`, `UHM236.20431_S60_mean`, `UHM238.20407_S57_mean`, `UHM245.20538_S85_mean`, `UHM252.20558_S40_mean`, `UHM267.20400_S68_mean`, `UHM274.20581_S31_mean`, `UHM276.20586_S91_mean`, `UHM280.20401_S80_mean`, `UHM286.20425_S83_mean`, `UHM289.20426_S95_mean`, `UHM294.20427_S12_mean`, `UHM298.20600_S69_mean`, `UHM325.20548_S15_mean`, `UHM337.20412_S22_mean`, `UHM354.20535_S49_mean`, `UHM356.20415_S58_mean`, `UHM369.20773_S31_mean`, `UHM370.20774_S43_mean`, `UHM372.20775_S55_mean`, `UHM373.20776_S67_mean`, `UHM374.20777_S79_mean`, `UHM375.20778_S91_mean`, `UHM377.20779_S8_mean`, `UHM38.3376_S36_mean`, `UHM386.20781_S32_mean`, `UHM387.20782_S44_mean`, `UHM414.20583_S55_mean`, `UHM418.20765_S30_mean`, `UHM422.20766_S42_mean`, `UHM425.20767_S54_mean`, `UHM426.20534_S37_mean`, `UHM428.20544_S62_mean`, `UHM429.20559_S52_mean`, `UHM435.20547_S3_mean`, `UHM437.20768_S66_mean`, `UHM439.20564_S17_mean`, `UHM44.3526_S31_mean`, `UHM445.20569_S77_mean`, `UHM447.20783_S56_mean`, `UHM448.20769_S78_mean`, `UHM45.3539_S92_mean`, `UHM454.20770_S90_mean`, `UHM455.20785_S80_mean`, `UHM458.20786_S92_mean`, `UHM459.20787_S9_mean`, `UHM461.20771_S7_mean`, `UHM467.20772_S19_mean`, `UHM470.20533_S25_mean`, `UHM476.20414_S46_mean`, `UHM478.20549_S27_mean`, `UHM479.20551_S51_mean`, `UHM481.20403_S9_mean`, `UHM482.20590_S44_mean`, `UHM483.20603_S10_mean`, `UHM519.20582_S43_mean`, `UHM520.20573_S30_mean`, `UHM746.21478_S117_mean`, `UHM747.21477_S106_mean`, `UHM748.21467_S170_mean`, `UHM748.21487_S129_mean`, `UHM749.21479_S128_mean`, `UHM759.21466_S159_mean`, `UHM759.21486_S118_mean`, `UHM775.21485_S107_mean`, `UHM776.21482_S161_mean`, `UHM777.21484_S183_mean`, `UHM779.21468_S181_mean`, `UHM779.21488_S140_mean`, `UHM782.21480_S139_mean`, `UHM810.21472_S138_mean`, `UHM811.21471_S127_mean`, `UHM813.21481_S150_mean`, `UHM818.21469_S105_mean`, `UHM818.21489_S151_mean`, `UHM819.21473_S149_mean`, `UHM820.21470_S116_mean`, `UHM820.21490_S162_mean`, `UHM827.21474_S160_mean`, `UHM829.21476_S182_mean`, `UHM832.21483_S172_mean`, `UHM836.20385_S78_mean`, `UHM837.20386_S90_mean`, `UHM838.20387_S7_mean`, `UHM891.20384_S66_mean`, `UHM892.20532_S13_mean`, `UHM893.20595_S9_mean`, `UHM894.20540_S14_mean`, `UHM895.20536_S61_mean`, `UHM896.20601_S81_mean`, `UHM897.20591_S56_mean`, `UHM898.20394_S91_mean`, `UHM899.20588_S20_mean`, `UHM900.20395_S8_mean`, `UHM901.20542_S38_mean`, `UHM902.20584_S67_mean`, `UHM903.20587_S8_mean`, `UHM904.20567_S53_mean`, `UHM905.20598_S45_mean`, `UHM906.20565_S29_mean`, `UHM907.20592_S68_mean`, `UHM908.20396_S20_mean`, `UHM909.20557_S28_mean`, `UHM910.20562_S88_mean`, `UHM965.20537_S73_mean`, `UHM966.20743_S51_mean`, `UHM967.20744_S63_mean`, `UHM968.20571_S6_mean`, `UHM969.20745_S75_mean`, `UHM971.20746_S87_mean`, `UHM973.20578_S90_mean`, `UHM974.20432_S72_mean`, `UHM975.20747_S4_mean`, `UHM977.20748_S16_mean`, `UHM978.20749_S28_mean`, `UHM979.20750_S40_mean`, `UHM980.20731_S2_mean`, `UHM981.20539_S2_mean`, `UHM982.20740_S15_mean`, `UHM983.20556_S16_mean`, `UHM984.20751_S52_mean`, `UHM985.20752_S64_mean`, `UHM988.20753_S76_mean`, `UHM989.20754_S88_mean`, `UHM991.20755_S5_mean`, `UHM993.20741_S27_mean`, `UHM996.20610_S94_mean`, `UHM997.20553_S75_mean`, `UHM998.20618_S95_mean`, `UHM999.20617_S83_mean`, `spiked.blank.20433_S84_sd`, `spiked.blank.20817_S84_sd`, `Std2uL.20625_S84_sd`, `StdSwab1uL.20624_S72_sd`, `STP1719.20422_S47_sd`, `STP213.20423_S59_sd`, `STP268.20424_S71_sd`, `STP544.20419_S11_sd`, `STP570.20420_S23_sd`, `STP579.20421_S35_sd`, `STP614.20418_S94_sd`, `UHM1000.20604_S22_sd`, `UHM1001.20609_S82_sd`, `UHM1007.20622_S48_sd`, `UHM1009.20614_S47_sd`, `UHM1010.20621_S36_sd`, `UHM1011.20606_S46_sd`, `UHM1024.20620_S24_sd`, `UHM1026.20607_S58_sd`, `UHM1028.20613_S35_sd`, `UHM1032.20605_S34_sd`, `UHM1033.20619_S12_sd`, `UHM1034.20616_S71_sd`, `UHM1035.20611_S11_sd`, `UHM1036.20612_S23_sd`, `UHM1052.20615_S59_sd`, `UHM1060.20723_S1_sd`, `UHM1065.20724_S13_sd`, `UHM1068.20732_S14_sd`, `UHM1069.20742_S39_sd`, `UHM1070.20725_S25_sd`, `UHM1071.20733_S26_sd`, `UHM1072.20734_S38_sd`, `UHM1073.20735_S50_sd`, `UHM1075.20726_S37_sd`, `UHM1077.20736_S62_sd`, `UHM1078.20727_S49_sd`, `UHM1080.20737_S74_sd`, `UHM1081.20728_S61_sd`, `UHM1088.20738_S86_sd`, `UHM1090.20739_S3_sd`, `UHM1093.20729_S73_sd`, `UHM1095.20730_S85_sd`, `UHM1097.20623_S60_sd`, `UHM1099.20608_S70_sd`, `UHM1100.20788_S21_sd`, `UHM1102.20789_S33_sd`, `UHM1104.20790_S45_sd`, `UHM1105.20791_S57_sd`, `UHM1109.20531_S1_sd`, `UHM1110.20568_S65_sd`, `UHM1113.20792_S69_sd`, `UHM1114.20793_S81_sd`, `UHM1115.20794_S93_sd`, `UHM1117.20795_S10_sd`, `UHM1118.20796_S22_sd`, `UHM1120.20797_S34_sd`, `UHM1124.20798_S46_sd`, `UHM1126.20799_S58_sd`, `UHM1128.20800_S70_sd`, `UHM1140.20555_S4_sd`, `UHM1145.20801_S82_sd`, `UHM1163.20405_S33_sd`, `UHM1164.20402_S92_sd`, `UHM1169.20552_S63_sd`, `UHM1171.20579_S7_sd`, `UHM1176.20404_S21_sd`, `UHM1177.20546_S86_sd`, `UHM1182.20576_S66_sd`, `UHM1210.20802_S94_sd`, `UHM1212.20803_S11_sd`, `UHM1217.20804_S23_sd`, `UHM1218.20805_S35_sd`, `UHM1219.20806_S47_sd`, `UHM1220.20807_S59_sd`, `UHM1221.20808_S71_sd`, `UHM1222.20809_S83_sd`, `UHM1223.20810_S95_sd`, `UHM1225.20811_S12_sd`, `UHM1227.20812_S24_sd`, `UHM1228.20813_S36_sd`, `UHM1237.20814_S48_sd`, `UHM1240.20566_S41_sd`, `UHM1246.20815_S60_sd`, `UHM1247.20816_S72_sd`, `UHM1248.20575_S54_sd`, `UHM1256.20570_S89_sd`, `UHM1260.20596_S21_sd`, `UHM1270.20577_S78_sd`, `UHM1271.20397_S32_sd`, `UHM1272.20398_S44_sd`, `UHM1274.20554_S87_sd`, `UHM1275.20597_S33_sd`, `UHM1282.20599_S57_sd`, `UHM1287.20543_S50_sd`, `UHM1291.20416_S70_sd`, `UHM1296.20550_S39_sd`, `UHM1319.20561_S76_sd`, `UHM1324.20413_S34_sd`, `UHM1327.20545_S74_sd`, `UHM1328.20572_S18_sd`, `UHM1334.20417_S82_sd`, `UHM1338.20399_S56_sd`, `UHM1341.20602_S93_sd`, `UHM1356.20541_S26_sd`, `UHM1380.20580_S19_sd`, `UHM1383.20594_S92_sd`, `UHM1385.20563_S5_sd`, `UHM1399.20756_S17_sd`, `UHM1400.20757_S29_sd`, `UHM1401.20758_S41_sd`, `UHM1402.20759_S53_sd`, `UHM1403.20760_S65_sd`, `UHM1405.20761_S77_sd`, `UHM1406.20762_S89_sd`, `UHM1414.20763_S6_sd`, `UHM1419.20764_S18_sd`, `UHM1427.20389_S31_sd`, `UHM1428.20390_S43_sd`, `UHM1429.20391_S55_sd`, `UHM1430.20392_S67_sd`, `UHM1432.20393_S79_sd`, `UHM1435.20388_S19_sd`, `UHM162.20560_S64_sd`, `UHM198.20585_S79_sd`, `UHM20.3314_S52_sd`, `UHM20.3315_S64_sd`, `UHM204.20409_S81_sd`, `UHM206.20410_S93_sd`, `UHM207.20593_S80_sd`, `UHM208.20411_S10_sd`, 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`UHM356.20415_S58_q75`, `UHM369.20773_S31_q75`, `UHM370.20774_S43_q75`, `UHM372.20775_S55_q75`, `UHM373.20776_S67_q75`, `UHM374.20777_S79_q75`, `UHM375.20778_S91_q75`, `UHM377.20779_S8_q75`, `UHM38.3376_S36_q75`, `UHM386.20781_S32_q75`, `UHM387.20782_S44_q75`, `UHM414.20583_S55_q75`, `UHM418.20765_S30_q75`, `UHM422.20766_S42_q75`, `UHM425.20767_S54_q75`, `UHM426.20534_S37_q75`, `UHM428.20544_S62_q75`, `UHM429.20559_S52_q75`, `UHM435.20547_S3_q75`, `UHM437.20768_S66_q75`, `UHM439.20564_S17_q75`, `UHM44.3526_S31_q75`, `UHM445.20569_S77_q75`, `UHM447.20783_S56_q75`, `UHM448.20769_S78_q75`, `UHM45.3539_S92_q75`, `UHM454.20770_S90_q75`, `UHM455.20785_S80_q75`, `UHM458.20786_S92_q75`, `UHM459.20787_S9_q75`, `UHM461.20771_S7_q75`, `UHM467.20772_S19_q75`, `UHM470.20533_S25_q75`, `UHM476.20414_S46_q75`, `UHM478.20549_S27_q75`, `UHM479.20551_S51_q75`, `UHM481.20403_S9_q75`, `UHM482.20590_S44_q75`, `UHM483.20603_S10_q75`, `UHM519.20582_S43_q75`, `UHM520.20573_S30_q75`, `UHM746.21478_S117_q75`, `UHM747.21477_S106_q75`, `UHM748.21467_S170_q75`, `UHM748.21487_S129_q75`, `UHM749.21479_S128_q75`, `UHM759.21466_S159_q75`, `UHM759.21486_S118_q75`, `UHM775.21485_S107_q75`, `UHM776.21482_S161_q75`, `UHM777.21484_S183_q75`, `UHM779.21468_S181_q75`, `UHM779.21488_S140_q75`, `UHM782.21480_S139_q75`, `UHM810.21472_S138_q75`, `UHM811.21471_S127_q75`, `UHM813.21481_S150_q75`, `UHM818.21469_S105_q75`, `UHM818.21489_S151_q75`, `UHM819.21473_S149_q75`, `UHM820.21470_S116_q75`, `UHM820.21490_S162_q75`, `UHM827.21474_S160_q75`, `UHM829.21476_S182_q75`, `UHM832.21483_S172_q75`, `UHM836.20385_S78_q75`, `UHM837.20386_S90_q75`, `UHM838.20387_S7_q75`, `UHM891.20384_S66_q75`, `UHM892.20532_S13_q75`, `UHM893.20595_S9_q75`, `UHM894.20540_S14_q75`, `UHM895.20536_S61_q75`, `UHM896.20601_S81_q75`, `UHM897.20591_S56_q75`, `UHM898.20394_S91_q75`, `UHM899.20588_S20_q75`, `UHM900.20395_S8_q75`, `UHM901.20542_S38_q75`, `UHM902.20584_S67_q75`, `UHM903.20587_S8_q75`, `UHM904.20567_S53_q75`, `UHM905.20598_S45_q75`, `UHM906.20565_S29_q75`, `UHM907.20592_S68_q75`, `UHM908.20396_S20_q75`, `UHM909.20557_S28_q75`, `UHM910.20562_S88_q75`, `UHM965.20537_S73_q75`, `UHM966.20743_S51_q75`, `UHM967.20744_S63_q75`, `UHM968.20571_S6_q75`, `UHM969.20745_S75_q75`, `UHM971.20746_S87_q75`, `UHM973.20578_S90_q75`, `UHM974.20432_S72_q75`, `UHM975.20747_S4_q75`, `UHM977.20748_S16_q75`, `UHM978.20749_S28_q75`, `UHM979.20750_S40_q75`, `UHM980.20731_S2_q75`, `UHM981.20539_S2_q75`, `UHM982.20740_S15_q75`, `UHM983.20556_S16_q75`, `UHM984.20751_S52_q75`, `UHM985.20752_S64_q75`, `UHM988.20753_S76_q75`, `UHM989.20754_S88_q75`, `UHM991.20755_S5_q75`, `UHM993.20741_S27_q75`, `UHM996.20610_S94_q75`, `UHM997.20553_S75_q75`, `UHM998.20618_S95_q75`, `UHM999.20617_S83_q75` 
## header has 1 row(s) 
## body has 1 row(s) 
## original dataset sample: 
##   spiked.blank.20433_S84_mean spiked.blank.20817_S84_mean Std2uL.20625_S84_mean
## 1                 0.004776379                    39.99696              357.6517
##   StdSwab1uL.20624_S72_mean STP1719.20422_S47_mean STP213.20423_S59_mean
## 1                  115.5526               6.016175              5.578485
##   STP268.20424_S71_mean STP544.20419_S11_mean STP570.20420_S23_mean
## 1              9.198111              1.443443              5.135258
##   STP579.20421_S35_mean STP614.20418_S94_mean UHM1000.20604_S22_mean
## 1              9.599436            0.02051672               9.208207
##   UHM1001.20609_S82_mean UHM1007.20622_S48_mean UHM1009.20614_S47_mean
## 1               5.057642               8.157403               40.14351
##   UHM1010.20621_S36_mean UHM1011.20606_S46_mean UHM1024.20620_S24_mean
## 1               6.117347               11.24587               21.00988
##   UHM1026.20607_S58_mean UHM1028.20613_S35_mean UHM1032.20605_S34_mean
## 1               4.341077               7.477964              0.9516934
##   UHM1033.20619_S12_mean UHM1034.20616_S71_mean UHM1035.20611_S11_mean
## 1               8.003474               4.375163               2.745983
##   UHM1036.20612_S23_mean UHM1052.20615_S59_mean UHM1060.20723_S1_mean
## 1               10.70918               13.34064              20.61572
##   UHM1065.20724_S13_mean UHM1068.20732_S14_mean UHM1069.20742_S39_mean
## 1               24.97482               31.81253               6.660551
##   UHM1070.20725_S25_mean UHM1071.20733_S26_mean UHM1072.20734_S38_mean
## 1               27.98871               2.735454               3.985997
##   UHM1073.20735_S50_mean UHM1075.20726_S37_mean UHM1077.20736_S62_mean
## 1               13.96255               12.68986               216.4361
##   UHM1078.20727_S49_mean UHM1080.20737_S74_mean UHM1081.20728_S61_mean
## 1               5.548632               28.64383               9.183565
##   UHM1088.20738_S86_mean UHM1090.20739_S3_mean UHM1093.20729_S73_mean
## 1                12.4188              10.33076               3.932479
##   UHM1095.20730_S85_mean UHM1097.20623_S60_mean UHM1099.20608_S70_mean
## 1               9.067412               14.07827             0.09433348
##   UHM1100.20788_S21_mean UHM1102.20789_S33_mean UHM1104.20790_S45_mean
## 1               8.293096               6.559488               5.100087
##   UHM1105.20791_S57_mean UHM1109.20531_S1_mean UHM1110.20568_S65_mean
## 1               5.874729              9.408055               12.44551
##   UHM1113.20792_S69_mean UHM1114.20793_S81_mean UHM1115.20794_S93_mean
## 1               41.73838               4.717759               3.341294
##   UHM1117.20795_S10_mean UHM1118.20796_S22_mean UHM1120.20797_S34_mean
## 1               2.830547                6.70343               14.52909
##   UHM1124.20798_S46_mean UHM1126.20799_S58_mean UHM1128.20800_S70_mean
## 1               20.90056               9.393834               8.405341
##   UHM1140.20555_S4_mean UHM1145.20801_S82_mean UHM1163.20405_S33_mean
## 1              6.603669               6.443118                9.66294
##   UHM1164.20402_S92_mean UHM1169.20552_S63_mean UHM1171.20579_S7_mean
## 1               1.670538                1.79581               7.85812
##   UHM1176.20404_S21_mean UHM1177.20546_S86_mean UHM1182.20576_S66_mean
## 1                10.0457               14.30525               8.088906
##   UHM1210.20802_S94_mean UHM1212.20803_S11_mean UHM1217.20804_S23_mean
## 1               9.148068               12.88537               14.45647
##   UHM1218.20805_S35_mean UHM1219.20806_S47_mean UHM1220.20807_S59_mean
## 1               5.822514               8.245007               3.155341
##   UHM1221.20808_S71_mean UHM1222.20809_S83_mean UHM1223.20810_S95_mean
## 1               2.778224               14.42651               3.856817
##   UHM1225.20811_S12_mean UHM1227.20812_S24_mean UHM1228.20813_S36_mean
## 1                5.58033               18.29223               9.268129
##   UHM1237.20814_S48_mean UHM1240.20566_S41_mean UHM1246.20815_S60_mean
## 1                8.67564               22.78669               8.846613
##   UHM1247.20816_S72_mean UHM1248.20575_S54_mean UHM1256.20570_S89_mean
## 1               7.938233               39.53702               93.17173
##   UHM1260.20596_S21_mean UHM1270.20577_S78_mean UHM1271.20397_S32_mean
## 1               60.85345               4.723621                29.5673
##   UHM1272.20398_S44_mean UHM1274.20554_S87_mean UHM1275.20597_S33_mean
## 1               45.55243               7.605623               18.65317
##   UHM1282.20599_S57_mean UHM1287.20543_S50_mean UHM1291.20416_S70_mean
## 1               35.85041               5.013352               9.975033
##   UHM1296.20550_S39_mean UHM1319.20561_S76_mean UHM1324.20413_S34_mean
## 1               17.27714               39.08554               16.08652
##   UHM1327.20545_S74_mean UHM1328.20572_S18_mean UHM1334.20417_S82_mean
## 1               26.65849               23.61116               5.170756
##   UHM1338.20399_S56_mean UHM1341.20602_S93_mean UHM1356.20541_S26_mean
## 1               16.45864               44.83836               30.36029
##   UHM1380.20580_S19_mean UHM1383.20594_S92_mean UHM1385.20563_S5_mean
## 1               26.76335               16.14698               19.0152
##   UHM1399.20756_S17_mean UHM1400.20757_S29_mean UHM1401.20758_S41_mean
## 1               9.562961               8.302323               11.33891
##   UHM1402.20759_S53_mean UHM1403.20760_S65_mean UHM1405.20761_S77_mean
## 1               13.06524               34.02746                8.87462
##   UHM1406.20762_S89_mean UHM1414.20763_S6_mean UHM1419.20764_S18_mean
## 1               18.33923              21.46939               4.909249
##   UHM1427.20389_S31_mean UHM1428.20390_S43_mean UHM1429.20391_S55_mean
## 1               5.721667               23.09574               2.641337
##   UHM1430.20392_S67_mean UHM1432.20393_S79_mean UHM1435.20388_S19_mean
## 1               19.55645               4.863439               9.075554
##   UHM162.20560_S64_mean UHM198.20585_S79_mean UHM20.3314_S52_mean
## 1              39.94214              21.60139            23.85117
##   UHM20.3315_S64_mean UHM204.20409_S81_mean UHM206.20410_S93_mean
## 1            13.14796                4.2132             0.7453322
##   UHM207.20593_S80_mean UHM208.20411_S10_mean UHM211.20406_S45_mean
## 1              11.44019              24.49077               113.244
##   UHM215.20408_S69_mean UHM216.20429_S36_mean UHM219.20430_S48_mean
## 1              3.450825              2.892531              126.0759
##   UHM236.20431_S60_mean UHM238.20407_S57_mean UHM245.20538_S85_mean
## 1              5.773556              18.91696              42.26617
##   UHM252.20558_S40_mean UHM267.20400_S68_mean UHM274.20581_S31_mean
## 1              13.40328              18.07165              25.07208
##   UHM276.20586_S91_mean UHM280.20401_S80_mean UHM286.20425_S83_mean
## 1              13.81828              25.21092              1.470365
##   UHM289.20426_S95_mean UHM294.20427_S12_mean UHM298.20600_S69_mean
## 1           0.001411203              6.288428              31.25326
##   UHM325.20548_S15_mean UHM337.20412_S22_mean UHM354.20535_S49_mean
## 1               5.97449              6.219713              34.74294
##   UHM356.20415_S58_mean UHM369.20773_S31_mean UHM370.20774_S43_mean
## 1              15.17792               17.3604              14.53506
##   UHM372.20775_S55_mean UHM373.20776_S67_mean UHM374.20777_S79_mean
## 1              2.690187              10.41424              8.884824
##   UHM375.20778_S91_mean UHM377.20779_S8_mean UHM38.3376_S36_mean
## 1              23.03495             11.99077            52.33402
##   UHM386.20781_S32_mean UHM387.20782_S44_mean UHM414.20583_S55_mean
## 1              12.90881              3.533652              15.70332
##   UHM418.20765_S30_mean UHM422.20766_S42_mean UHM425.20767_S54_mean
## 1              11.05319              27.84835              9.920538
##   UHM426.20534_S37_mean UHM428.20544_S62_mean UHM429.20559_S52_mean
## 1              30.10237              2.388841              27.78506
##   UHM435.20547_S3_mean UHM437.20768_S66_mean UHM439.20564_S17_mean
## 1             16.30938              3.992076              8.962657
##   UHM44.3526_S31_mean UHM445.20569_S77_mean UHM447.20783_S56_mean
## 1            4.654147              4.048089                29.118
##   UHM448.20769_S78_mean UHM45.3539_S92_mean UHM454.20770_S90_mean
## 1              21.14525            25.97959              23.51129
##   UHM455.20785_S80_mean UHM458.20786_S92_mean UHM459.20787_S9_mean
## 1              19.06633              4.557317             8.370386
##   UHM461.20771_S7_mean UHM467.20772_S19_mean UHM470.20533_S25_mean
## 1             20.42271              21.53246              2.409249
##   UHM476.20414_S46_mean UHM478.20549_S27_mean UHM479.20551_S51_mean
## 1              7.973947              2.148176              5.745332
##   UHM481.20403_S9_mean UHM482.20590_S44_mean UHM483.20603_S10_mean
## 1             2.293964            0.03538862             0.8365176
##   UHM519.20582_S43_mean UHM520.20573_S30_mean UHM746.21478_S117_mean
## 1              21.75119              14.97243               503.4356
##   UHM747.21477_S106_mean UHM748.21467_S170_mean UHM748.21487_S129_mean
## 1              0.3376031                237.051                 244.72
##   UHM749.21479_S128_mean UHM759.21466_S159_mean UHM759.21486_S118_mean
## 1               293.4701               10.37961                34.6738
##   UHM775.21485_S107_mean UHM776.21482_S161_mean UHM777.21484_S183_mean
## 1               26.00423               49.50836                134.679
##   UHM779.21468_S181_mean UHM779.21488_S140_mean UHM782.21480_S139_mean
## 1               451.2466                      0                1.69442
##   UHM810.21472_S138_mean UHM811.21471_S127_mean UHM813.21481_S150_mean
## 1               176.2893                19.5787               31.72471
##   UHM818.21469_S105_mean UHM818.21489_S151_mean UHM819.21473_S149_mean
## 1               56.20614              0.1389492               9.364416
##   UHM820.21470_S116_mean UHM820.21490_S162_mean UHM827.21474_S160_mean
## 1               7.281698            0.003039514               24.91609
##   UHM829.21476_S182_mean UHM832.21483_S172_mean UHM836.20385_S78_mean
## 1               40.24837               775.9983              5.111051
##   UHM837.20386_S90_mean UHM838.20387_S7_mean UHM891.20384_S66_mean
## 1              1.526704             15.05211               3.83782
##   UHM892.20532_S13_mean UHM893.20595_S9_mean UHM894.20540_S14_mean
## 1                20.637             5.598567              4.601607
##   UHM895.20536_S61_mean UHM896.20601_S81_mean UHM897.20591_S56_mean
## 1              20.01064              28.09944              52.68519
##   UHM898.20394_S91_mean UHM899.20588_S20_mean UHM900.20395_S8_mean
## 1              3.050912              19.07816             13.20104
##   UHM901.20542_S38_mean UHM902.20584_S67_mean UHM903.20587_S8_mean
## 1              33.00836              2.835432             3.879614
##   UHM904.20567_S53_mean UHM905.20598_S45_mean UHM906.20565_S29_mean
## 1              19.00499              11.23849               18.5787
##   UHM907.20592_S68_mean UHM908.20396_S20_mean UHM909.20557_S28_mean
## 1              5.182154              9.693443              2.078702
##   UHM910.20562_S88_mean UHM965.20537_S73_mean UHM966.20743_S51_mean
## 1              8.762918              8.188884              6.056557
##   UHM967.20744_S63_mean UHM968.20571_S6_mean UHM969.20745_S75_mean
## 1               10.9556             14.32469              17.09824
##   UHM971.20746_S87_mean UHM973.20578_S90_mean UHM974.20432_S72_mean
## 1              8.536257              16.88276              1.862245
##   UHM975.20747_S4_mean UHM977.20748_S16_mean UHM978.20749_S28_mean
## 1             12.05818              26.11442               5.38211
##   UHM979.20750_S40_mean UHM980.20731_S2_mean UHM981.20539_S2_mean
## 1              5.266717             2.911203             11.09878
##   UHM982.20740_S15_mean UHM983.20556_S16_mean UHM984.20751_S52_mean
## 1              5.355623               1.79277              10.18519
##   UHM985.20752_S64_mean UHM988.20753_S76_mean UHM989.20754_S88_mean
## 1              2.953647              11.38081              16.42966
##   UHM991.20755_S5_mean UHM993.20741_S27_mean UHM996.20610_S94_mean
## 1             17.04798              17.47612              8.971559
##   UHM997.20553_S75_mean UHM998.20618_S95_mean UHM999.20617_S83_mean
## 1              9.519214              16.21461              14.60975
##   spiked.blank.20433_S84_sd spiked.blank.20817_S84_sd Std2uL.20625_S84_sd
## 1                 0.4584328                  3837.822            34327.02
##   StdSwab1uL.20624_S72_sd STP1719.20422_S47_sd STP213.20423_S59_sd
## 1                9457.827             199.4625            181.4103
##   STP268.20424_S71_sd STP544.20419_S11_sd STP570.20420_S23_sd
## 1            340.4533            137.5725            375.7074
##   STP579.20421_S35_sd STP614.20418_S94_sd UHM1000.20604_S22_sd
## 1            673.8552            1.763978             260.5709
##   UHM1001.20609_S82_sd UHM1007.20622_S48_sd UHM1009.20614_S47_sd
## 1             156.7285             428.6303             3431.514
##   UHM1010.20621_S36_sd UHM1011.20606_S46_sd UHM1024.20620_S24_sd
## 1             120.6173             573.8612             1919.708
##   UHM1026.20607_S58_sd UHM1028.20613_S35_sd UHM1032.20605_S34_sd
## 1             172.5067              349.934             34.10332
##   UHM1033.20619_S12_sd UHM1034.20616_S71_sd UHM1035.20611_S11_sd
## 1             413.4289             224.0273             135.4633
##   UHM1036.20612_S23_sd UHM1052.20615_S59_sd UHM1060.20723_S1_sd
## 1             789.8326             690.6257            1548.774
##   UHM1065.20724_S13_sd UHM1068.20732_S14_sd UHM1069.20742_S39_sd
## 1             2281.347               2336.6             187.0706
##   UHM1070.20725_S25_sd UHM1071.20733_S26_sd UHM1072.20734_S38_sd
## 1             1997.883             121.9915              121.262
##   UHM1073.20735_S50_sd UHM1075.20726_S37_sd UHM1077.20736_S62_sd
## 1             1075.641             656.7168             20605.39
##   UHM1078.20727_S49_sd UHM1080.20737_S74_sd UHM1081.20728_S61_sd
## 1             181.8163             1441.164             874.3637
##   UHM1088.20738_S86_sd UHM1090.20739_S3_sd UHM1093.20729_S73_sd
## 1             349.6617            249.1892             320.7827
##   UHM1095.20730_S85_sd UHM1097.20623_S60_sd UHM1099.20608_S70_sd
## 1             334.9327             488.1832             5.515083
##   UHM1100.20788_S21_sd UHM1102.20789_S33_sd UHM1104.20790_S45_sd
## 1             258.4523             301.2004             279.7654
##   UHM1105.20791_S57_sd UHM1109.20531_S1_sd UHM1110.20568_S65_sd
## 1             318.8914            892.8903             379.6909
##   UHM1113.20792_S69_sd UHM1114.20793_S81_sd UHM1115.20794_S93_sd
## 1             3771.379             200.0252             138.7811
##   UHM1117.20795_S10_sd UHM1118.20796_S22_sd UHM1120.20797_S34_sd
## 1             55.02554             241.7785             1208.683
##   UHM1124.20798_S46_sd UHM1126.20799_S58_sd UHM1128.20800_S70_sd
## 1             670.5941             260.1035             344.3808
##   UHM1140.20555_S4_sd UHM1145.20801_S82_sd UHM1163.20405_S33_sd
## 1            240.9509             370.6076              361.684
##   UHM1164.20402_S92_sd UHM1169.20552_S63_sd UHM1171.20579_S7_sd
## 1              74.1127             92.15168            253.1672
##   UHM1176.20404_S21_sd UHM1177.20546_S86_sd UHM1182.20576_S66_sd
## 1             520.6518             557.3127             570.4734
##   UHM1210.20802_S94_sd UHM1212.20803_S11_sd UHM1217.20804_S23_sd
## 1             264.6138             541.0537             998.1715
##   UHM1218.20805_S35_sd UHM1219.20806_S47_sd UHM1220.20807_S59_sd
## 1             273.0741             331.6981             92.97026
##   UHM1221.20808_S71_sd UHM1222.20809_S83_sd UHM1223.20810_S95_sd
## 1             131.1366             533.4219             101.1954
##   UHM1225.20811_S12_sd UHM1227.20812_S24_sd UHM1228.20813_S36_sd
## 1             222.6452             946.0996             263.6471
##   UHM1237.20814_S48_sd UHM1240.20566_S41_sd UHM1246.20815_S60_sd
## 1             409.4388              875.684             326.1371
##   UHM1247.20816_S72_sd UHM1248.20575_S54_sd UHM1256.20570_S89_sd
## 1             336.4837              1864.08             4702.348
##   UHM1260.20596_S21_sd UHM1270.20577_S78_sd UHM1271.20397_S32_sd
## 1              4666.64             380.3785             1390.051
##   UHM1272.20398_S44_sd UHM1274.20554_S87_sd UHM1275.20597_S33_sd
## 1             3630.122             302.3414             708.7168
##   UHM1282.20599_S57_sd UHM1287.20543_S50_sd UHM1291.20416_S70_sd
## 1             1282.894             338.5289              283.284
##   UHM1296.20550_S39_sd UHM1319.20561_S76_sd UHM1324.20413_S34_sd
## 1             1087.751             1889.755             478.8152
##   UHM1327.20545_S74_sd UHM1328.20572_S18_sd UHM1334.20417_S82_sd
## 1              1263.95              919.316              161.838
##   UHM1338.20399_S56_sd UHM1341.20602_S93_sd UHM1356.20541_S26_sd
## 1             534.3128             3452.914             1052.043
##   UHM1380.20580_S19_sd UHM1383.20594_S92_sd UHM1385.20563_S5_sd
## 1             944.1403             621.2758            1554.309
##   UHM1399.20756_S17_sd UHM1400.20757_S29_sd UHM1401.20758_S41_sd
## 1             300.5565             537.7485             390.1608
##   UHM1402.20759_S53_sd UHM1403.20760_S65_sd UHM1405.20761_S77_sd
## 1             372.4807             1991.607              224.322
##   UHM1406.20762_S89_sd UHM1414.20763_S6_sd UHM1419.20764_S18_sd
## 1             443.1395            912.4244             144.0148
##   UHM1427.20389_S31_sd UHM1428.20390_S43_sd UHM1429.20391_S55_sd
## 1             247.6804              1821.52             129.5644
##   UHM1430.20392_S67_sd UHM1432.20393_S79_sd UHM1435.20388_S19_sd
## 1              1197.89             239.0004             219.5548
##   UHM162.20560_S64_sd UHM198.20585_S79_sd UHM20.3314_S52_sd UHM20.3315_S64_sd
## 1            2038.443            1264.205          1967.319          883.3827
##   UHM204.20409_S81_sd UHM206.20410_S93_sd UHM207.20593_S80_sd
## 1            146.0356            28.41686            787.1001
##   UHM208.20411_S10_sd UHM211.20406_S45_sd UHM215.20408_S69_sd
## 1            1333.483            10462.81            298.0452
##   UHM216.20429_S36_sd UHM219.20430_S48_sd UHM236.20431_S60_sd
## 1            194.6522            11577.25            201.1663
##   UHM238.20407_S57_sd UHM245.20538_S85_sd UHM252.20558_S40_sd
## 1             1077.58            3191.541            454.7642
##   UHM267.20400_S68_sd UHM274.20581_S31_sd UHM276.20586_S91_sd
## 1            569.1757            1133.963            624.3576
##   UHM280.20401_S80_sd UHM286.20425_S83_sd UHM289.20426_S95_sd
## 1            1469.155            79.44984           0.1026104
##   UHM294.20427_S12_sd UHM298.20600_S69_sd UHM325.20548_S15_sd
## 1            224.4329            1887.009            166.0294
##   UHM337.20412_S22_sd UHM354.20535_S49_sd UHM356.20415_S58_sd
## 1            286.5993            1370.193             450.903
##   UHM369.20773_S31_sd UHM370.20774_S43_sd UHM372.20775_S55_sd
## 1            550.5194            487.7792            211.0535
##   UHM373.20776_S67_sd UHM374.20777_S79_sd UHM375.20778_S91_sd
## 1            444.2917            293.5235            1359.093
##   UHM377.20779_S8_sd UHM38.3376_S36_sd UHM386.20781_S32_sd UHM387.20782_S44_sd
## 1           398.5069          3713.544            354.3424            149.9313
##   UHM414.20583_S55_sd UHM418.20765_S30_sd UHM422.20766_S42_sd
## 1            631.9773            365.6069            1550.099
##   UHM425.20767_S54_sd UHM426.20534_S37_sd UHM428.20544_S62_sd
## 1             466.705            1484.465            157.6026
##   UHM429.20559_S52_sd UHM435.20547_S3_sd UHM437.20768_S66_sd
## 1            825.3063           530.5878            139.5958
##   UHM439.20564_S17_sd UHM44.3526_S31_sd UHM445.20569_S77_sd UHM447.20783_S56_sd
## 1            352.0468          316.0349            214.4998            1224.856
##   UHM448.20769_S78_sd UHM45.3539_S92_sd UHM454.20770_S90_sd UHM455.20785_S80_sd
## 1            1342.785          1771.043            1338.427            1069.783
##   UHM458.20786_S92_sd UHM459.20787_S9_sd UHM461.20771_S7_sd UHM467.20772_S19_sd
## 1            151.8565           318.5813            594.151            1038.911
##   UHM470.20533_S25_sd UHM476.20414_S46_sd UHM478.20549_S27_sd
## 1            167.2901            268.0634            170.0588
##   UHM479.20551_S51_sd UHM481.20403_S9_sd UHM482.20590_S44_sd
## 1            368.5505           62.60031             1.99909
##   UHM483.20603_S10_sd UHM519.20582_S43_sd UHM520.20573_S30_sd
## 1            27.60242            776.8161            585.7043
##   UHM746.21478_S117_sd UHM747.21477_S106_sd UHM748.21467_S170_sd
## 1             48204.54             13.36252             22638.64
##   UHM748.21487_S129_sd UHM749.21479_S128_sd UHM759.21466_S159_sd
## 1             23388.98             28095.95             942.4137
##   UHM759.21486_S118_sd UHM775.21485_S107_sd UHM776.21482_S161_sd
## 1             3240.704             2487.594             4742.853
##   UHM777.21484_S183_sd UHM779.21468_S181_sd UHM779.21488_S140_sd
## 1             12912.56             43285.63                    0
##   UHM782.21480_S139_sd UHM810.21472_S138_sd UHM811.21471_S127_sd
## 1             160.5278             16876.08              1833.49
##   UHM813.21481_S150_sd UHM818.21469_S105_sd UHM818.21489_S151_sd
## 1             3026.918             5360.311             9.956992
##   UHM819.21473_S149_sd UHM820.21470_S116_sd UHM820.21490_S162_sd
## 1             869.4057             688.4577            0.2083677
##   UHM827.21474_S160_sd UHM829.21476_S182_sd UHM832.21483_S172_sd
## 1             2047.245             3760.014             73237.08
##   UHM836.20385_S78_sd UHM837.20386_S90_sd UHM838.20387_S7_sd
## 1            279.8225             98.6592           788.1735
##   UHM891.20384_S66_sd UHM892.20532_S13_sd UHM893.20595_S9_sd
## 1             252.509            1371.546           144.8056
##   UHM894.20540_S14_sd UHM895.20536_S61_sd UHM896.20601_S81_sd
## 1            255.6911            854.5812            1367.993
##   UHM897.20591_S56_sd UHM898.20394_S91_sd UHM899.20588_S20_sd
## 1            3726.469             171.383            651.9474
##   UHM900.20395_S8_sd UHM901.20542_S38_sd UHM902.20584_S67_sd UHM903.20587_S8_sd
## 1           495.6867            1621.214            141.9833           207.1982
##   UHM904.20567_S53_sd UHM905.20598_S45_sd UHM906.20565_S29_sd
## 1             665.932            606.1551            1174.737
##   UHM907.20592_S68_sd UHM908.20396_S20_sd UHM909.20557_S28_sd
## 1            179.2343            487.3568            99.12479
##   UHM910.20562_S88_sd UHM965.20537_S73_sd UHM966.20743_S51_sd
## 1            304.6754             714.661             178.339
##   UHM967.20744_S63_sd UHM968.20571_S6_sd UHM969.20745_S75_sd
## 1            490.4001           1331.936            759.0453
##   UHM971.20746_S87_sd UHM973.20578_S90_sd UHM974.20432_S72_sd
## 1            283.7502            1452.297            121.4982
##   UHM975.20747_S4_sd UHM977.20748_S16_sd UHM978.20749_S28_sd
## 1           333.5943            1200.685            178.5628
##   UHM979.20750_S40_sd UHM980.20731_S2_sd UHM981.20539_S2_sd UHM982.20740_S15_sd
## 1            128.1956           124.3727           551.9762            120.5603
##   UHM983.20556_S16_sd UHM984.20751_S52_sd UHM985.20752_S64_sd
## 1            99.79664            445.6342            81.83254
##   UHM988.20753_S76_sd UHM989.20754_S88_sd UHM991.20755_S5_sd
## 1            512.3247            644.4926           586.2617
##   UHM993.20741_S27_sd UHM996.20610_S94_sd UHM997.20553_S75_sd
## 1            677.6175            556.4158            689.3695
##   UHM998.20618_S95_sd UHM999.20617_S83_sd spiked.blank.20433_S84_se
## 1            362.4453            714.6812               0.004776379
##   spiked.blank.20817_S84_se Std2uL.20625_S84_se StdSwab1uL.20624_S72_se
## 1                    39.986            357.6508                98.54042
##   STP1719.20422_S47_se STP213.20423_S59_se STP268.20424_S71_se
## 1             2.078185              1.8901            3.547159
##   STP544.20419_S11_se STP570.20420_S23_se STP579.20421_S35_se
## 1            1.433358            3.914469            7.020848
##   STP614.20418_S94_se UHM1000.20604_S22_se UHM1001.20609_S82_se
## 1          0.01837876             2.714869             1.632943
##   UHM1007.20622_S48_se UHM1009.20614_S47_se UHM1010.20621_S36_se
## 1             4.465868              35.7527             1.256702
##   UHM1011.20606_S46_se UHM1024.20620_S24_se UHM1026.20607_S58_se
## 1             5.979019             20.00129             1.797335
##   UHM1028.20613_S35_se UHM1032.20605_S34_se UHM1033.20619_S12_se
## 1             3.645937              0.35532             4.307486
##   UHM1034.20616_S71_se UHM1035.20611_S11_se UHM1036.20612_S23_se
## 1             2.334125             1.411382             8.229209
##   UHM1052.20615_S59_se UHM1060.20723_S1_se UHM1065.20724_S13_se
## 1             7.195579            16.13657             23.76919
##   UHM1068.20732_S14_se UHM1069.20742_S39_se UHM1070.20725_S25_se
## 1             24.34487             1.949075              20.8158
##   UHM1071.20733_S26_se UHM1072.20734_S38_se UHM1073.20735_S50_se
## 1             1.271021              1.26342             11.20702
##   UHM1075.20726_S37_se UHM1077.20736_S62_se UHM1078.20727_S49_se
## 1             6.842285             214.6861             1.894331
##   UHM1080.20737_S74_se UHM1081.20728_S61_se UHM1088.20738_S86_se
## 1             15.01538             9.109932               3.6431
##   UHM1090.20739_S3_se UHM1093.20729_S73_se UHM1095.20730_S85_se
## 1            2.596284             3.342212             3.489639
##   UHM1097.20623_S60_se UHM1099.20608_S70_se UHM1100.20788_S21_se
## 1             5.086346           0.05746125             2.692795
##   UHM1102.20789_S33_se UHM1104.20790_S45_se UHM1105.20791_S57_se
## 1             3.138186             2.914855             3.322506
##   UHM1109.20531_S1_se UHM1110.20568_S65_se UHM1113.20792_S69_se
## 1            9.302959             3.955972             39.29372
##   UHM1114.20793_S81_se UHM1115.20794_S93_se UHM1117.20795_S10_se
## 1             2.084048              1.44595            0.5733071
##   UHM1118.20796_S22_se UHM1120.20797_S34_se UHM1124.20798_S46_se
## 1             2.519073             12.59319             6.986872
##   UHM1126.20799_S58_se UHM1128.20800_S70_se UHM1140.20555_S4_se
## 1                 2.71             3.588079             2.51045
##   UHM1145.20801_S82_se UHM1163.20405_S33_se UHM1164.20402_S92_se
## 1             3.861334             3.768359            0.7721749
##   UHM1169.20552_S63_se UHM1171.20579_S7_se UHM1176.20404_S21_se
## 1            0.9601217            2.637731             5.424634
##   UHM1177.20546_S86_se UHM1182.20576_S66_se UHM1210.20802_S94_se
## 1             5.806601             5.943721             2.756993
##   UHM1212.20803_S11_se UHM1217.20804_S23_se UHM1218.20805_S35_se
## 1             5.637199             10.39988             2.845139
##   UHM1219.20806_S47_se UHM1220.20807_S59_se UHM1221.20808_S71_se
## 1             3.455938            0.9686505             1.366303
##   UHM1222.20809_S83_se UHM1223.20810_S95_se UHM1225.20811_S12_se
## 1             5.557684             1.054348             2.319724
##   UHM1227.20812_S24_se UHM1228.20813_S36_se UHM1237.20814_S48_se
## 1             9.857344              2.74692             4.265913
##   UHM1240.20566_S41_se UHM1246.20815_S60_se UHM1247.20816_S72_se
## 1             9.123688             3.397999             3.505799
##   UHM1248.20575_S54_se UHM1256.20570_S89_se UHM1260.20596_S21_se
## 1             19.42172             48.99343             48.62138
##   UHM1270.20577_S78_se UHM1271.20397_S32_se UHM1272.20398_S44_se
## 1             3.963136             14.48284             37.82198
##   UHM1274.20554_S87_se UHM1275.20597_S33_se UHM1282.20599_S57_se
## 1             3.150073             7.384069             13.36638
##   UHM1287.20543_S50_se UHM1291.20416_S70_se UHM1296.20550_S39_se
## 1             3.527109             2.951515              11.3332
##   UHM1319.20561_S76_se UHM1324.20413_S34_se UHM1327.20545_S74_se
## 1             19.68922             4.988741             13.16901
##   UHM1328.20572_S18_se UHM1334.20417_S82_se UHM1338.20399_S56_se
## 1             9.578287             1.686179             5.566967
##   UHM1341.20602_S93_se UHM1356.20541_S26_se UHM1380.20580_S19_se
## 1             35.97566             10.96116              9.83693
##   UHM1383.20594_S92_se UHM1385.20563_S5_se UHM1399.20756_S17_se
## 1             6.473027            16.19424             3.131477
##   UHM1400.20757_S29_se UHM1401.20758_S41_se UHM1402.20759_S53_se
## 1             5.602763             4.065057              3.88085
##   UHM1403.20760_S65_se UHM1405.20761_S77_se UHM1406.20762_S89_se
## 1             20.75041             2.337195             4.617039
##   UHM1414.20763_S6_se UHM1419.20764_S18_se UHM1427.20389_S31_se
## 1            9.506484              1.50048             2.580564
##   UHM1428.20390_S43_se UHM1429.20391_S55_se UHM1430.20392_S67_se
## 1             18.97828             1.349922             12.48073
##   UHM1432.20393_S79_se UHM1435.20388_S19_se UHM162.20560_S64_se
## 1             2.490128             2.287526             21.2384
##   UHM198.20585_S79_se UHM20.3314_S52_se UHM20.3315_S64_se UHM204.20409_S81_se
## 1            13.17166          20.49736          9.203901            1.521534
##   UHM206.20410_S93_se UHM207.20593_S80_se UHM208.20411_S10_se
## 1           0.2960732            8.200739            13.89346
##   UHM211.20406_S45_se UHM215.20408_S69_se UHM216.20429_S36_se
## 1            109.0113            3.105312            2.028067
##   UHM219.20430_S48_se UHM236.20431_S60_se UHM238.20407_S57_se
## 1            120.6226            2.095937            11.22723
##   UHM245.20538_S85_se UHM252.20558_S40_se UHM267.20400_S68_se
## 1            33.25243            4.738156            5.930201
##   UHM274.20581_S31_se UHM276.20586_S91_se UHM280.20401_S80_se
## 1            11.81468            6.505137            15.30702
##   UHM286.20425_S83_se UHM289.20426_S95_se UHM294.20427_S12_se
## 1           0.8277822          0.00106909            2.338351
##   UHM298.20600_S69_se UHM325.20548_S15_se UHM337.20412_S22_se
## 1            19.66061            1.729849            2.986058
##   UHM354.20535_S49_se UHM356.20415_S58_se UHM369.20773_S31_se
## 1            14.27594            4.697926            5.735822
##   UHM370.20774_S43_se UHM372.20775_S55_se UHM373.20776_S67_se
## 1            5.082136            2.198951            4.629043
##   UHM374.20777_S79_se UHM375.20778_S91_se UHM377.20779_S8_se UHM38.3376_S36_se
## 1            3.058201            14.16029           4.152015          38.69115
##   UHM386.20781_S32_se UHM387.20782_S44_se UHM414.20583_S55_se
## 1            3.691868            1.562123            6.584526
##   UHM418.20765_S30_se UHM422.20766_S42_se UHM425.20767_S54_se
## 1            3.809232            16.15037            4.862566
##   UHM426.20534_S37_se UHM428.20544_S62_se UHM429.20559_S52_se
## 1            15.46654             1.64205            8.598807
##   UHM435.20547_S3_se UHM437.20768_S66_se UHM439.20564_S17_se UHM44.3526_S31_se
## 1           5.528156            1.454439             3.66795          3.292745
##   UHM445.20569_S77_se UHM447.20783_S56_se UHM448.20769_S78_se UHM45.3539_S92_se
## 1            2.234857            12.76168            13.99039          18.45237
##   UHM454.20770_S90_se UHM455.20785_S80_se UHM458.20786_S92_se
## 1            13.94498            11.14599            1.582182
##   UHM459.20787_S9_se UHM461.20771_S7_se UHM467.20772_S19_se UHM470.20533_S25_se
## 1           3.319276           6.190416            10.82434            1.742983
##   UHM476.20414_S46_se UHM478.20549_S27_se UHM479.20551_S51_se
## 1            2.792933             1.77183            3.839901
##   UHM481.20403_S9_se UHM482.20590_S44_se UHM483.20603_S10_se
## 1          0.6522281          0.02082837           0.2875876
##   UHM519.20582_S43_se UHM520.20573_S30_se UHM746.21478_S117_se
## 1            8.093591             6.10241             502.2397
##   UHM747.21477_S106_se UHM748.21467_S170_se UHM748.21487_S129_se
## 1            0.1392231             235.8704             243.6881
##   UHM749.21479_S128_se UHM759.21466_S159_se UHM759.21486_S118_se
## 1             292.7296             9.818941             33.76467
##   UHM775.21485_S107_se UHM776.21482_S161_se UHM777.21484_S183_se
## 1             25.91807             49.41544             134.5351
##   UHM779.21468_S181_se UHM779.21488_S140_se UHM782.21480_S139_se
## 1             450.9899                    0             1.672527
##   UHM810.21472_S138_se UHM811.21471_S127_se UHM813.21481_S150_se
## 1             175.8307               19.103             31.53725
##   UHM818.21469_S105_se UHM818.21489_S151_se UHM819.21473_S149_se
## 1              55.8487            0.1037412             9.058275
##   UHM820.21470_S116_se UHM820.21490_S162_se UHM827.21474_S160_se
## 1             7.172992          0.002170968              21.3301
##   UHM829.21476_S182_se UHM832.21483_S172_se UHM836.20385_S78_se
## 1             39.17531             763.0519             2.91545
##   UHM837.20386_S90_se UHM838.20387_S7_se UHM891.20384_S66_se
## 1            1.027923           8.211923            2.630873
##   UHM892.20532_S13_se UHM893.20595_S9_se UHM894.20540_S14_se
## 1            14.29003           1.508719            2.664027
##   UHM895.20536_S61_se UHM896.20601_S81_se UHM897.20591_S56_se
## 1             8.90382            14.25302            38.82581
##   UHM898.20394_S91_se UHM899.20588_S20_se UHM900.20395_S8_se
## 1            1.785627            6.792593           5.164524
##   UHM901.20542_S38_se UHM902.20584_S67_se UHM903.20587_S8_se
## 1            16.89131            1.479314           2.158784
##   UHM904.20567_S53_se UHM905.20598_S45_se UHM906.20565_S29_se
## 1            6.938297            6.315486            12.23951
##   UHM907.20592_S68_se UHM908.20396_S20_se UHM909.20557_S28_se
## 1            1.867429            5.077736            1.032774
##   UHM910.20562_S88_se UHM965.20537_S73_se UHM966.20743_S51_se
## 1            3.174392            7.446002            1.858101
##   UHM967.20744_S63_se UHM968.20571_S6_se UHM969.20745_S75_se
## 1            5.109443           13.87734            7.908438
##   UHM971.20746_S87_se UHM973.20578_S90_se UHM974.20432_S72_se
## 1            2.956373            15.13138            1.265881
##   UHM975.20747_S4_se UHM977.20748_S16_se UHM978.20749_S28_se
## 1           3.475695            12.50985            1.860433
##   UHM979.20750_S40_se UHM980.20731_S2_se UHM981.20539_S2_se UHM982.20740_S15_se
## 1             1.33566            1.29583           5.751001            1.256109
##   UHM983.20556_S16_se UHM984.20751_S52_se UHM985.20752_S64_se
## 1            1.039774             4.64303           0.8526073
##   UHM988.20753_S76_se UHM989.20754_S88_se UHM991.20755_S5_se
## 1            5.337874            6.714922           6.108219
##   UHM993.20741_S27_se UHM996.20610_S94_se UHM997.20553_S75_se
## 1            7.060048            5.797256            7.182491
##   UHM998.20618_S95_se UHM999.20617_S83_se spiked.blank.20433_S84_q25
## 1            3.776291            7.446212                          0
##   spiked.blank.20817_S84_q25 Std2uL.20625_S84_q25 StdSwab1uL.20624_S72_q25
## 1                          0                    0                        0
##   STP1719.20422_S47_q25 STP213.20423_S59_q25 STP268.20424_S71_q25
## 1                     0                    0                    0
##   STP544.20419_S11_q25 STP570.20420_S23_q25 STP579.20421_S35_q25
## 1                    0                    0                    0
##   STP614.20418_S94_q25 UHM1000.20604_S22_q25 UHM1001.20609_S82_q25
## 1                    0                     0                     0
##   UHM1007.20622_S48_q25 UHM1009.20614_S47_q25 UHM1010.20621_S36_q25
## 1                     0                     0                     0
##   UHM1011.20606_S46_q25 UHM1024.20620_S24_q25 UHM1026.20607_S58_q25
## 1                     0                     0                     0
##   UHM1028.20613_S35_q25 UHM1032.20605_S34_q25 UHM1033.20619_S12_q25
## 1                     0                     0                     0
##   UHM1034.20616_S71_q25 UHM1035.20611_S11_q25 UHM1036.20612_S23_q25
## 1                     0                     0                     0
##   UHM1052.20615_S59_q25 UHM1060.20723_S1_q25 UHM1065.20724_S13_q25
## 1                     0                    0                     0
##   UHM1068.20732_S14_q25 UHM1069.20742_S39_q25 UHM1070.20725_S25_q25
## 1                     0                     0                     0
##   UHM1071.20733_S26_q25 UHM1072.20734_S38_q25 UHM1073.20735_S50_q25
## 1                     0                     0                     0
##   UHM1075.20726_S37_q25 UHM1077.20736_S62_q25 UHM1078.20727_S49_q25
## 1                     0                     0                     0
##   UHM1080.20737_S74_q25 UHM1081.20728_S61_q25 UHM1088.20738_S86_q25
## 1                     0                     0                     0
##   UHM1090.20739_S3_q25 UHM1093.20729_S73_q25 UHM1095.20730_S85_q25
## 1                    0                     0                     0
##   UHM1097.20623_S60_q25 UHM1099.20608_S70_q25 UHM1100.20788_S21_q25
## 1                     0                     0                     0
##   UHM1102.20789_S33_q25 UHM1104.20790_S45_q25 UHM1105.20791_S57_q25
## 1                     0                     0                     0
##   UHM1109.20531_S1_q25 UHM1110.20568_S65_q25 UHM1113.20792_S69_q25
## 1                    0                     0                     0
##   UHM1114.20793_S81_q25 UHM1115.20794_S93_q25 UHM1117.20795_S10_q25
## 1                     0                     0                     0
##   UHM1118.20796_S22_q25 UHM1120.20797_S34_q25 UHM1124.20798_S46_q25
## 1                     0                     0                     0
##   UHM1126.20799_S58_q25 UHM1128.20800_S70_q25 UHM1140.20555_S4_q25
## 1                     0                     0                    0
##   UHM1145.20801_S82_q25 UHM1163.20405_S33_q25 UHM1164.20402_S92_q25
## 1                     0                     0                     0
##   UHM1169.20552_S63_q25 UHM1171.20579_S7_q25 UHM1176.20404_S21_q25
## 1                     0                    0                     0
##   UHM1177.20546_S86_q25 UHM1182.20576_S66_q25 UHM1210.20802_S94_q25
## 1                     0                     0                     0
##   UHM1212.20803_S11_q25 UHM1217.20804_S23_q25 UHM1218.20805_S35_q25
## 1                     0                     0                     0
##   UHM1219.20806_S47_q25 UHM1220.20807_S59_q25 UHM1221.20808_S71_q25
## 1                     0                     0                     0
##   UHM1222.20809_S83_q25 UHM1223.20810_S95_q25 UHM1225.20811_S12_q25
## 1                     0                     0                     0
##   UHM1227.20812_S24_q25 UHM1228.20813_S36_q25 UHM1237.20814_S48_q25
## 1                     0                     0                     0
##   UHM1240.20566_S41_q25 UHM1246.20815_S60_q25 UHM1247.20816_S72_q25
## 1                     0                     0                     0
##   UHM1248.20575_S54_q25 UHM1256.20570_S89_q25 UHM1260.20596_S21_q25
## 1                     0                     0                     0
##   UHM1270.20577_S78_q25 UHM1271.20397_S32_q25 UHM1272.20398_S44_q25
## 1                     0                     0                     0
##   UHM1274.20554_S87_q25 UHM1275.20597_S33_q25 UHM1282.20599_S57_q25
## 1                     0                     0                     0
##   UHM1287.20543_S50_q25 UHM1291.20416_S70_q25 UHM1296.20550_S39_q25
## 1                     0                     0                     0
##   UHM1319.20561_S76_q25 UHM1324.20413_S34_q25 UHM1327.20545_S74_q25
## 1                     0                     0                     0
##   UHM1328.20572_S18_q25 UHM1334.20417_S82_q25 UHM1338.20399_S56_q25
## 1                     0                     0                     0
##   UHM1341.20602_S93_q25 UHM1356.20541_S26_q25 UHM1380.20580_S19_q25
## 1                     0                     0                     0
##   UHM1383.20594_S92_q25 UHM1385.20563_S5_q25 UHM1399.20756_S17_q25
## 1                     0                    0                     0
##   UHM1400.20757_S29_q25 UHM1401.20758_S41_q25 UHM1402.20759_S53_q25
## 1                     0                     0                     0
##   UHM1403.20760_S65_q25 UHM1405.20761_S77_q25 UHM1406.20762_S89_q25
## 1                     0                     0                     0
##   UHM1414.20763_S6_q25 UHM1419.20764_S18_q25 UHM1427.20389_S31_q25
## 1                    0                     0                     0
##   UHM1428.20390_S43_q25 UHM1429.20391_S55_q25 UHM1430.20392_S67_q25
## 1                     0                     0                     0
##   UHM1432.20393_S79_q25 UHM1435.20388_S19_q25 UHM162.20560_S64_q25
## 1                     0                     0                    0
##   UHM198.20585_S79_q25 UHM20.3314_S52_q25 UHM20.3315_S64_q25
## 1                    0                  0                  0
##   UHM204.20409_S81_q25 UHM206.20410_S93_q25 UHM207.20593_S80_q25
## 1                    0                    0                    0
##   UHM208.20411_S10_q25 UHM211.20406_S45_q25 UHM215.20408_S69_q25
## 1                    0                    0                    0
##   UHM216.20429_S36_q25 UHM219.20430_S48_q25 UHM236.20431_S60_q25
## 1                    0                    0                    0
##   UHM238.20407_S57_q25 UHM245.20538_S85_q25 UHM252.20558_S40_q25
## 1                    0                    0                    0
##   UHM267.20400_S68_q25 UHM274.20581_S31_q25 UHM276.20586_S91_q25
## 1                    0                    0                    0
##   UHM280.20401_S80_q25 UHM286.20425_S83_q25 UHM289.20426_S95_q25
## 1                    0                    0                    0
##   UHM294.20427_S12_q25 UHM298.20600_S69_q25 UHM325.20548_S15_q25
## 1                    0                    0                    0
##   UHM337.20412_S22_q25 UHM354.20535_S49_q25 UHM356.20415_S58_q25
## 1                    0                    0                    0
##   UHM369.20773_S31_q25 UHM370.20774_S43_q25 UHM372.20775_S55_q25
## 1                    0                    0                    0
##   UHM373.20776_S67_q25 UHM374.20777_S79_q25 UHM375.20778_S91_q25
## 1                    0                    0                    0
##   UHM377.20779_S8_q25 UHM38.3376_S36_q25 UHM386.20781_S32_q25
## 1                   0                  0                    0
##   UHM387.20782_S44_q25 UHM414.20583_S55_q25 UHM418.20765_S30_q25
## 1                    0                    0                    0
##   UHM422.20766_S42_q25 UHM425.20767_S54_q25 UHM426.20534_S37_q25
## 1                    0                    0                    0
##   UHM428.20544_S62_q25 UHM429.20559_S52_q25 UHM435.20547_S3_q25
## 1                    0                    0                   0
##   UHM437.20768_S66_q25 UHM439.20564_S17_q25 UHM44.3526_S31_q25
## 1                    0                    0                  0
##   UHM445.20569_S77_q25 UHM447.20783_S56_q25 UHM448.20769_S78_q25
## 1                    0                    0                    0
##   UHM45.3539_S92_q25 UHM454.20770_S90_q25 UHM455.20785_S80_q25
## 1                  0                    0                    0
##   UHM458.20786_S92_q25 UHM459.20787_S9_q25 UHM461.20771_S7_q25
## 1                    0                   0                   0
##   UHM467.20772_S19_q25 UHM470.20533_S25_q25 UHM476.20414_S46_q25
## 1                    0                    0                    0
##   UHM478.20549_S27_q25 UHM479.20551_S51_q25 UHM481.20403_S9_q25
## 1                    0                    0                   0
##   UHM482.20590_S44_q25 UHM483.20603_S10_q25 UHM519.20582_S43_q25
## 1                    0                    0                    0
##   UHM520.20573_S30_q25 UHM746.21478_S117_q25 UHM747.21477_S106_q25
## 1                    0                     0                     0
##   UHM748.21467_S170_q25 UHM748.21487_S129_q25 UHM749.21479_S128_q25
## 1                     0                     0                     0
##   UHM759.21466_S159_q25 UHM759.21486_S118_q25 UHM775.21485_S107_q25
## 1                     0                     0                     0
##   UHM776.21482_S161_q25 UHM777.21484_S183_q25 UHM779.21468_S181_q25
## 1                     0                     0                     0
##   UHM779.21488_S140_q25 UHM782.21480_S139_q25 UHM810.21472_S138_q25
## 1                     0                     0                     0
##   UHM811.21471_S127_q25 UHM813.21481_S150_q25 UHM818.21469_S105_q25
## 1                     0                     0                     0
##   UHM818.21489_S151_q25 UHM819.21473_S149_q25 UHM820.21470_S116_q25
## 1                     0                     0                     0
##   UHM820.21490_S162_q25 UHM827.21474_S160_q25 UHM829.21476_S182_q25
## 1                     0                     0                     0
##   UHM832.21483_S172_q25 UHM836.20385_S78_q25 UHM837.20386_S90_q25
## 1                     0                    0                    0
##   UHM838.20387_S7_q25 UHM891.20384_S66_q25 UHM892.20532_S13_q25
## 1                   0                    0                    0
##   UHM893.20595_S9_q25 UHM894.20540_S14_q25 UHM895.20536_S61_q25
## 1                   0                    0                    0
##   UHM896.20601_S81_q25 UHM897.20591_S56_q25 UHM898.20394_S91_q25
## 1                    0                    0                    0
##   UHM899.20588_S20_q25 UHM900.20395_S8_q25 UHM901.20542_S38_q25
## 1                    0                   0                    0
##   UHM902.20584_S67_q25 UHM903.20587_S8_q25 UHM904.20567_S53_q25
## 1                    0                   0                    0
##   UHM905.20598_S45_q25 UHM906.20565_S29_q25 UHM907.20592_S68_q25
## 1                    0                    0                    0
##   UHM908.20396_S20_q25 UHM909.20557_S28_q25 UHM910.20562_S88_q25
## 1                    0                    0                    0
##   UHM965.20537_S73_q25 UHM966.20743_S51_q25 UHM967.20744_S63_q25
## 1                    0                    0                    0
##   UHM968.20571_S6_q25 UHM969.20745_S75_q25 UHM971.20746_S87_q25
## 1                   0                    0                    0
##   UHM973.20578_S90_q25 UHM974.20432_S72_q25 UHM975.20747_S4_q25
## 1                    0                    0                   0
##   UHM977.20748_S16_q25 UHM978.20749_S28_q25 UHM979.20750_S40_q25
## 1                    0                    0                    0
##   UHM980.20731_S2_q25 UHM981.20539_S2_q25 UHM982.20740_S15_q25
## 1                   0                   0                    0
##   UHM983.20556_S16_q25 UHM984.20751_S52_q25 UHM985.20752_S64_q25
## 1                    0                    0                    0
##   UHM988.20753_S76_q25 UHM989.20754_S88_q25 UHM991.20755_S5_q25
## 1                    0                    0                   0
##   UHM993.20741_S27_q25 UHM996.20610_S94_q25 UHM997.20553_S75_q25
## 1                    0                    0                    0
##   UHM998.20618_S95_q25 UHM999.20617_S83_q25 spiked.blank.20433_S84_median
## 1                    0                    0                             0
##   spiked.blank.20817_S84_median Std2uL.20625_S84_median
## 1                             0                       0
##   StdSwab1uL.20624_S72_median STP1719.20422_S47_median STP213.20423_S59_median
## 1                           0                        0                       0
##   STP268.20424_S71_median STP544.20419_S11_median STP570.20420_S23_median
## 1                       0                       0                       0
##   STP579.20421_S35_median STP614.20418_S94_median UHM1000.20604_S22_median
## 1                       0                       0                        0
##   UHM1001.20609_S82_median UHM1007.20622_S48_median UHM1009.20614_S47_median
## 1                        0                        0                        0
##   UHM1010.20621_S36_median UHM1011.20606_S46_median UHM1024.20620_S24_median
## 1                        0                        0                        0
##   UHM1026.20607_S58_median UHM1028.20613_S35_median UHM1032.20605_S34_median
## 1                        0                        0                        0
##   UHM1033.20619_S12_median UHM1034.20616_S71_median UHM1035.20611_S11_median
## 1                        0                        0                        0
##   UHM1036.20612_S23_median UHM1052.20615_S59_median UHM1060.20723_S1_median
## 1                        0                        0                       0
##   UHM1065.20724_S13_median UHM1068.20732_S14_median UHM1069.20742_S39_median
## 1                        0                        0                        0
##   UHM1070.20725_S25_median UHM1071.20733_S26_median UHM1072.20734_S38_median
## 1                        0                        0                        0
##   UHM1073.20735_S50_median UHM1075.20726_S37_median UHM1077.20736_S62_median
## 1                        0                        0                        0
##   UHM1078.20727_S49_median UHM1080.20737_S74_median UHM1081.20728_S61_median
## 1                        0                        0                        0
##   UHM1088.20738_S86_median UHM1090.20739_S3_median UHM1093.20729_S73_median
## 1                        0                       0                        0
##   UHM1095.20730_S85_median UHM1097.20623_S60_median UHM1099.20608_S70_median
## 1                        0                        0                        0
##   UHM1100.20788_S21_median UHM1102.20789_S33_median UHM1104.20790_S45_median
## 1                        0                        0                        0
##   UHM1105.20791_S57_median UHM1109.20531_S1_median UHM1110.20568_S65_median
## 1                        0                       0                        0
##   UHM1113.20792_S69_median UHM1114.20793_S81_median UHM1115.20794_S93_median
## 1                        0                        0                        0
##   UHM1117.20795_S10_median UHM1118.20796_S22_median UHM1120.20797_S34_median
## 1                        0                        0                        0
##   UHM1124.20798_S46_median UHM1126.20799_S58_median UHM1128.20800_S70_median
## 1                        0                        0                        0
##   UHM1140.20555_S4_median UHM1145.20801_S82_median UHM1163.20405_S33_median
## 1                       0                        0                        0
##   UHM1164.20402_S92_median UHM1169.20552_S63_median UHM1171.20579_S7_median
## 1                        0                        0                       0
##   UHM1176.20404_S21_median UHM1177.20546_S86_median UHM1182.20576_S66_median
## 1                        0                        0                        0
##   UHM1210.20802_S94_median UHM1212.20803_S11_median UHM1217.20804_S23_median
## 1                        0                        0                        0
##   UHM1218.20805_S35_median UHM1219.20806_S47_median UHM1220.20807_S59_median
## 1                        0                        0                        0
##   UHM1221.20808_S71_median UHM1222.20809_S83_median UHM1223.20810_S95_median
## 1                        0                        0                        0
##   UHM1225.20811_S12_median UHM1227.20812_S24_median UHM1228.20813_S36_median
## 1                        0                        0                        0
##   UHM1237.20814_S48_median UHM1240.20566_S41_median UHM1246.20815_S60_median
## 1                        0                        0                        0
##   UHM1247.20816_S72_median UHM1248.20575_S54_median UHM1256.20570_S89_median
## 1                        0                        0                        0
##   UHM1260.20596_S21_median UHM1270.20577_S78_median UHM1271.20397_S32_median
## 1                        0                        0                        0
##   UHM1272.20398_S44_median UHM1274.20554_S87_median UHM1275.20597_S33_median
## 1                        0                        0                        0
##   UHM1282.20599_S57_median UHM1287.20543_S50_median UHM1291.20416_S70_median
## 1                        0                        0                        0
##   UHM1296.20550_S39_median UHM1319.20561_S76_median UHM1324.20413_S34_median
## 1                        0                        0                        0
##   UHM1327.20545_S74_median UHM1328.20572_S18_median UHM1334.20417_S82_median
## 1                        0                        0                        0
##   UHM1338.20399_S56_median UHM1341.20602_S93_median UHM1356.20541_S26_median
## 1                        0                        0                        0
##   UHM1380.20580_S19_median UHM1383.20594_S92_median UHM1385.20563_S5_median
## 1                        0                        0                       0
##   UHM1399.20756_S17_median UHM1400.20757_S29_median UHM1401.20758_S41_median
## 1                        0                        0                        0
##   UHM1402.20759_S53_median UHM1403.20760_S65_median UHM1405.20761_S77_median
## 1                        0                        0                        0
##   UHM1406.20762_S89_median UHM1414.20763_S6_median UHM1419.20764_S18_median
## 1                        0                       0                        0
##   UHM1427.20389_S31_median UHM1428.20390_S43_median UHM1429.20391_S55_median
## 1                        0                        0                        0
##   UHM1430.20392_S67_median UHM1432.20393_S79_median UHM1435.20388_S19_median
## 1                        0                        0                        0
##   UHM162.20560_S64_median UHM198.20585_S79_median UHM20.3314_S52_median
## 1                       0                       0                     0
##   UHM20.3315_S64_median UHM204.20409_S81_median UHM206.20410_S93_median
## 1                     0                       0                       0
##   UHM207.20593_S80_median UHM208.20411_S10_median UHM211.20406_S45_median
## 1                       0                       0                       0
##   UHM215.20408_S69_median UHM216.20429_S36_median UHM219.20430_S48_median
## 1                       0                       0                       0
##   UHM236.20431_S60_median UHM238.20407_S57_median UHM245.20538_S85_median
## 1                       0                       0                       0
##   UHM252.20558_S40_median UHM267.20400_S68_median UHM274.20581_S31_median
## 1                       0                       0                       0
##   UHM276.20586_S91_median UHM280.20401_S80_median UHM286.20425_S83_median
## 1                       0                       0                       0
##   UHM289.20426_S95_median UHM294.20427_S12_median UHM298.20600_S69_median
## 1                       0                       0                       0
##   UHM325.20548_S15_median UHM337.20412_S22_median UHM354.20535_S49_median
## 1                       0                       0                       0
##   UHM356.20415_S58_median UHM369.20773_S31_median UHM370.20774_S43_median
## 1                       0                       0                       0
##   UHM372.20775_S55_median UHM373.20776_S67_median UHM374.20777_S79_median
## 1                       0                       0                       0
##   UHM375.20778_S91_median UHM377.20779_S8_median UHM38.3376_S36_median
## 1                       0                      0                     0
##   UHM386.20781_S32_median UHM387.20782_S44_median UHM414.20583_S55_median
## 1                       0                       0                       0
##   UHM418.20765_S30_median UHM422.20766_S42_median UHM425.20767_S54_median
## 1                       0                       0                       0
##   UHM426.20534_S37_median UHM428.20544_S62_median UHM429.20559_S52_median
## 1                       0                       0                       0
##   UHM435.20547_S3_median UHM437.20768_S66_median UHM439.20564_S17_median
## 1                      0                       0                       0
##   UHM44.3526_S31_median UHM445.20569_S77_median UHM447.20783_S56_median
## 1                     0                       0                       0
##   UHM448.20769_S78_median UHM45.3539_S92_median UHM454.20770_S90_median
## 1                       0                     0                       0
##   UHM455.20785_S80_median UHM458.20786_S92_median UHM459.20787_S9_median
## 1                       0                       0                      0
##   UHM461.20771_S7_median UHM467.20772_S19_median UHM470.20533_S25_median
## 1                      0                       0                       0
##   UHM476.20414_S46_median UHM478.20549_S27_median UHM479.20551_S51_median
## 1                       0                       0                       0
##   UHM481.20403_S9_median UHM482.20590_S44_median UHM483.20603_S10_median
## 1                      0                       0                       0
##   UHM519.20582_S43_median UHM520.20573_S30_median UHM746.21478_S117_median
## 1                       0                       0                        0
##   UHM747.21477_S106_median UHM748.21467_S170_median UHM748.21487_S129_median
## 1                        0                        0                        0
##   UHM749.21479_S128_median UHM759.21466_S159_median UHM759.21486_S118_median
## 1                        0                        0                        0
##   UHM775.21485_S107_median UHM776.21482_S161_median UHM777.21484_S183_median
## 1                        0                        0                        0
##   UHM779.21468_S181_median UHM779.21488_S140_median UHM782.21480_S139_median
## 1                        0                        0                        0
##   UHM810.21472_S138_median UHM811.21471_S127_median UHM813.21481_S150_median
## 1                        0                        0                        0
##   UHM818.21469_S105_median UHM818.21489_S151_median UHM819.21473_S149_median
## 1                        0                        0                        0
##   UHM820.21470_S116_median UHM820.21490_S162_median UHM827.21474_S160_median
## 1                        0                        0                        0
##   UHM829.21476_S182_median UHM832.21483_S172_median UHM836.20385_S78_median
## 1                        0                        0                       0
##   UHM837.20386_S90_median UHM838.20387_S7_median UHM891.20384_S66_median
## 1                       0                      0                       0
##   UHM892.20532_S13_median UHM893.20595_S9_median UHM894.20540_S14_median
## 1                       0                      0                       0
##   UHM895.20536_S61_median UHM896.20601_S81_median UHM897.20591_S56_median
## 1                       0                       0                       0
##   UHM898.20394_S91_median UHM899.20588_S20_median UHM900.20395_S8_median
## 1                       0                       0                      0
##   UHM901.20542_S38_median UHM902.20584_S67_median UHM903.20587_S8_median
## 1                       0                       0                      0
##   UHM904.20567_S53_median UHM905.20598_S45_median UHM906.20565_S29_median
## 1                       0                       0                       0
##   UHM907.20592_S68_median UHM908.20396_S20_median UHM909.20557_S28_median
## 1                       0                       0                       0
##   UHM910.20562_S88_median UHM965.20537_S73_median UHM966.20743_S51_median
## 1                       0                       0                       0
##   UHM967.20744_S63_median UHM968.20571_S6_median UHM969.20745_S75_median
## 1                       0                      0                       0
##   UHM971.20746_S87_median UHM973.20578_S90_median UHM974.20432_S72_median
## 1                       0                       0                       0
##   UHM975.20747_S4_median UHM977.20748_S16_median UHM978.20749_S28_median
## 1                      0                       0                       0
##   UHM979.20750_S40_median UHM980.20731_S2_median UHM981.20539_S2_median
## 1                       0                      0                      0
##   UHM982.20740_S15_median UHM983.20556_S16_median UHM984.20751_S52_median
## 1                       0                       0                       0
##   UHM985.20752_S64_median UHM988.20753_S76_median UHM989.20754_S88_median
## 1                       0                       0                       0
##   UHM991.20755_S5_median UHM993.20741_S27_median UHM996.20610_S94_median
## 1                      0                       0                       0
##   UHM997.20553_S75_median UHM998.20618_S95_median UHM999.20617_S83_median
## 1                       0                       0                       0
##   spiked.blank.20433_S84_q75 spiked.blank.20817_S84_q75 Std2uL.20625_S84_q75
## 1                          0                          0                    0
##   StdSwab1uL.20624_S72_q75 STP1719.20422_S47_q75 STP213.20423_S59_q75
## 1                        0                     0                    0
##   STP268.20424_S71_q75 STP544.20419_S11_q75 STP570.20420_S23_q75
## 1                    0                    0                    0
##   STP579.20421_S35_q75 STP614.20418_S94_q75 UHM1000.20604_S22_q75
## 1                    0                    0                     0
##   UHM1001.20609_S82_q75 UHM1007.20622_S48_q75 UHM1009.20614_S47_q75
## 1                     0                     0                     0
##   UHM1010.20621_S36_q75 UHM1011.20606_S46_q75 UHM1024.20620_S24_q75
## 1                     0                     0                     0
##   UHM1026.20607_S58_q75 UHM1028.20613_S35_q75 UHM1032.20605_S34_q75
## 1                     0                     0                     0
##   UHM1033.20619_S12_q75 UHM1034.20616_S71_q75 UHM1035.20611_S11_q75
## 1                     0                     0                     0
##   UHM1036.20612_S23_q75 UHM1052.20615_S59_q75 UHM1060.20723_S1_q75
## 1                     0                     0                    0
##   UHM1065.20724_S13_q75 UHM1068.20732_S14_q75 UHM1069.20742_S39_q75
## 1                     0                     0                     0
##   UHM1070.20725_S25_q75 UHM1071.20733_S26_q75 UHM1072.20734_S38_q75
## 1                     0                     0                     0
##   UHM1073.20735_S50_q75 UHM1075.20726_S37_q75 UHM1077.20736_S62_q75
## 1                     0                     0                     0
##   UHM1078.20727_S49_q75 UHM1080.20737_S74_q75 UHM1081.20728_S61_q75
## 1                     0                     0                     0
##   UHM1088.20738_S86_q75 UHM1090.20739_S3_q75 UHM1093.20729_S73_q75
## 1                     0                    0                     0
##   UHM1095.20730_S85_q75 UHM1097.20623_S60_q75 UHM1099.20608_S70_q75
## 1                     0                     0                     0
##   UHM1100.20788_S21_q75 UHM1102.20789_S33_q75 UHM1104.20790_S45_q75
## 1                     0                     0                     0
##   UHM1105.20791_S57_q75 UHM1109.20531_S1_q75 UHM1110.20568_S65_q75
## 1                     0                    0                     0
##   UHM1113.20792_S69_q75 UHM1114.20793_S81_q75 UHM1115.20794_S93_q75
## 1                     0                     0                     0
##   UHM1117.20795_S10_q75 UHM1118.20796_S22_q75 UHM1120.20797_S34_q75
## 1                     0                     0                     0
##   UHM1124.20798_S46_q75 UHM1126.20799_S58_q75 UHM1128.20800_S70_q75
## 1                     0                     0                     0
##   UHM1140.20555_S4_q75 UHM1145.20801_S82_q75 UHM1163.20405_S33_q75
## 1                    0                     0                     0
##   UHM1164.20402_S92_q75 UHM1169.20552_S63_q75 UHM1171.20579_S7_q75
## 1                     0                     0                    0
##   UHM1176.20404_S21_q75 UHM1177.20546_S86_q75 UHM1182.20576_S66_q75
## 1                     0                     0                     0
##   UHM1210.20802_S94_q75 UHM1212.20803_S11_q75 UHM1217.20804_S23_q75
## 1                     0                     0                     0
##   UHM1218.20805_S35_q75 UHM1219.20806_S47_q75 UHM1220.20807_S59_q75
## 1                     0                     0                     0
##   UHM1221.20808_S71_q75 UHM1222.20809_S83_q75 UHM1223.20810_S95_q75
## 1                     0                     0                     0
##   UHM1225.20811_S12_q75 UHM1227.20812_S24_q75 UHM1228.20813_S36_q75
## 1                     0                     0                     0
##   UHM1237.20814_S48_q75 UHM1240.20566_S41_q75 UHM1246.20815_S60_q75
## 1                     0                     0                     0
##   UHM1247.20816_S72_q75 UHM1248.20575_S54_q75 UHM1256.20570_S89_q75
## 1                     0                     0                     0
##   UHM1260.20596_S21_q75 UHM1270.20577_S78_q75 UHM1271.20397_S32_q75
## 1                     0                     0                     0
##   UHM1272.20398_S44_q75 UHM1274.20554_S87_q75 UHM1275.20597_S33_q75
## 1                     0                     0                     0
##   UHM1282.20599_S57_q75 UHM1287.20543_S50_q75 UHM1291.20416_S70_q75
## 1                     0                     0                     0
##   UHM1296.20550_S39_q75 UHM1319.20561_S76_q75 UHM1324.20413_S34_q75
## 1                     0                     0                     0
##   UHM1327.20545_S74_q75 UHM1328.20572_S18_q75 UHM1334.20417_S82_q75
## 1                     0                     0                     0
##   UHM1338.20399_S56_q75 UHM1341.20602_S93_q75 UHM1356.20541_S26_q75
## 1                     0                     0                     0
##   UHM1380.20580_S19_q75 UHM1383.20594_S92_q75 UHM1385.20563_S5_q75
## 1                     0                     0                    0
##   UHM1399.20756_S17_q75 UHM1400.20757_S29_q75 UHM1401.20758_S41_q75
## 1                     0                     0                     0
##   UHM1402.20759_S53_q75 UHM1403.20760_S65_q75 UHM1405.20761_S77_q75
## 1                     0                     0                     0
##   UHM1406.20762_S89_q75 UHM1414.20763_S6_q75 UHM1419.20764_S18_q75
## 1                     0                    0                     0
##   UHM1427.20389_S31_q75 UHM1428.20390_S43_q75 UHM1429.20391_S55_q75
## 1                     0                     0                     0
##   UHM1430.20392_S67_q75 UHM1432.20393_S79_q75 UHM1435.20388_S19_q75
## 1                     0                     0                     0
##   UHM162.20560_S64_q75 UHM198.20585_S79_q75 UHM20.3314_S52_q75
## 1                    0                    0                  0
##   UHM20.3315_S64_q75 UHM204.20409_S81_q75 UHM206.20410_S93_q75
## 1                  0                    0                    0
##   UHM207.20593_S80_q75 UHM208.20411_S10_q75 UHM211.20406_S45_q75
## 1                    0                    0                    0
##   UHM215.20408_S69_q75 UHM216.20429_S36_q75 UHM219.20430_S48_q75
## 1                    0                    0                    0
##   UHM236.20431_S60_q75 UHM238.20407_S57_q75 UHM245.20538_S85_q75
## 1                    0                    0                    0
##   UHM252.20558_S40_q75 UHM267.20400_S68_q75 UHM274.20581_S31_q75
## 1                    0                    0                    0
##   UHM276.20586_S91_q75 UHM280.20401_S80_q75 UHM286.20425_S83_q75
## 1                    0                    0                    0
##   UHM289.20426_S95_q75 UHM294.20427_S12_q75 UHM298.20600_S69_q75
## 1                    0                    0                    0
##   UHM325.20548_S15_q75 UHM337.20412_S22_q75 UHM354.20535_S49_q75
## 1                    0                    0                    0
##   UHM356.20415_S58_q75 UHM369.20773_S31_q75 UHM370.20774_S43_q75
## 1                    0                    0                    0
##   UHM372.20775_S55_q75 UHM373.20776_S67_q75 UHM374.20777_S79_q75
## 1                    0                    0                    0
##   UHM375.20778_S91_q75 UHM377.20779_S8_q75 UHM38.3376_S36_q75
## 1                    0                   0                  0
##   UHM386.20781_S32_q75 UHM387.20782_S44_q75 UHM414.20583_S55_q75
## 1                    0                    0                    0
##   UHM418.20765_S30_q75 UHM422.20766_S42_q75 UHM425.20767_S54_q75
## 1                    0                    0                    0
##   UHM426.20534_S37_q75 UHM428.20544_S62_q75 UHM429.20559_S52_q75
## 1                    0                    0                    0
##   UHM435.20547_S3_q75 UHM437.20768_S66_q75 UHM439.20564_S17_q75
## 1                   0                    0                    0
##   UHM44.3526_S31_q75 UHM445.20569_S77_q75 UHM447.20783_S56_q75
## 1                  0                    0                    0
##   UHM448.20769_S78_q75 UHM45.3539_S92_q75 UHM454.20770_S90_q75
## 1                    0                  0                    0
##   UHM455.20785_S80_q75 UHM458.20786_S92_q75 UHM459.20787_S9_q75
## 1                    0                    0                   0
##   UHM461.20771_S7_q75 UHM467.20772_S19_q75 UHM470.20533_S25_q75
## 1                   0                    0                    0
##   UHM476.20414_S46_q75 UHM478.20549_S27_q75 UHM479.20551_S51_q75
## 1                    0                    0                    0
##   UHM481.20403_S9_q75 UHM482.20590_S44_q75 UHM483.20603_S10_q75
## 1                   0                    0                    0
##   UHM519.20582_S43_q75 UHM520.20573_S30_q75 UHM746.21478_S117_q75
## 1                    0                    0                     0
##   UHM747.21477_S106_q75 UHM748.21467_S170_q75 UHM748.21487_S129_q75
## 1                     0                     0                     0
##   UHM749.21479_S128_q75 UHM759.21466_S159_q75 UHM759.21486_S118_q75
## 1                     0                     0                     0
##   UHM775.21485_S107_q75 UHM776.21482_S161_q75 UHM777.21484_S183_q75
## 1                     0                     0                     0
##   UHM779.21468_S181_q75 UHM779.21488_S140_q75 UHM782.21480_S139_q75
## 1                     0                     0                     0
##   UHM810.21472_S138_q75 UHM811.21471_S127_q75 UHM813.21481_S150_q75
## 1                     0                     0                     0
##   UHM818.21469_S105_q75 UHM818.21489_S151_q75 UHM819.21473_S149_q75
## 1                     0                     0                     0
##   UHM820.21470_S116_q75 UHM820.21490_S162_q75 UHM827.21474_S160_q75
## 1                     0                     0                     0
##   UHM829.21476_S182_q75 UHM832.21483_S172_q75 UHM836.20385_S78_q75
## 1                     0                     0                    0
##   UHM837.20386_S90_q75 UHM838.20387_S7_q75 UHM891.20384_S66_q75
## 1                    0                   0                    0
##   UHM892.20532_S13_q75 UHM893.20595_S9_q75 UHM894.20540_S14_q75
## 1                    0                   0                    0
##   UHM895.20536_S61_q75 UHM896.20601_S81_q75 UHM897.20591_S56_q75
## 1                    0                    0                    0
##   UHM898.20394_S91_q75 UHM899.20588_S20_q75 UHM900.20395_S8_q75
## 1                    0                    0                   0
##   UHM901.20542_S38_q75 UHM902.20584_S67_q75 UHM903.20587_S8_q75
## 1                    0                    0                   0
##   UHM904.20567_S53_q75 UHM905.20598_S45_q75 UHM906.20565_S29_q75
## 1                    0                    0                    0
##   UHM907.20592_S68_q75 UHM908.20396_S20_q75 UHM909.20557_S28_q75
## 1                    0                    0                    0
##   UHM910.20562_S88_q75 UHM965.20537_S73_q75 UHM966.20743_S51_q75
## 1                    0                    0                    0
##   UHM967.20744_S63_q75 UHM968.20571_S6_q75 UHM969.20745_S75_q75
## 1                    0                   0                    0
##   UHM971.20746_S87_q75 UHM973.20578_S90_q75 UHM974.20432_S72_q75
## 1                    0                    0                    0
##   UHM975.20747_S4_q75 UHM977.20748_S16_q75 UHM978.20749_S28_q75
## 1                   0                    0                    0
##   UHM979.20750_S40_q75 UHM980.20731_S2_q75 UHM981.20539_S2_q75
## 1                    0                   0                   0
##   UHM982.20740_S15_q75 UHM983.20556_S16_q75 UHM984.20751_S52_q75
## 1                    0                    0                    0
##   UHM985.20752_S64_q75 UHM988.20753_S76_q75 UHM989.20754_S88_q75
## 1                    0                    0                    0
##   UHM991.20755_S5_q75 UHM993.20741_S27_q75 UHM996.20610_S94_q75
## 1                   0                    0                    0
##   UHM997.20553_S75_q75 UHM998.20618_S95_q75 UHM999.20617_S83_q75
## 1                    0                    0                    0

# conclusion # needs phyloseq obj
# Define the parameters
max_passed_range <- 12 # depends on your model system
output_path <- "spike_success_report.docx"

# Subset the phyloseq object to exclude blank samples (optional step)
physeq_16S_adj_scaled_perc <- phyloseq::subset_samples(physeq_absolute_abundance_16S_OTU, sample.or.blank != "blank")

# Generate the spike success report and calculate summary statistics
summary_stats <- conclusion(physeq_16S_adj_scaled_perc, 
                            merged_spiked_species, 
                            max_passed_range, 
                            output_path)

## Warning in prune_taxa(taxa, phy_tree(x)): prune_taxa attempted to reduce tree to 1 or fewer tips.
##  tree replaced with NULL.

## Table saved in docx format: spike_success_report.docx 
## Merged data saved as CSV: spike_success_report.csv 
## Structure of spike_success_report:
## 'data.frame':    260 obs. of  5 variables:
##  $ Sample            : chr  "STP1719.20422_S47" "STP213.20423_S59" "STP268.20424_S71" "STP544.20419_S11" ...
##  $ Total_Reads_total : num  55421 51389 84733 13297 47306 ...
##  $ Total_Reads_spiked: num  243 33 291 13204 3676 ...
##  $ Percentage        : num  0.4385 0.0642 0.3434 99.3006 7.7707 ...
##  $ Result            : chr  "passed" "failed" "passed" "failed" ...
## First few rows of spike_success_report:
##              Sample Total_Reads_total Total_Reads_spiked  Percentage Result
## 1 STP1719.20422_S47             55421                243  0.43846195 passed
## 2  STP213.20423_S59             51389                 33  0.06421608 failed
## 3  STP268.20424_S71             84733                291  0.34343172 passed
## 4  STP544.20419_S11             13297              13204 99.30059412 failed
## 5  STP570.20420_S23             47306               3676  7.77068448 passed
## 6  STP579.20421_S35             88430              17950 20.29854122 failed
## Unique values in the 'Result' column after filtering :
## [1] "passed" "failed"
## Table saved in docx format: spike_success_report.docx 
## Summary statistics saved as CSV: spike_success_report.csv

# Print the summary statistics
print(summary_stats)

##   mean_total_reads_spiked sd_total_reads_spiked se_total_reads_spiked
## 1                124139.9              646162.8              40150.61
##   q25_total_reads_spiked median_total_reads_spiked q75_total_reads_spiked
## 1                     79                      1309                   9363
##   mean_percentage sd_percentage se_percentage q25_percentage median_percentage
## 1        16.60193      30.70811      1.908109      0.1098736          1.320221
##   q75_percentage passed_count failed_count
## 1       12.85727          128          131