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Muhammed-Shikhani authored Nov 22, 2023
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Binary file added data_for_figures/AllsamplesGCresults.xlsx
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30 changes: 30 additions & 0 deletions data_for_figures/Bubble_MS_sample_data_20221018.csv
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R_name,sample_number,Temp,pH,SpCond,Sal,TDG,Depth_Hydrolab,LDO.,LDO,IBatt,Start_Date,End_Date,Duration_h,Depth_meter,Gas_amount,Volume_ml,Plant,EGM_before,EGM_after,Oxygen_percent,rO2,pch,ol
m10,21,20.60838323,7.703552894,14.64670659,0.01,793.7904192,0.22245509,0,0,0,16.12.2021 10:40,16.12.2021 20:40,10,0.3,100,4,Echinodorus python,NA,NA,32.6,0.233009708737864,1,4
m14,25,18.850181,6.988959276,23.53393665,0.02,823.1538462,0.382217195,97.860181,9.102941176,24.58823529,11.01.2022 10:54,11.01.2022 15:40,4.75,0.3,100,4,Anubias bateri,NA,NA,37.8,0.233009708737864,19,1
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m21,32,18.93817427,6.97966805,22.97510373,0.02,904.1950207,1.683941909,95.23983402,8.844356846,40.17012448,21.01.2022 12:18,21.01.2022 16:35,4.3,2,100,4,Echinodorus python,NA,NA,41.9,0.341666666666667,19,1
m5,16,19.27023904,6.789083665,9,0.01,806.3426295,1.983386454,87.47370518,8.069721116,43.6812749,08.12.2021 14:53,08.12.2021 20:15,5.35,2.5,50,4,Echinodorus python,NA,NA,34.8,0.368,1,4
m12,23,18.11681275,7.012031873,15.47410359,0.01,847.250996,1.958286853,98.99521912,9.347968127,20.94820717,20.12.2021 11:38,20.12.2021 17:52,6.25,2.5,80,4,Echinodorus small bear,NA,NA,37.3,0.368,19,1
m18,29,19.03961832,6.825572519,26.29770992,0.02,887.6183206,1.815801527,95.78473282,8.877022901,41.18320611,19.01.2022 11:08,19.01.2022 13:15,2.1,2.5,90,4,Echinodorus python,NA,NA,42.9,0.368,19,1
m25,36,18.84950276,6.801491713,30.7679558,0.02,933.1878453,1.814861878,94.84475138,8.822596685,62.17679558,02.02.2022 11:30,02.02.2022 14:00,2.5,2.5,100,4,Echinodorus python,48000,48700,41,0.368,19,1
m2,13,18.55689342,6.960816327,9.464852608,0.01,800.2176871,2.489501134,97.80498866,9.153265306,39.18820862,07.12.2021 09:10,07.12.2021 16:35,7.45,3,100,4,Echinodorus small bear,NA,NA,41.7,0.392307692307692,1,4
m22,33,18.05670996,7.122813853,28.66666667,0.02,975.4329004,2.4695671,101.252381,9.572294372,22.59307359,24.01.2022 12:30,24.01.2022 16:23,3.9,3,100,4,Echinodorus python,NA,NA,36.2,0.392307692307692,19,1
m16,27,18.53360544,7.04877551,26.06802721,0.02,856.1814059,2.828231293,99.99002268,9.361496599,25.91156463,17.01.2022 09:25,17.01.2022 17:00,7.55,3.35,80,4,Anubias bateri,NA,NA,30.9,0.408239700374532,1,4
m7,18,19.03120582,6.858170478,12.27650728,0.01,799.8794179,2.851309771,87.02120582,8.066590437,60.18503119,10.12.2021 10:24,10.12.2021 19:10,8.75,3.5,100,4,Echinodorus python,NA,NA,42.8,0.414814814814815,1,4
NA,38,NA,NA,NA,NA,NA,3.5,NA,NA,NA,03.02.2022 10:40,03.02.2022 16:25,5.75,3.5,100,4,Echinodorus python,44000,37300,43,0.414814814814815,19,1
m4,15,18.63965636,6.749106529,9.759450172,0.01,805.7250859,3.416666667,88.6371134,8.281580756,64.65979381,08.12.2021 09:32,08.12.2021 14:30,5,4,100,4,Echinodorus python,NA,NA,44,0.435714285714286,19,1
m23,34,18.8263017,7.035328467,30.15571776,0.020024331,1047.83455,3.402335766,102.8970803,9.57729927,62.79075426,26.01.2022 12:50,26.01.2022 19:55,7.1,4,70,4,Echinodorus python,NA,NA,38.6,0.435714285714286,1,4
m24,35,18.77399202,6.897724551,28.13972056,0.02,1044.05988,3.364690619,91.03792415,8.482634731,29.78243513,28.01.2022 10:13,28.01.2022 19:30,9.25,4,100,4,Echinodorus python,NA,NA,38.2,0.435714285714286,1,4
m19,30,19.21080997,6.769875389,20.85981308,0.02,942.4018692,3.617788162,98.48286604,9.095109034,20.45482866,19.01.2022 13:45,19.01.2022 19:48,6.05,4.25,60,4,Echinodorus python,NA,NA,40.3,0.445614035087719,1,4
m6,17,18.79884244,6.759742765,10.68488746,0.01,807.9871383,3.883054662,86.9829582,8.10096463,22.2829582,09.12.2021 09:35,09.12.2021 20:05,10.5,4.5,60,4,Echinodorus python,NA,NA,41.4,0.455172413793103,1,4
61 changes: 61 additions & 0 deletions data_for_figures/Fig3_o2_plot_4panels.R
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setwd("/home/shikhani/Documents/Bubble_data/Data_2022_08_13/")
data <- read.csv("Bubble_MS_sample_data_20221018.csv")
data=data[order(data$Depth_meter),]

data$rO2=1-(0.79/((data$Depth_meter*0.1)+1))

data$pch <- 19
data$pch[(which(data$Gas_amount<80 | data$Duration_h>7))] <- 1

data$ol <- 1
#data$ol[which(data$sample_number == 16 | data$sample_number== 37)] <- 2
data$ol[(which(data$Gas_amount<80 | data$Duration_h>7))] <- 4
data19 <- data[which(data$pch==19),]
data1 <- data[which(data$pch==1),]

h19 <- hist(data19$Oxygen_percent,breaks=c(20,25, 30, 35,40, 45,50))


dat19 <- rbind(h19$counts)

h1 <- hist(data1$Oxygen_percent,breaks=c(20,25, 30, 35,40, 45,50))

dat1 <- rbind(h1$counts)



png(filename = "O2_depth_4panels.png",width = 250,height = 200,units = "mm",res = 300)


l <-layout(matrix(c(1:4), 2, 2, byrow = TRUE), widths=c(0.67, 0.33))
par(mar=c(1, 1, 1, 1),
oma = c(3, 3, 0.2, 0.2))

plot((data19$Depth_meter), data19$Oxygen_percent,pch=data19$pch, xlim = c(0,5), ylab="Oxygen (%)", xlab="Depth (m)", ylim=c(20,50), las=1, col= data19$ol)
arrows((data19$Depth_meter)+0.2, data19$Oxygen_percent,(data19$Depth_meter)-0.2, data19$Oxygen_percent,length=0.05, angle=90, code=3, col=data19$ol)
lines((c(0,data1$Depth_meter)*1),c(0.21,data1$rO2)*100, col="red")
mtext("Oxygen (%)",side=2,col="black",line=2.5)
text(0.1,48,"(A)")


barplot(as.matrix(dat19),col=c(1), space = 0, axes = FALSE, horiz=T)
axis(side = 2, at=c(0,1,2,3,4,5,6),labels = c(20,25, 30, 35,40, 45,50),las=2)
axis(side = 1)
text(0.5,5.7,"(B)")

plot((data1$Depth_meter), data1$Oxygen_percent,pch=data1$pch, xlim = c(0,5), ylab="Oxygen (%)", xlab="Depth (m)", ylim=c(20,50), las=1, col= data1$ol)
arrows((data1$Depth_meter)+0.2, data1$Oxygen_percent,(data1$Depth_meter)-0.2, data1$Oxygen_percent,length=0.05, angle=90, code=3, col=data1$ol)
lines((c(0,data1$Depth_meter)*1),c(0.21,data1$rO2)*100, col="red")
mtext("Oxygen (%)",side=2,col="black",line=2.5)
mtext("Depth (m)",side=1,col="black",line=2.5)
legend("bottomright", legend =c( "fast experiment", "slow experiment","Theory"),pch = c(19,1,NA), lty = c(NA,NA,1), col=c(1,4,2),bty = "n",)
text(0.1,48,"(C)")

b1 <- barplot(as.matrix(dat1),col=c("lightblue2"), space = 0, axes = FALSE, horiz=T)
axis(side = 2, at=c(0,1,2,3,4,5,6),labels = c(20,25, 30, 35,40, 45,50),las=2)
axis(side = 1)
mtext("count",side=1,col="black",line=2.5)
text(0.5,5.7,"(D)")
dev.off()


Binary file added data_for_figures/GC-Calibrations.docx
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30 changes: 30 additions & 0 deletions data_for_figures/GC_RawData_20220805.csv
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sample;Sample Volume (ml);Amount of gas (%);Withdrawal for GC1 (ml) _injected into GC1;Withdrawal GC2 for dilution (ml)_injected into dilution exetainer;Dilution exetainer volume (ml);Diluted volume for GC2 (ml) _injected into GC2;GC2 date_ name of GC2 Data;co2;co2_a;co2_b;co2_results_raw;ch4;ch4_a;ch4_b;ch4_result_raw;sample;GC1 date_name of GC1 data;N2;N2_a;N2_b;N2_result_raw;Ar;Ar_a;Ar_b;Ar_result_raw
Sample 12;4;95;0.5;0.4;12.02;0.6;20220125-9;Y=0.0758x-2.7683;0.0758;-2.7683;17579.868;Y=0.0591x+0.9083;0.0591;0.9083;18.472;Sample 12;20211220-16;Y=0.0891x+8.1503;0.0891;8.1503;224.2156;Y=0.1519x-0.2411;0.1519;-0.2411;4.3818
Sample 13;4;100;0.5;0.45;11.93;0.65;20220125-10;Y=0.0758x-2.7683;0.0758;-2.7683;21794.366;Y=0.0591x+0.9083;0.0591;0.9083;17.8792;Sample 13;20211220-17;Y=0.0891x+8.1503;0.0891;8.1503;217.6878;Y=0.1519x-0.2411;0.1519;-0.2411;4.1736
Sample 14;4;50;0.5;0.325;12.15;0.7;20220125-11;Y=0.0758x-2.7683;0.0758;-2.7683;19617.051;Y=0.0591x+0.9083;0.0591;0.9083;29.5988;Sample 14;20211221-04;Y=0.0891x+8.1503;0.0891;8.1503;251.355;Y=0.1519x-0.2411;0.1519;-0.2411;4.5668
Sample 15;4;100;0.5;0.4;12.09;0.6;20220125-12;Y=0.0758x-2.7683;0.0758;-2.7683;21076.127;Y=0.0591x+0.9083;0.0591;0.9083;17.184;Sample 15;20211221-05 ;Y=0.0891x+8.1503;0.0891;8.1503;201.8364;Y=0.1519x-0.2411;0.1519;-0.2411;3.4676
Sample 16;4;50;0.225;0.35;11.99;0.6;20220125-13;Y=0.0758x-2.7683;0.0758;-2.7683;27729.6228;Y=0.0591x+0.9083;0.0591;0.9083;13.6524;Sample 16;20220127-16;Y=0.1078x+4.1363;0.1078;4.1363;108.2436;Y=0.0108x-0.0078;0.0108;-0.0078;2.99
Sample 17;4;60;0.4;0.55;12.05;0.65;20220125-14;Y=0.0758x-2.7683;0.0758;-2.7683;35048.207;Y=0.0591x+0.9083;0.0591;0.9083;12.0606;Sample 17;20220127-17;Y=0.1078x+4.1363;0.1078;4.1363;168.6202;Y=0.0108x-0.0078;0.0108;-0.0078;3.3078
Sample 18;4;100;0.5;0.6;12.05;0.6;20220125-15;Y=0.0758x-2.7683;0.0758;-2.7683;34175.1326;Y=0.0591x+0.9083;0.0591;0.9083;18.962;Sample 18;20220127-18;Y=0.1078x+4.1363;0.1078;4.1363;201.3074;Y=0.0108x-0.0078;0.0108;-0.0078;4.6892
Sample 19;4;90;0.4;0.65;11.95;0.65;20220125-16;Y=0.0758x-2.7683;0.0758;-2.7683;9442.265;Y=0.0591x+0.9083;0.0591;0.9083;22.1182;Sample 19;20220127-19;Y=0.1078x+4.1363;0.1078;4.1363;203.0664;Y=0.0108x-0.0078;0.0108;-0.0078;3.508
Sample 20;6;100;0.45;0.45;12.01;0.55;20220125-17;Y=0.0758x-2.7683;0.0758;-2.7683;14974.906;Y=0.0591x+0.9083;0.0591;0.9083;16.6492;Sample 20;20220127-20;Y=0.1078x+4.1363;0.1078;4.1363;187.8234;Y=0.0108x-0.0078;0.0108;-0.0078;3.6032
Sample 21;4;100;0.425;0.4;12.08;0.55;20220126-08;Y=0.0739x+75.912;0.0739;75.912;6593.2312;Y=0.0741x+0.3909;0.0741;0.3909;4.6682;Sample 21;20220127-21;Y=0.1078x+4.1363;0.1078;4.1363;222.8908;Y=0.0108x-0.0078;0.0108;-0.0078;2.9288
Sample 22;4;85;0.45;0.4;11.95;0.5;20220126-09;Y=0.0739x+75.912;0.0739;75.912;7824.6564;Y=0.0741x+0.3909;0.0741;0.3909;4.6004;Sample 22;20220127-22;Y=0.1078x+4.1363;0.1078;4.1363;217.1272;Y=0.0108x-0.0078;0.0108;-0.0078;3.6958
Sample 23;4;80;0.45;0.4;12.01;0.5;20220126-10;Y=0.0739x+75.912;0.0739;75.912;8541.5204;Y=0.0741x+0.3909;0.0741;0.3909;4.985;Sample 23;20220127-23;Y=0.1078x+4.1363;0.1078;4.1363;214.3932;Y=0.0108x-0.0078;0.0108;-0.0078;3.4872
Sample 24;4;100;0.4;0.4;12;0.5;20220126-11;Y=0.0739x+75.912;0.0739;75.912;10692.6076;Y=0.0741x+0.3909;0.0741;0.3909;3.6772;Sample 24;20220127-24;Y=0.1078x+4.1363;0.1078;4.1363;179.8954;Y=0.0108x-0.0078;0.0108;-0.0078;3.6936
Sample 25;4;100;0.45;0.4;12.04;0.5;20220126-12;Y=0.0739x+75.912;0.0739;75.912;12926.7292;Y=0.0741x+0.3909;0.0741;0.3909;4.4808;Sample 25;20220127-25;Y=0.1078x+4.1363;0.1078;4.1363;201.97;Y=0.0108x-0.0078;0.0108;-0.0078;4.35
Sample 26;4;100;0.45;0.4;12.09;0.5;20220126-13;Y=0.0739x+75.912;0.0739;75.912;14671.4576;Y=0.0741x+0.3909;0.0741;0.3909;5.8126;Sample 26;20220127-26;Y=0.1078x+4.1363;0.1078;4.1363;217.8138;Y=0.0108x-0.0078;0.0108;-0.0078;4.5668
Sample 27;4;80;0.45;0.4;12.09;0.5;20220126-14;Y=0.0739x+75.912;0.0739;75.912;9291.7148;Y=0.0741x+0.3909;0.0741;0.3909;3.5532;Sample 27;20220127-27;Y=0.1078x+4.1363;0.1078;4.1363;224.4332;Y=0.0108x-0.0078;0.0108;-0.0078;4.4594
Sample 28;4;100;0.45;0.4;12;0.5;20220126-15;Y=0.0739x+75.912;0.0739;75.912;9194.9944;Y=0.0741x+0.3909;0.0741;0.3909;4.1644;Sample 28;20220127-28;Y=0.1078x+4.1363;0.1078;4.1363;206.572;Y=0.0108x-0.0078;0.0108;-0.0078;3.8144
Sample 29;4;90;0.4;0.4;11.84;0.5;20220126-16;Y=0.0739x+75.912;0.0739;75.912;13226.4676;Y=0.0741x+0.3909;0.0741;0.3909;3.6912;Sample 29;20220127-29;Y=0.1078x+4.1363;0.1078;4.1363;157.3384;Y=0.0108x-0.0078;0.0108;-0.0078;3.7176
Sample 30;4;60;0.4;0.4;12.08;0.5;20220126-17;Y=0.0739x+75.912;0.0739;75.912;14849.4706;Y=0.0741x+0.3909;0.0741;0.3909;3.7356;Sample 30;20220127-30;Y=0.1078x+4.1363;0.1078;4.1363;166.1035;Y=0.0108x-0.0078;0.0108;-0.0078;4.108
Sample 31;6;100;0.5;0.4;12.03;0.5;20220126-18;Y=0.0739x+75.912;0.0739;75.912;6597.3042;Y=0.0741x+0.3909;0.0741;0.3909;4.3512;Sample 31;20220127-31;Y=0.1078x+4.1363;0.1078;4.1363;219.3492;Y=0.0108x-0.0078;0.0108;-0.0078;4.5188
Sample 32;4;100;0.4;0.4;11.68;0.5;20220126-19;Y=0.0739x+75.912;0.0739;75.912;13085.0228;Y=0.0741x+0.3909;0.0741;0.3909;5.6504;Sample 32;20220127-32;Y=0.1078x+4.1363;0.1078;4.1363;161.2428;Y=0.0108x-0.0078;0.0108;-0.0078;2.7204
Sample 33;4;100;0.4;0.4;11.69;0.5;20220126-20;Y=0.0739x+75.912;0.0739;75.912;7682.2232;Y=0.0741x+0.3909;0.0741;0.3909;3.7582;Sample 33;20220127-33;Y=0.1078x+4.1363;0.1078;4.1363;179.77;Y=0.0108x-0.0078;0.0108;-0.0078;2.7916
Sample 34;4;70;0.45;0.4;11.94;0.5;20220204-08;Y=0.0872x-26.718;0.0872;26.718;14479.3896;Y=0.0839x-0.9596;0.0839;-0.9596;7.1564;Sample 34;20220127-34;Y=0.1078x+4.1363;0.1078;4.1363;193.1496;Y=0.0108x-0.0078;0.0108;-0.0078;2.902
Sample 35;4;100;0.5;0.4;12.18;0.5;20220204-09;Y=0.0872x-26.718;0.0872;26.718;15219.7016;Y=0.0839x-0.9596;0.0839;-0.9596;7.9958;Sample 35;20220204-10;Y=0.1009x+4.7812;0.1009;4.7812;227.0172;Y=0.1217x-0.1072;0.1217;-0.1072;3.8432
Sample 36;4;100;0.5;0.8;12.2;0.5;20220204-10;Y=0.0872x-26.718;0.0872;26.718;31609.3016;Y=0.0839x-0.9596;0.0839;-0.9596;6.749;Sample 36;20220204-11;Y=0.1009x+4.7812;0.1009;4.7812;203.2336;Y=0.1217x-0.1072;0.1217;-0.1072;4.0844
Sample 37;4;100;0.5;0.4;12.19;0.5;20220204-11;Y=0.0872x-26.718;0.0872;26.718;2868.742;Y=0.0839x-0.9596;0.0839;-0.9596;6.5344;Sample 37;20220204-12;Y=0.1009x+4.7812;0.1009;4.7812;207.1108;Y=0.1217x-0.1072;0.1217;-0.1072;3.5534
Sample 38;4;100;0.5;0.4;12.16;0.5;20220204-12;Y=0.0872x-26.718;0.0872;26.718;16502.9076;Y=0.0839x-0.9596;0.0839;-0.9596;4.548;Sample 38;20220204-13;Y=0.1009x+4.7812;0.1009;4.7812;207.085;Y=0.1217x-0.1072;0.1217;-0.1072;4.0708
Sample 39;4;60;0.5;0.4;12;0.5;20220204-13;Y=0.0872x-26.718;0.0872;26.718;11075.8098;Y=0.0839x-0.9596;0.0839;-0.9596;6.7956;Sample 39;20220204-14;Y=0.1009x+4.7812;0.1009;4.7812;275.5084;Y=0.1217x-0.1072;0.1217;-0.1072;4.6278
Sample 40;4;100;0.5;0.4;12.23;0.5;20220204-15;Y=0.0872x-26.718;0.0872;26.718;17160.078;Y=0.0839x-0.9596;0.0839;-0.9596;4.8958;Sample 40;20220204-15;Y=0.1009x+4.7812;0.1009;4.7812;200.3156;Y=0.1217x-0.1072;0.1217;-0.1072;3.6208
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