From 861e955073fdfb6ee5088a1adf667b3a116c585d Mon Sep 17 00:00:00 2001 From: Sam Gurr Date: Sun, 17 Dec 2023 23:32:54 -0500 Subject: [PATCH] first commit, added some data, very rough draft orgnaization --- RAnalysis/Data/Dstage.data.csv | 88 ++++ RAnalysis/Data/larval_growth.csv | 132 ++++++ RAnalysis/Data/larval_survival.csv | 259 +++++++++++ RAnalysis/Data/metamorphosis.csv | 61 +++ .../Respiration/data/RR_bad_data_larvae.csv | 93 ++++ .../data/RR_blanks_means_larvae.csv | 13 + .../Respiration/data/RR_calc_raw_larvae.csv | 119 +++++ .../Output/Respiration/plots/F2_RR_larvae.pdf | Bin 0 -> 11112 bytes .../Respiration/plots/F3_RR_larvae_16DPF.pdf | Bin 0 -> 12368 bytes .../Respiration/plots/F3_RR_larvae_2DPF.pdf | Bin 0 -> 13033 bytes .../Respiration/plots/F3_RR_larvae_7DPF.pdf | Bin 0 -> 12282 bytes .../BaySacllopLarvae_Dstage_Abnormality.Rmd | 419 ++++++++++++++++++ RAnalysis/Scripts/LarvalGrowth.Rmd | 121 +++++ RAnalysis/Scripts/LarvalSurvival.Rmd | 154 +++++++ RAnalysis/Scripts/Metamorphosis.Rmd | 141 ++++++ 15 files changed, 1600 insertions(+) create mode 100644 RAnalysis/Data/Dstage.data.csv create mode 100644 RAnalysis/Data/larval_growth.csv create mode 100644 RAnalysis/Data/larval_survival.csv create mode 100644 RAnalysis/Data/metamorphosis.csv create mode 100644 RAnalysis/Output/Respiration/data/RR_bad_data_larvae.csv create mode 100644 RAnalysis/Output/Respiration/data/RR_blanks_means_larvae.csv create mode 100644 RAnalysis/Output/Respiration/data/RR_calc_raw_larvae.csv create mode 100644 RAnalysis/Output/Respiration/plots/F2_RR_larvae.pdf create mode 100644 RAnalysis/Output/Respiration/plots/F3_RR_larvae_16DPF.pdf create mode 100644 RAnalysis/Output/Respiration/plots/F3_RR_larvae_2DPF.pdf create mode 100644 RAnalysis/Output/Respiration/plots/F3_RR_larvae_7DPF.pdf create mode 100644 RAnalysis/Scripts/BaySacllopLarvae_Dstage_Abnormality.Rmd create mode 100644 RAnalysis/Scripts/LarvalGrowth.Rmd create mode 100644 RAnalysis/Scripts/LarvalSurvival.Rmd create mode 100644 RAnalysis/Scripts/Metamorphosis.Rmd diff --git a/RAnalysis/Data/Dstage.data.csv b/RAnalysis/Data/Dstage.data.csv new file mode 100644 index 0000000..6eb9083 --- /dev/null +++ b/RAnalysis/Data/Dstage.data.csv @@ -0,0 +1,88 @@ +Parent,Treatment,Rep,ID,Generation,Year,Run ,Length,Survival ,Normal,Lethal.Deformities,dead,Percent.deformed,total individuals +LOW,Low OA,A,1,1,2021,2,96.86492308,37%,23,1,0,0.042,24 +LOW,Low OA,B,2,1,2021,2,99.87604545,26%,28,2,6,0.067,36 +LOW,Low OA,C,3,1,2021,2,96.0788125,30%,50,2,4,0.038,56 +LOW,Low OA,D,4,1,2021,2,96.11265625,32%,55,5,5,0.083,65 +LOW,Low OA,E,5,1,2021,2,95.12751429,31%,46,4,6,0.08,56 +MODERATE,Moderate OA,A,6,1,2021,2,,20%,,,,,0 +MODERATE,Moderate OA,B,7,1,2021,2,95.27536,22%,63,0,3,0,66 +MODERATE,Moderate OA,C,8,1,2021,2,95.39796,18%,51,7,8,0.121,66 +MODERATE,Moderate OA,D,9,1,2021,2,93.86782,22%,47,2,4,0.041,53 +MODERATE,Moderate OA,E,10,1,2021,2,93.93840426,24%,45,0,4,0,49 +HIGH,High OA,A,11,1,2021,2,68.86038889,14%,4,40,0,0.909,44 +HIGH,High OA,B,12,1,2021,2,70.2973,11%,3,21,0,0.875,24 +HIGH,High OA,C,13,1,2021,2,66.45377778,10%,2,17,1,0.895,20 +HIGH,High OA,D,14,1,2021,2,76.81166667,7%,1,23,3,0.958,27 +HIGH,High OA,E,15,1,2021,2,,9%,,,,,0 +LOW,Low OA,A,1,1,2021,1,,,30,2,10,0.063,42 +LOW,Low OA,B,2,1,2021,1,,,32,0,2,0,34 +LOW,Low OA,C,3,1,2021,1,,,61,3,10,0.047,74 +LOW,Low OA,D,4,1,2021,1,,,42,2,4,0.045,48 +MODERATE,Moderate OA,A,5,1,2021,1,,,74,2,6,0.026,82 +MODERATE,Moderate OA,B,6,1,2021,1,,,54,2,5,0.036,61 +MODERATE,Moderate OA,C,7,1,2021,1,,,18,4,3,0.182,25 +MODERATE,Moderate OA,D,8,1,2021,1,,,59,5,10,0.078,74 +HIGH,High OA,A,9,1,2021,1,,,2,4,1,0.667,7 +HIGH,High OA,B,10,1,2021,1,,,3,21,0,0.875,24 +HIGH,High OA,C,11,1,2021,1,,,3,17,0,0.85,20 +HIGH,High OA,D,12,1,2021,1,,,4,51,4,0.927,59 +LOW,Low OA,A,1,2,2022,3,,,21,1,,0.045,22 +LOW,Low OA,B,2,2,2022,3,,,27,4,,0.129,31 +LOW,Low OA,C,3,2,2022,3,,,31,5,,0.139,36 +MODERATE,Low OA,A,4,2,2022,3,,,8,5,,0.385,13 +MODERATE,Low OA,B,5,2,2022,3,,,34,6,,0.15,40 +MODERATE,Low OA,C,6,2,2022,3,,,18,2,,0.1,20 +HIGH,Low OA,A,7,2,2022,3,,,13,3,,0.188,16 +HIGH,Low OA,B,8,2,2022,3,,,23,5,,0.179,28 +HIGH,Low OA,C,9,2,2022,3,,,22,4,,0.154,26 +LOW,Moderate OA,A,10,2,2022,3,,,30,4,,0.118,34 +LOW,Moderate OA,B,11,2,2022,3,,,48,11,,0.186,59 +LOW,Moderate OA,C,12,2,2022,3,,,45,4,,0.082,49 +MODERATE,Moderate OA,A,13,2,2022,3,,,16,3,,0.158,19 +MODERATE,Moderate OA,B,14,2,2022,3,,,14,8,,0.364,22 +MODERATE,Moderate OA,C,15,2,2022,3,,,20,7,,0.259,27 +HIGH,Moderate OA,A,16,2,2022,3,,,17,0,,0,17 +HIGH,Moderate OA,B,17,2,2022,3,,,19,5,,0.208,24 +HIGH,Moderate OA,C,18,2,2022,3,,,14,8,,0.364,22 +LOW,High OA,A,19,2,2022,3,,,3,27,,0.9,30 +LOW,High OA,B,20,2,2022,3,,,3,29,,0.906,32 +LOW,High OA,C,21,2,2022,3,,,2,64,,0.97,66 +MODERATE,High OA,A,22,2,2022,3,,,2,30,,0.938,32 +MODERATE,High OA,B,23,2,2022,3,,,1,42,,0.977,43 +MODERATE,High OA,C,24,2,2022,3,,,1,15,,0.938,16 +HIGH,High OA,A,25,2,2022,3,,,1,24,,0.96,25 +HIGH,High OA,B,26,2,2022,3,,,1,22,,0.957,23 +HIGH,High OA,C,27,2,2022,3,,,1,36,,0.973,37 +LOW,Low OA,A,1,2,2022,4,,,54,4,4,0.069,62 +LOW,Low OA,B,2,2,2022,4,,,28,2,1,0.067,31 +lOW,Low OA,C,3,2,2022,4,,,44,7,4,0.137,55 +MODERATE,Moderate OA,A,10,2,2022,4,,,41,10,2,0.196,53 +MODERATE,Moderate OA,B,11,2,2022,4,,,63,3,6,0.045,72 +MODERATE,Moderate OA,C,12,2,2022,4,,,48,4,2,0.077,54 +LOW,Low OA,A,1,3,2023,6,,,44,11,1,0.2,56 +LOW,Low OA,B,2,3,2023,6,,,14,2,0,0.125,16 +LOW,Low OA,C,3,3,2023,6,,,63,27,9,0.3,99 +MODERATE,Low OA,A,4,3,2023,6,,,41,20,1,0.328,62 +MODERATE,Low OA,B,5,3,2023,6,,,37,6,0,0.14,43 +MODERATE,Low OA,C,6,3,2023,6,,,31,19,0,0.38,50 +LOW,Moderate OA,A,7,3,2023,6,,,17,15,0,0.469,32 +LOW,Moderate OA,B,8,3,2023,6,,,33,15,0,0.313,48 +LOW,Moderate OA,C,9,3,2023,6,,,20,15,1,0.429,36 +MODERATE,Moderate OA,A,10,3,2023,6,,,17,7,0,0.292,24 +MODERATE,Moderate OA,B,11,3,2023,6,,,12,23,0,0.657,35 +MODERATE,Moderate OA,C,12,3,2023,6,,,18,21,0,0.538,39 +LOW,High OA,A,13,3,2023,6,,,,,,,0 +LOW,High OA,B,14,3,2023,6,,,41,30,1,0.423,72 +LOW,High OA,C,15,3,2023,6,,,6,21,0,0.778,27 +MODERATE,High OA,A,16,3,2023,6,,,42,34,2,0.447,78 +MODERATE,High OA,B,17,3,2023,6,,,22,38,2,0.633,62 +MODERATE,High OA,C,18,3,2023,6,,,48,52,3,0.52,103 +HIGH,Low OA,A,19,3,2023,6,,,32,23,2,0.418,57 +HIGH,Low OA,B,20,3,2023,6,,,20,21,1,0.512,42 +HIGH,Low OA,C,21,3,2023,6,,,35,24,1,0.407,60 +HIGH,Moderate OA,A,22,3,2023,6,,,12,10,1,0.455,23 +HIGH,Moderate OA,B,23,3,2023,6,,,29,17,0,0.37,46 +HIGH,Moderate OA,C,24,3,2023,6,,,15,14,0,0.483,29 +HIGH,High OA,A,25,3,2023,6,,,39,29,0,0.426,68 +HIGH,High OA,B,26,3,2023,6,,,51,28,0,0.354,79 +HIGH,High OA,C,27,3,2023,6,,,28,30,0,0.517,58 diff --git a/RAnalysis/Data/larval_growth.csv b/RAnalysis/Data/larval_growth.csv new file mode 100644 index 0000000..5579757 --- /dev/null +++ b/RAnalysis/Data/larval_growth.csv @@ -0,0 +1,132 @@ +Generation,Age,Parental_OA,treatment,Rep,ID,Length +2,2,LOW,Low OA,A,1,104.70 +2,2,LOW,Low OA,B,2,100.10 +2,2,LOW,Low OA,C,3,104.50 +2,2,MODERATE,Moderate OA,A,10,104.10 +2,2,MODERATE,Moderate OA,B,11,99.20 +2,2,MODERATE,Moderate OA,C,12,99.60 +2,4,LOW,Low OA,A,1,111.20 +2,4,LOW,Low OA,B,2,109.30 +2,4,LOW,Low OA,C,3,109.60 +2,4,MODERATE,Moderate OA,A,10,108.30 +2,4,MODERATE,Moderate OA,B,11,107.10 +2,4,MODERATE,Moderate OA,C,12,106.20 +2,6,LOW,Low OA,A,1,129.80 +2,6,LOW,Low OA,B,2,133.00 +2,6,LOW,Low OA,C,3,129.80 +2,6,MODERATE,Moderate OA,A,10,128.30 +2,6,MODERATE,Moderate OA,B,11,127.90 +2,6,MODERATE,Moderate OA,C,12,124.70 +2,8,LOW,Low OA,A,1,139.30 +2,8,LOW,Low OA,B,2,144.40 +2,8,LOW,Low OA,C,3,147.90 +2,8,MODERATE,Moderate OA,A,10,142.00 +2,8,MODERATE,Moderate OA,B,11,143.30 +2,8,MODERATE,Moderate OA,C,12,139.20 +2,10,LOW,Low OA,A,1,165.40 +2,10,LOW,Low OA,B,2,168.90 +2,10,LOW,Low OA,C,3,177.50 +2,10,MODERATE,Moderate OA,A,10,169.10 +2,10,MODERATE,Moderate OA,B,11,167.60 +2,10,MODERATE,Moderate OA,C,12,149.40 +2,12,LOW,Low OA,A,1,181.60 +2,12,LOW,Low OA,B,2,187.70 +2,12,LOW,Low OA,C,3,188.80 +2,12,MODERATE,Moderate OA,A,10,175.20 +2,12,MODERATE,Moderate OA,B,11,173.30 +2,12,MODERATE,Moderate OA,C,12,176.70 +2,14,LOW,Low OA,A,1,201.10 +2,14,LOW,Low OA,B,2,206.60 +2,14,LOW,Low OA,C,3,203.10 +2,14,MODERATE,Moderate OA,A,10,194.60 +2,14,MODERATE,Moderate OA,B,11,194.80 +2,14,MODERATE,Moderate OA,C,12,198.30 +2,21,LOW,Low OA,A,1,350.60 +2,21,LOW,Low OA,B,2,349.70 +2,21,LOW,Low OA,C,3,315.10 +2,21,MODERATE,Moderate OA,A,10,320.60 +2,21,MODERATE,Moderate OA,B,11,267.20 +2,21,MODERATE,Moderate OA,C,12,317.70 +1,2,WILD,Low OA,A,1,96.86 +1,2,WILD,Low OA,B,2,99.88 +1,2,WILD,Low OA,C,3,96.08 +1,2,WILD,Low OA,D,4,96.11 +1,2,WILD,Low OA,E,5,95.13 +1,2,WILD,Moderate OA,B,7,95.28 +1,2,WILD,Moderate OA,C,8,95.40 +1,2,WILD,Moderate OA,D,9,93.87 +1,2,WILD,Moderate OA,E,10,93.94 +1,2,WILD,High OA,A,11,68.86 +1,2,WILD,High OA,B,12,70.30 +1,2,WILD,High OA,C,13,66.45 +1,2,WILD,High OA,D,14,76.81 +1,4,WILD,Low OA,A,1,107.06 +1,4,WILD,Low OA,B,2,110.54 +1,4,WILD,Low OA,C,3,106.23 +1,4,WILD,Low OA,D,4,107.49 +1,4,WILD,Low OA,E,5,107.78 +1,4,WILD,Moderate OA,B,7,106.24 +1,4,WILD,Moderate OA,C,8,103.19 +1,4,WILD,Moderate OA,D,9,102.34 +1,4,WILD,Moderate OA,E,10,102.42 +1,4,WILD,High OA,A,11,83.00 +1,4,WILD,High OA,B,12,79.70 +1,4,WILD,High OA,C,13,69.58 +1,4,WILD,High OA,D,14,78.50 +1,8,WILD,Low OA,A,1,181.13 +1,8,WILD,Low OA,B,2,166.50 +1,8,WILD,Low OA,C,3,161.25 +1,8,WILD,Low OA,D,4,159.13 +1,8,WILD,Low OA,E,5,153.31 +1,8,WILD,Moderate OA,A,6,146.08 +1,8,WILD,Moderate OA,B,7,162.35 +1,8,WILD,Moderate OA,C,8,165.43 +1,8,WILD,Moderate OA,D,9,156.14 +1,8,WILD,Moderate OA,E,10,158.59 +1,8,WILD,High OA,A,11,110.00 +1,8,WILD,High OA,B,12,83.44 +1,8,WILD,High OA,C,13,113.75 +1,8,WILD,High OA,D,14,90.58 +1,8,WILD,High OA,E,15,93.36 +1,10,WILD,Low OA,A,1,193.76 +1,10,WILD,Low OA,B,2,174.93 +1,10,WILD,Low OA,C,3,181.32 +1,10,WILD,Low OA,D,4,177.87 +1,10,WILD,Low OA,E,5,183.72 +1,10,WILD,Moderate OA,A,6,156.64 +1,10,WILD,Moderate OA,B,7,177.28 +1,10,WILD,Moderate OA,C,8,178.12 +1,10,WILD,Moderate OA,D,9,168.02 +1,10,WILD,Moderate OA,E,10,166.61 +1,10,WILD,High OA,A,11,136.91 +1,10,WILD,High OA,B,12,95.91 +1,10,WILD,High OA,C,13,121.27 +1,10,WILD,High OA,D,14,90.14 +1,10,WILD,High OA,E,15,80.38 +1,14,WILD,Low OA,A,1,318.43 +1,14,WILD,Low OA,B,2,338.52 +1,14,WILD,Low OA,C,3,298.22 +1,14,WILD,Low OA,D,4,343.28 +1,14,WILD,Low OA,E,5,279.22 +1,14,WILD,Moderate OA,A,6,272.64 +1,14,WILD,Moderate OA,B,7,284.98 +1,14,WILD,Moderate OA,C,8,351.71 +1,14,WILD,Moderate OA,D,9,276.39 +1,14,WILD,Moderate OA,E,10,298.18 +1,14,WILD,High OA,A,11,200.48 +1,14,WILD,High OA,B,12,233.26 +1,14,WILD,High OA,C,13,192.52 +1,14,WILD,High OA,D,14,161.11 +1,14,WILD,High OA,E,15,206.54 +1,18,WILD,Low OA,A,1,528.73 +1,18,WILD,Low OA,B,2,584.18 +1,18,WILD,Low OA,C,3,513.17 +1,18,WILD,Low OA,D,4,557.09 +1,18,WILD,Low OA,E,5,556.62 +1,18,WILD,Moderate OA,A,6,533.34 +1,18,WILD,Moderate OA,B,7,539.39 +1,18,WILD,Moderate OA,C,8,582.50 +1,18,WILD,Moderate OA,D,9,595.27 +1,18,WILD,Moderate OA,E,10,493.50 +1,18,WILD,High OA,A,11,472.62 +1,18,WILD,High OA,B,12,384.06 diff --git a/RAnalysis/Data/larval_survival.csv b/RAnalysis/Data/larval_survival.csv new file mode 100644 index 0000000..09dc430 --- /dev/null +++ b/RAnalysis/Data/larval_survival.csv @@ -0,0 +1,259 @@ +Parental_OA,Exposure_OA,treatment,Generation,Tank,Tank_Number,Date,Age,Count,proportion,Percent_Survival +LOW,LOW,Low OA,2,A,1,8/18/2022,2,"60,667",1,100 +LOW,LOW,Low OA,2,B,2,8/18/2022,2,"40,133",1,100 +LOW,LOW,Low OA,2,C,3,8/18/2022,2,"49,200",1,100 +MODERATE,MODERATE,Moderate OA,2,A,10,8/18/2022,2,"63,600",1,100 +MODERATE,MODERATE,Moderate OA,2,B,11,8/18/2022,2,"64,000",1,100 +MODERATE,MODERATE,Moderate OA,2,C,12,8/18/2022,2,"74,200",1,100 +LOW,LOW,Low OA,2,A,1,8/22/2022,6,"16,800",0.28,28 +LOW,LOW,Low OA,2,B,2,8/22/2022,6,"11,250",0.28,28 +LOW,LOW,Low OA,2,C,3,8/22/2022,6,"17,400",0.35,35 +MODERATE,MODERATE,Moderate OA,2,A,10,8/22/2022,6,"37,200",0.58,58 +MODERATE,MODERATE,Moderate OA,2,B,11,8/22/2022,6,"30,000",0.47,47 +MODERATE,MODERATE,Moderate OA,2,C,12,8/22/2022,6,"26,600",0.36,36 +LOW,LOW,Low OA,2,A,1,8/24/2022,8,"12,333",0.2,20 +LOW,LOW,Low OA,2,B,2,8/24/2022,8,"5,867",0.15,15 +LOW,LOW,Low OA,2,C,3,8/24/2022,8,"13,770",0.28,28 +MODERATE,MODERATE,Moderate OA,2,A,10,8/24/2022,8,"18,000",0.28,28 +MODERATE,MODERATE,Moderate OA,2,B,11,8/24/2022,8,"25,250",0.39,39 +MODERATE,MODERATE,Moderate OA,2,C,12,8/24/2022,8,"19,000",0.26,26 +LOW,LOW,Low OA,2,A,1,8/26/2022,10,"5,800",0.1,10 +LOW,LOW,Low OA,2,B,2,8/26/2022,10,"3,200",0.08,8 +LOW,LOW,Low OA,2,C,3,8/26/2022,10,"6,000",0.12,12 +MODERATE,MODERATE,Moderate OA,2,A,10,8/26/2022,10,"17,200",0.27,27 +MODERATE,MODERATE,Moderate OA,2,B,11,8/26/2022,10,"17,000",0.27,27 +MODERATE,MODERATE,Moderate OA,2,C,12,8/26/2022,10,"15,000",0.2,20 +LOW,LOW,Low OA,2,A,1,8/30/2022,14,"2,400",0.04,4 +LOW,LOW,Low OA,2,B,2,8/30/2022,14,"1,333",0.03,3 +LOW,LOW,Low OA,2,C,3,8/30/2022,14,"6,000",0.12,12 +MODERATE,MODERATE,Moderate OA,2,A,10,8/30/2022,14,"11,167",0.18,18 +MODERATE,MODERATE,Moderate OA,2,B,11,8/30/2022,14,"9,000",0.14,14 +MODERATE,MODERATE,Moderate OA,2,C,12,8/30/2022,14,"12,000",0.16,16 +LOW,LOW,Low OA,2,A,1,9/6/2022,21,"1,139.00",0.02,2 +LOW,LOW,Low OA,2,B,2,9/6/2022,21,"2,208.00",0.06,6 +LOW,LOW,Low OA,2,C,3,9/6/2022,21,700,0.01,1 +MODERATE,MODERATE,Moderate OA,2,A,10,9/6/2022,21,600,0.01,1 +MODERATE,MODERATE,Moderate OA,2,B,11,9/6/2022,21,399,0.01,1 +MODERATE,MODERATE,Moderate OA,2,C,12,9/6/2022,21,348,0,0 +WILD,LOW,Low OA,1,A,1,7/28/2021,2,91250,0.38,38 +WILD,LOW,Low OA,1,B,2,7/28/2021,2,64375,0.27,27 +WILD,LOW,Low OA,1,C,3,7/28/2021,2,75625,0.32,32 +WILD,LOW,Low OA,1,D,4,7/28/2021,2,79375,0.33,33 +WILD,LOW,Low OA,1,E,5,7/28/2021,2,76875,0.32,32 +WILD,MODERATE,Moderate OA,1,A,6,7/28/2021,2,50000,0.21,21 +WILD,MODERATE,Moderate OA,1,B,7,7/28/2021,2,55000,0.23,23 +WILD,MODERATE,Moderate OA,1,C,8,7/28/2021,2,45625,0.19,19 +WILD,MODERATE,Moderate OA,1,D,9,7/28/2021,2,55625,0.23,23 +WILD,MODERATE,Moderate OA,1,E,10,7/28/2021,2,60000,0.22,22 +WILD,HIGH,High OA,1,A,11,7/28/2021,2,35000,0.15,15 +WILD,HIGH,High OA,1,B,12,7/28/2021,2,28125,0.12,12 +WILD,HIGH,High OA,1,C,13,7/28/2021,2,25000,0.1,10 +WILD,HIGH,High OA,1,D,14,7/28/2021,2,16875,0.07,7 +WILD,HIGH,High OA,1,E,15,7/28/2021,2,22500,0.09,9 +WILD,LOW,Low OA,1,A,1,7/30/2021,4,58667,0.07,7.08557 +WILD,LOW,Low OA,1,B,2,7/30/2021,4,61500,0.09,9.44743 +WILD,LOW,Low OA,1,C,3,7/30/2021,4,48000,0.2,20.15452 +WILD,LOW,Low OA,1,D,4,7/30/2021,4,51500,0.22,21.62412 +WILD,LOW,Low OA,1,E,5,7/30/2021,4,56500,0.24,23.72355 +WILD,MODERATE,Moderate OA,1,A,6,7/30/2021,4,50000,0.21,20.99429 +WILD,MODERATE,Moderate OA,1,B,7,7/30/2021,4,38500,0.16,16.1656 +WILD,MODERATE,Moderate OA,1,C,8,7/30/2021,4,35333,0.15,14.83596 +WILD,MODERATE,Moderate OA,1,D,9,7/30/2021,4,41500,0.17,17.42526 +WILD,MODERATE,Moderate OA,1,E,10,7/30/2021,4,50500,0.19,18.68848 +WILD,HIGH,High OA,1,A,11,7/30/2021,4,14500,0.06,6.08834 +WILD,HIGH,High OA,1,B,12,7/30/2021,4,12500,0.05,5.24857 +WILD,HIGH,High OA,1,C,13,7/30/2021,4,12000,0.05,5.03863 +WILD,HIGH,High OA,1,D,14,7/30/2021,4,7000,0.03,2.9392 +WILD,HIGH,High OA,1,E,15,7/30/2021,4,11000,0.05,4.61874 +WILD,LOW,Low OA,1,A,1,8/3/2021,8,34500,0.14,14.48606 +WILD,LOW,Low OA,1,B,2,8/3/2021,8,43000,0.18,18.05509 +WILD,LOW,Low OA,1,C,3,8/3/2021,8,20500,0.09,8.60766 +WILD,LOW,Low OA,1,D,4,8/3/2021,8,31000,0.13,13.01646 +WILD,LOW,Low OA,1,E,5,8/3/2021,8,26000,0.11,10.91703 +WILD,MODERATE,Moderate OA,1,A,6,8/3/2021,8,20000,0.08,8.39772 +WILD,MODERATE,Moderate OA,1,B,7,8/3/2021,8,26000,0.11,10.91703 +WILD,MODERATE,Moderate OA,1,C,8,8/3/2021,8,26500,0.11,11.12697 +WILD,MODERATE,Moderate OA,1,D,9,8/3/2021,8,25000,0.1,10.49714 +WILD,MODERATE,Moderate OA,1,E,10,8/3/2021,8,22500,0.08,8.32655 +WILD,HIGH,High OA,1,A,11,8/3/2021,8,5500,0.02,2.30937 +WILD,HIGH,High OA,1,B,12,8/3/2021,8,3733,0.02,1.56757 +WILD,HIGH,High OA,1,C,13,8/3/2021,8,1867,0.01,0.78379 +WILD,HIGH,High OA,1,D,14,8/3/2021,8,3200,0.01,1.34363 +WILD,HIGH,High OA,1,E,15,8/3/2021,8,10667,0.04,4.47878 +WILD,LOW,Low OA,1,A,1,8/5/2021,10,20600,0.09,8.64965 +WILD,LOW,Low OA,1,B,2,8/5/2021,10,23960,0.1,10.06046 +WILD,LOW,Low OA,1,C,3,8/5/2021,10,16000,0.07,6.71817 +WILD,LOW,Low OA,1,D,4,8/5/2021,10,23000,0.1,9.65737 +WILD,LOW,Low OA,1,E,5,8/5/2021,10,27500,0.12,11.54686 +WILD,MODERATE,Moderate OA,1,A,6,8/5/2021,10,16500,0.07,6.92812 +WILD,MODERATE,Moderate OA,1,B,7,8/5/2021,10,16500,0.07,6.92812 +WILD,MODERATE,Moderate OA,1,C,8,8/5/2021,10,19000,0.08,7.97783 +WILD,MODERATE,Moderate OA,1,D,9,8/5/2021,10,19500,0.08,8.18777 +WILD,MODERATE,Moderate OA,1,E,10,8/5/2021,10,19500,0.07,7.21634 +WILD,HIGH,High OA,1,A,11,8/5/2021,10,1800,0.01,0.75579 +WILD,HIGH,High OA,1,B,12,8/5/2021,10,1000,0,0.41989 +WILD,HIGH,High OA,1,C,13,8/5/2021,10,800,0,0.33591 +WILD,HIGH,High OA,1,D,14,8/5/2021,10,200,0,0.08398 +WILD,HIGH,High OA,1,E,15,8/5/2021,10,500,0,0.20994 +WILD,LOW,Low OA,1,A,1,8/9/2021,14,21077,0.09,8.84979 +WILD,LOW,Low OA,1,B,2,8/9/2021,14,21000,0.09,8.8176 +WILD,LOW,Low OA,1,C,3,8/9/2021,14,14567,0.06,6.11634 +WILD,LOW,Low OA,1,D,4,8/9/2021,14,15400,0.06,6.46624 +WILD,LOW,Low OA,1,E,5,8/9/2021,14,24725,0.1,10.38168 +WILD,MODERATE,Moderate OA,1,A,6,8/9/2021,14,19067,0.08,8.00582 +WILD,MODERATE,Moderate OA,1,B,7,8/9/2021,14,17600,0.07,7.38999 +WILD,MODERATE,Moderate OA,1,C,8,8/9/2021,14,28800,0.12,12.09271 +WILD,MODERATE,Moderate OA,1,D,9,8/9/2021,14,15600,0.07,6.55022 +WILD,MODERATE,Moderate OA,1,E,10,8/9/2021,14,2520,0.01,0.93257 +WILD,HIGH,High OA,1,A,11,8/9/2021,14,61,0,0.026 +WILD,HIGH,High OA,1,B,12,8/9/2021,14,8,0,0.003 +WILD,HIGH,High OA,1,C,13,8/9/2021,14,4,0,0.002 +WILD,HIGH,High OA,1,D,14,8/9/2021,14,6,0,0.003 +WILD,HIGH,High OA,1,E,15,8/9/2021,14,3,0,0.001 +WILD,LOW,Low OA,1,A,1,8/13/2021,18,6583,0.03,2.63333 +WILD,LOW,Low OA,1,B,2,8/13/2021,18,4300,0.02,1.72 +WILD,LOW,Low OA,1,C,3,8/13/2021,18,2200,0.01,0.88 +WILD,LOW,Low OA,1,D,4,8/13/2021,18,10533,0.04,4.21333 +WILD,LOW,Low OA,1,E,5,8/13/2021,18,15083,0.06,6.03333 +WILD,MODERATE,Moderate OA,1,A,6,8/13/2021,18,623,0,0.24933 +WILD,MODERATE,Moderate OA,1,B,7,8/13/2021,18,433,0,0.17333 +WILD,MODERATE,Moderate OA,1,C,8,8/13/2021,18,3960,0.02,1.584 +WILD,MODERATE,Moderate OA,1,D,9,8/13/2021,18,1733,0.01,0.69333 +WILD,MODERATE,Moderate OA,1,E,10,8/13/2021,18,400,0,0.16 +WILD,HIGH,High OA,1,A,11,8/13/2021,18,61,0,0.0244 +WILD,HIGH,High OA,1,B,12,8/13/2021,18,23,0,0.0092 +LOW,LOW,Low OA,3,A,1,4/7/2023,2,"76,128.00",0.19,19.28 +LOW,LOW,Low OA,3,B,2,4/7/2023,2,"60,090.67",0.15,15.15 +LOW,LOW,Low OA,3,C,3,4/7/2023,2,"91,466.67",0.23,23.37 +MODERATE,LOW,Low OA,3,A,4,4/7/2023,2,"74,612.00",0.19,18.93 +MODERATE,LOW,Low OA,3,B,5,4/7/2023,2,"106,358.00",0.27,27 +MODERATE,LOW,Low OA,3,C,6,4/7/2023,2,"96,238.67",0.25,24.53 +LOW,MODERATE,Moderate OA,3,A,7,4/7/2023,2,"70,286.67",0.18,17.82 +LOW,MODERATE,Moderate OA,3,B,8,4/7/2023,2,"68,715.33",0.17,17.4 +LOW,MODERATE,Moderate OA,3,C,9,4/7/2023,2,"68,908.00",0.17,17.4 +MODERATE,MODERATE,Moderate OA,3,A,10,4/7/2023,2,"87,360.00",0.22,22.17 +MODERATE,MODERATE,Moderate OA,3,B,11,4/7/2023,2,"74,612.00",0.19,18.93 +MODERATE,MODERATE,Moderate OA,3,C,12,4/7/2023,2,"93,600.00",0.24,23.78 +LOW,HIGH,High OA,3,A,13,4/7/2023,2,"59,453.33",0.15,15.07 +LOW,HIGH,High OA,3,B,14,4/7/2023,2,"85,064.00",0.22,21.7 +LOW,HIGH,High OA,3,C,15,4/7/2023,2,"67,392.00",0.17,17.04 +MODERATE,HIGH,High OA,3,A,16,4/7/2023,2,"117,417.33",0.3,29.88 +MODERATE,HIGH,High OA,3,B,17,4/7/2023,2,"87,360.00",0.22,22.17 +MODERATE,HIGH,High OA,3,C,18,4/7/2023,2,"111,589.33",0.29,28.64 +HIGH,LOW,Low OA,3,A,19,4/7/2023,2,"90,844.00",0.23,23.1 +HIGH,LOW,Low OA,3,B,20,4/7/2023,2,"70,286.67",0.18,17.82 +HIGH,LOW,Low OA,3,C,21,4/7/2023,2,"77,376.00",0.2,19.6 +HIGH,MODERATE,Moderate OA,3,A,22,4/7/2023,2,"106,100.00",0.27,26.96 +HIGH,MODERATE,Moderate OA,3,B,23,4/7/2023,2,"80,838.00",0.21,20.56 +HIGH,MODERATE,Moderate OA,3,C,24,4/7/2023,2,"104,832.00",0.27,26.69 +HIGH,HIGH,High OA,3,A,25,4/7/2023,2,"94,076.00",0.24,23.96 +HIGH,HIGH,High OA,3,B,26,4/7/2023,2,"100,564.00",0.26,25.65 +HIGH,HIGH,High OA,3,C,27,4/7/2023,2,"76,774.67",0.19,19.49 +LOW,LOW,Low OA,3,A,1,4/10/2023,5,"36,135.67",0.09,9.15 +LOW,LOW,Low OA,3,B,2,4/10/2023,5,"46,953.00",0.12,11.84 +LOW,LOW,Low OA,3,C,3,4/10/2023,5,"29,964.00",0.08,7.65 +MODERATE,LOW,Low OA,3,A,4,4/10/2023,5,"46,953.00",0.12,11.92 +MODERATE,LOW,Low OA,3,B,5,4/10/2023,5,"58,941.00",0.15,14.96 +MODERATE,LOW,Low OA,3,C,6,4/10/2023,5,"58,283.33",0.15,14.85 +LOW,MODERATE,Moderate OA,3,A,7,4/10/2023,5,"40,959.00",0.1,10.38 +LOW,MODERATE,Moderate OA,3,B,8,4/10/2023,5,"32,638.67",0.08,8.26 +LOW,MODERATE,Moderate OA,3,C,9,4/10/2023,5,"46,631.67",0.12,11.77 +MODERATE,MODERATE,Moderate OA,3,A,10,4/10/2023,5,"58,622.67",0.15,14.88 +MODERATE,MODERATE,Moderate OA,3,B,11,4/10/2023,5,"51,961.00",0.13,13.19 +MODERATE,MODERATE,Moderate OA,3,C,12,4/10/2023,5,"69,930.00",0.18,17.77 +LOW,HIGH,High OA,3,A,13,4/10/2023,5,"45,778.33",0.12,11.61 +LOW,HIGH,High OA,3,B,14,4/10/2023,5,"36,135.67",0.09,9.22 +LOW,HIGH,High OA,3,C,15,4/10/2023,5,"44,295.33",0.11,11.2 +MODERATE,HIGH,High OA,3,A,16,4/10/2023,5,"53,269.33",0.14,13.56 +MODERATE,HIGH,High OA,3,B,17,4/10/2023,5,"30,796.33",0.08,7.82 +MODERATE,HIGH,High OA,3,C,18,4/10/2023,5,"48,275.33",0.12,12.39 +HIGH,LOW,Low OA,3,A,19,4/10/2023,5,"62,425.00",0.16,15.87 +HIGH,LOW,Low OA,3,B,20,4/10/2023,5,"69,940.00",0.18,17.73 +HIGH,LOW,Low OA,3,C,21,4/10/2023,5,"68,251.33",0.17,17.3 +HIGH,MODERATE,Moderate OA,3,A,22,4/10/2023,5,"64,935.00",0.17,16.5 +HIGH,MODERATE,Moderate OA,3,B,23,4/10/2023,5,"75,924.00",0.19,19.32 +HIGH,MODERATE,Moderate OA,3,C,24,4/10/2023,5,"41,958.00",0.11,10.68 +HIGH,HIGH,High OA,3,A,25,4/10/2023,5,"55,944.00",0.14,14.25 +HIGH,HIGH,High OA,3,B,26,4/10/2023,5,"66,443.00",0.17,16.95 +HIGH,HIGH,High OA,3,C,27,4/10/2023,5,"47,792.33",0.12,12.13 +LOW,LOW,Low OA,3,A,1,4/12/2023,7,"41,566.67",0.11,10.53 +LOW,LOW,Low OA,3,B,2,4/12/2023,7,"46,517.33",0.12,11.73 +LOW,LOW,Low OA,3,C,3,4/12/2023,7,"23,060.25",0.06,5.89 +MODERATE,LOW,Low OA,3,A,4,4/12/2023,7,"35,747.33",0.09,9.07 +MODERATE,LOW,Low OA,3,B,5,4/12/2023,7,"51,844.00",0.13,13.17 +MODERATE,LOW,Low OA,3,C,6,4/12/2023,7,"34,562.67",0.09,8.81 +LOW,MODERATE,Moderate OA,3,A,7,4/12/2023,7,"37,886.00",0.1,9.61 +LOW,MODERATE,Moderate OA,3,B,8,4/12/2023,7,"24,592.67",0.06,6.23 +LOW,MODERATE,Moderate OA,3,C,9,4/12/2023,7,"31,239.33",0.08,7.89 +MODERATE,MODERATE,Moderate OA,3,A,10,4/12/2023,7,"42,398.00",0.11,10.77 +MODERATE,MODERATE,Moderate OA,3,B,11,4/12/2023,7,"39,072.67",0.1,9.92 +MODERATE,MODERATE,Moderate OA,3,C,12,4/12/2023,7,"59,856.00",0.15,15.22 +LOW,HIGH,High OA,3,A,13,4/12/2023,7,"2,440.00",0.01,0.62 +LOW,HIGH,High OA,3,B,14,4/12/2023,7,"32,422.00",0.08,8.27 +LOW,HIGH,High OA,3,C,15,4/12/2023,7,"31,239.33",0.08,7.9 +MODERATE,HIGH,High OA,3,A,16,4/12/2023,7,"31,590.67",0.08,8.04 +MODERATE,HIGH,High OA,3,B,17,4/12/2023,7,"20,783.33",0.05,5.28 +MODERATE,HIGH,High OA,3,C,18,4/12/2023,7,"20,783.33",0.05,5.34 +HIGH,LOW,Low OA,3,A,19,4/12/2023,7,"41,874.00",0.11,10.65 +HIGH,LOW,Low OA,3,B,20,4/12/2023,7,"34,916.00",0.09,8.86 +HIGH,LOW,Low OA,3,C,21,4/12/2023,7,"41,209.33",0.1,10.45 +HIGH,MODERATE,Moderate OA,3,A,22,4/12/2023,7,"41,209.33",0.1,10.48 +HIGH,MODERATE,Moderate OA,3,B,23,4/12/2023,7,"66,506.67",0.17,16.93 +HIGH,MODERATE,Moderate OA,3,C,24,4/12/2023,7,"39,072.67",0.1,9.95 +HIGH,HIGH,High OA,3,A,25,4/12/2023,7,"22,446.00",0.06,5.72 +HIGH,HIGH,High OA,3,B,26,4/12/2023,7,"39,904.00",0.1,10.18 +HIGH,HIGH,High OA,3,C,27,4/12/2023,7,"32,409.00",0.08,8.23 +LOW,LOW,Low OA,3,A,1,4/17/2023,12,12173,0.03,3.04 +LOW,LOW,Low OA,3,B,2,4/17/2023,12,21249,0.05,5.32 +LOW,LOW,Low OA,3,C,3,4/17/2023,12,15899.56,0.04,3.98 +MODERATE,LOW,Low OA,3,A,4,4/17/2023,12,14428.33,0.04,3.61 +MODERATE,LOW,Low OA,3,B,5,4/17/2023,12,25446.33,0.06,6.37 +MODERATE,LOW,Low OA,3,C,6,4/17/2023,12,14244,0.04,3.56 +LOW,MODERATE,Moderate OA,3,A,7,4/17/2023,12,10354.26,0.03,2.59 +LOW,MODERATE,Moderate OA,3,B,8,4/17/2023,12,16121,0.04,4.03 +LOW,MODERATE,Moderate OA,3,C,9,4/17/2023,12,21056,0.05,5.27 +MODERATE,MODERATE,Moderate OA,3,A,10,4/17/2023,12,11805,0.03,2.95 +MODERATE,MODERATE,Moderate OA,3,B,11,4/17/2023,12,16618,0.04,4.16 +MODERATE,MODERATE,Moderate OA,3,C,12,4/17/2023,12,15463,0.04,3.87 +LOW,HIGH,High OA,3,A,13,4/17/2023,12,17212,0.04,4.3 +LOW,HIGH,High OA,3,B,14,4/17/2023,12,10613.33,0.03,2.65 +LOW,HIGH,High OA,3,C,15,4/17/2023,12,20242,0.05,5.06 +MODERATE,HIGH,High OA,3,A,16,4/17/2023,12,8704.67,0.02,2.18 +MODERATE,HIGH,High OA,3,B,17,4/17/2023,12,15035.33,0.04,3.76 +MODERATE,HIGH,High OA,3,C,18,4/17/2023,12,10199,0.03,2.55 +HIGH,LOW,Low OA,3,A,19,4/17/2023,12,19783.33,0.05,4.95 +HIGH,LOW,Low OA,3,B,20,4/17/2023,12,22157.33,0.06,5.54 +HIGH,LOW,Low OA,3,C,21,4/17/2023,12,25708.67,0.06,6.43 +HIGH,MODERATE,Moderate OA,3,A,22,4/17/2023,12,30597,0.08,7.66 +HIGH,MODERATE,Moderate OA,3,B,23,4/17/2023,12,21385,0.05,5.35 +HIGH,MODERATE,Moderate OA,3,C,24,4/17/2023,12,28294,0.07,7.08 +HIGH,HIGH,High OA,3,A,25,4/17/2023,12,17805,0.04,4.45 +HIGH,HIGH,High OA,3,B,26,4/17/2023,12,13641.33,0.03,3.41 +HIGH,HIGH,High OA,3,C,27,4/17/2023,12,13057,0.03,3.27 +LOW,LOW,Low OA,3,A,1,4/21/2023,16,"6,629.00",0.02,1.66 +LOW,LOW,Low OA,3,B,2,4/21/2023,16,"13,990.00",0.04,3.5 +LOW,LOW,Low OA,3,C,3,4/21/2023,16,"10,684.00",0.03,2.67 +MODERATE,LOW,Low OA,3,A,4,4/21/2023,16,"6,875.00",0.02,1.72 +MODERATE,LOW,Low OA,3,B,5,4/21/2023,16,"13,752.00",0.03,3.44 +MODERATE,LOW,Low OA,3,C,6,4/21/2023,16,"7,364.00",0.02,1.84 +LOW,MODERATE,Moderate OA,3,A,7,4/21/2023,16,"7,772.00",0.02,1.94 +LOW,MODERATE,Moderate OA,3,B,8,4/21/2023,16,"11,659.00",0.03,2.92 +LOW,MODERATE,Moderate OA,3,C,9,4/21/2023,16,"15,559.00",0.04,3.89 +MODERATE,MODERATE,Moderate OA,3,A,10,4/21/2023,16,"7,364.00",0.02,1.84 +MODERATE,MODERATE,Moderate OA,3,B,11,4/21/2023,16,"10,456.00",0.03,2.61 +MODERATE,MODERATE,Moderate OA,3,C,12,4/21/2023,16,"8,669.00",0.02,2.17 +LOW,HIGH,High OA,3,A,13,4/21/2023,16,"7,717.00",0.02,1.93 +LOW,HIGH,High OA,3,B,14,4/21/2023,16,"2,782.00",0.01,0.7 +LOW,HIGH,High OA,3,C,15,4/21/2023,16,"14,350.00",0.04,3.59 +MODERATE,HIGH,High OA,3,A,16,4/21/2023,16,"6,154.00",0.02,1.54 +MODERATE,HIGH,High OA,3,B,17,4/21/2023,16,"5,725.00",0.01,1.43 +MODERATE,HIGH,High OA,3,C,18,4/21/2023,16,"6,280.00",0.02,1.57 +HIGH,LOW,Low OA,3,A,19,4/21/2023,16,"14,051.00",0.04,3.51 +HIGH,LOW,Low OA,3,B,20,4/21/2023,16,"17,639.00",0.04,4.41 +HIGH,LOW,Low OA,3,C,21,4/21/2023,16,"13,693.00",0.03,3.42 +HIGH,MODERATE,Moderate OA,3,A,22,4/21/2023,16,"20,031.00",0.05,5.01 +HIGH,MODERATE,Moderate OA,3,B,23,4/21/2023,16,"8,218.00",0.02,2.05 +HIGH,MODERATE,Moderate OA,3,C,24,4/21/2023,16,"14,440.00",0.04,3.61 +HIGH,HIGH,High OA,3,A,25,4/21/2023,16,"16,432.00",0.04,4.11 +HIGH,HIGH,High OA,3,B,26,4/21/2023,16,"13,717.00",0.03,3.43 +HIGH,HIGH,High OA,3,C,27,4/21/2023,16,"11,142.00",0.03,2.79 diff --git a/RAnalysis/Data/metamorphosis.csv b/RAnalysis/Data/metamorphosis.csv new file mode 100644 index 0000000..234e982 --- /dev/null +++ b/RAnalysis/Data/metamorphosis.csv @@ -0,0 +1,61 @@ +Parent,Exposure OA,Treatment,Tank,Tank Number,Generation,Age,sucessful metamorphosis,metamorphesed +LOW,LOW,low OA,A,1,2,21,0.85,1 +LOW,LOW,low OA,B,2,2,21,0.75,1 +LOW,LOW,low OA,C,3,2,21,0.19,0.933333333 +MODERATE,MODERATE,moderate OA,A,10,2,21,0.08,0.6 +MODERATE,MODERATE,moderate OA,B,11,2,21,0.08,0.875 +MODERATE,MODERATE,moderate OA,C,12,2,21,0.11,0.6 +LOW,LOW,low OA,A,1,3,16,,0.33 +LOW,LOW,low OA,B,2,3,16,,0.56 +LOW,LOW,low OA,C,3,3,16,,0.19 +MODERATE,LOW,low OA,A,4,3,16,,0.4 +MODERATE,LOW,low OA,B,5,3,16,,0.35 +MODERATE,LOW,low OA,C,6,3,16,,0.52 +LOW,MODERATE,moderate OA,A,7,3,16,,0.49 +LOW,MODERATE,moderate OA,B,8,3,16,,0.06 +LOW,MODERATE,moderate OA,C,9,3,16,,0.4 +MODERATE,MODERATE,moderate OA,A,10,3,16,,0.42 +MODERATE,MODERATE,moderate OA,B,11,3,16,,0.27 +MODERATE,MODERATE,moderate OA,C,12,3,16,,0.28 +LOW,HIGH,high OA,A,13,3,16,,0.51 +LOW,HIGH,high OA,B,14,3,16,,0 +LOW,HIGH,high OA,C,15,3,16,,0.4 +MODERATE,HIGH,high OA,A,16,3,16,,0.18 +MODERATE,HIGH,high OA,B,17,3,16,,0.58 +MODERATE,HIGH,high OA,C,18,3,16,,0.56 +HIGH,LOW,low OA,A,19,3,16,,0.61 +HIGH,LOW,low OA,B,20,3,16,,0.25 +HIGH,LOW,low OA,C,21,3,16,,0.15 +HIGH,MODERATE,moderate OA,A,22,3,16,,0.44 +HIGH,MODERATE,moderate OA,B,23,3,16,,0.18 +HIGH,MODERATE,moderate OA,C,24,3,16,,0.42 +HIGH,HIGH,high OA,A,25,3,16,,0.49 +HIGH,HIGH,high OA,B,26,3,16,,0.45 +HIGH,HIGH,high OA,C,27,3,16,,0.32 +LOW,LOW,low OA,A,1,3,19,0.88,0.48 +LOW,LOW,low OA,B,2,3,19,0.97,0.78 +LOW,LOW,low OA,C,3,3,19,0.93,0.37 +MODERATE,LOW,low OA,A,4,3,19,0.98,0.87 +MODERATE,LOW,low OA,B,5,3,19,0.98,0.73 +MODERATE,LOW,low OA,C,6,3,19,0.97,0.86 +LOW,MODERATE,moderate OA,A,7,3,19,0.88,0.57 +LOW,MODERATE,moderate OA,B,8,3,19,1,0.41 +LOW,MODERATE,moderate OA,C,9,3,19,0.95,0.6 +MODERATE,MODERATE,moderate OA,A,10,3,19,0.63,0.88 +MODERATE,MODERATE,moderate OA,B,11,3,19,0.97,0.86 +MODERATE,MODERATE,moderate OA,C,12,3,19,0.95,0.71 +LOW,HIGH,high OA,A,13,3,19,0.97,0.88 +LOW,HIGH,high OA,B,14,3,19,1,0.25 +LOW,HIGH,high OA,C,15,3,19,0.97,0.83 +MODERATE,HIGH,high OA,A,16,3,19,0.88,0.62 +MODERATE,HIGH,high OA,B,17,3,19,0.92,0.43 +MODERATE,HIGH,high OA,C,18,3,19,0.93,0.65 +HIGH,LOW,low OA,A,19,3,19,0.37,0.3 +HIGH,LOW,low OA,B,20,3,19,0.6,0.23 +HIGH,LOW,low OA,C,21,3,19,0.6,0.46 +HIGH,MODERATE,moderate OA,A,22,3,19,1,0.4 +HIGH,MODERATE,moderate OA,B,23,3,19,0.79,0.72 +HIGH,MODERATE,moderate OA,C,24,3,19,0.96,0.77 +HIGH,HIGH,high OA,A,25,3,19,0.89,0.86 +HIGH,HIGH,high OA,B,26,3,19,1,0.63 +HIGH,HIGH,high OA,C,27,3,19,0.22,0.43 diff --git a/RAnalysis/Output/Respiration/data/RR_bad_data_larvae.csv b/RAnalysis/Output/Respiration/data/RR_bad_data_larvae.csv new file mode 100644 index 0000000..b07e120 --- /dev/null +++ b/RAnalysis/Output/Respiration/data/RR_bad_data_larvae.csv @@ -0,0 +1,93 @@ +"","Date","pH","Run","filetype","Channel","Filename","Lpc","Leq","Lz","alpha","Fed_Unfed","Food","pH_parents","Replicate","Chamber_tank","Number","Plate","Num_indivs","Date_formatted.x","BLANK.mean_Lpc","n","Date_formatted.y","resp_blankStand" +"1","3/16/2023",7,"1","SDR_data","A6","SDR_799_resp_Plate1.csv",-0.000203126,-0.000203126,-0.000316056,0.4,NA,NA,8,NA,"14",2,1,14,"20230316",0.0029864295,4,"20230316",-0.0027833035 +"2","3/16/2023",7,"1","SDR_data","A2","SDR_799_resp_Plate1.csv",-0.00065597,0.000894251,0.000894251,0.4,NA,NA,8,NA,"13",1,1,15,"20230316",0.0029864295,4,"20230316",-0.0023304595 +"3","3/16/2023",7,"1","SDR_data","A5","SDR_799_resp_Plate1.csv",-6.66e-05,-0.000319164,-0.000319164,0.4,NA,NA,8,NA,"14",1,1,14,"20230316",0.0029864295,4,"20230316",-0.0029198295 +"4","3/16/2023",7,"1","SDR_data","A3","SDR_799_resp_Plate1.csv",-1.66e-05,9.77e-05,0.000237288,0.4,NA,NA,8,NA,"13",2,1,15,"20230316",0.0029864295,4,"20230316",-0.0029698295 +"5","3/16/2023",7,"1","SDR_data","C1","SDR_799_resp_Plate1.csv",-0.00148428,-0.001574693,-0.001574693,0.4,NA,NA,8,NA,"13",3,1,15,"20230316",0.0029864295,4,"20230316",-0.0015021495 +"6","3/16/2023",7,"1","SDR_data","B4","SDR_799_resp_Plate1.csv",-0.002700023,-0.002700023,-0.000945537,0.4,NA,NA,8,NA,"14",3,1,14,"20230316",0.0029864295,4,"20230316",-0.0002864065 +"7","3/16/2023",7.5,"1","SDR_data","A2","SDR_979_resp_Plate3.csv",-0.000518386,-0.000349525,-0.000349525,0.4,NA,NA,7.5,NA,"10",1,3,17,"20230316",0.00285058933333333,3,"20230316",-0.00233220333333333 +"8","3/16/2023",7.5,"1","SDR_data","C6","SDR_799_resp_Plate1.csv",-0.001083221,-0.001083221,-0.002499077,0.4,NA,NA,8,NA,"9",2,1,12,"20230316",0.00285058933333333,3,"20230316",-0.00176736833333333 +"9","3/16/2023",7.5,"1","SDR_data","B1","SDR_799_resp_Plate1.csv",-0.00106502,-0.000968221,-0.000968221,0.4,NA,NA,8,NA,"8",2,1,19,"20230316",0.00285058933333333,3,"20230316",-0.00178556933333333 +"10","3/16/2023",8,"1","SDR_data","C3","SDR_873_resp_Plate2.csv",-0.001092579,-0.000518181,-0.000518181,0.4,NA,NA,7.5,NA,"4",2,2,10,"20230316",0.003310325,4,"20230316",-0.002217746 +"11","3/16/2023",8,"1","SDR_data","B3","SDR_873_resp_Plate2.csv",-0.001498019,-0.002442283,-0.001075898,0.4,NA,NA,7.5,NA,"4",1,2,10,"20230316",0.003310325,4,"20230316",-0.001812306 +"12","3/16/2023",8,"1","SDR_data","A1","SDR_873_resp_Plate2.csv",-0.000974896,-0.000966465,-0.001301313,0.4,NA,NA,7.5,NA,"5",1,2,13,"20230316",0.003310325,4,"20230316",-0.002335429 +"13","3/16/2023",8,"1","SDR_data","B6","SDR_799_resp_Plate1.csv",-0.002402508,-0.002557967,-0.002249946,0.4,NA,NA,8,NA,"1",1,1,16,"20230316",0.003310325,4,"20230316",-0.000907817 +"14","3/16/2023",8,"1","SDR_data","C4","SDR_799_resp_Plate1.csv",-0.000435613,-0.000435613,-0.000859389,0.4,NA,NA,8,NA,"1",2,1,16,"20230316",0.003310325,4,"20230316",-0.002874712 +"15","4/12/2023",7,"1","SDR_data","B1","SDR_979_resp_Plate3.csv",-0.015203886,-0.015395839,-0.015395839,0.4,NA,NA,8,NA,"14",2,3,4,"20230412",0.0160520011666667,6,"20230412",-0.000848115166666667 +"16","4/12/2023",7,"1","SDR_data","C5","SDR_979_resp_Plate3.csv",-0.008998846,-0.008998846,-0.007403163,0.4,NA,NA,7,NA,"25",1,3,7,"20230412",0.0160520011666667,6,"20230412",-0.00705315516666667 +"17","4/12/2023",7,"1","SDR_data","C4","SDR_979_resp_Plate3.csv",-0.013057591,-0.013236312,-0.013327561,0.4,NA,NA,8,NA,"13",1,3,4,"20230412",0.0160520011666667,6,"20230412",-0.00299441016666667 +"18","4/12/2023",7,"1","SDR_data","B6","SDR_979_resp_Plate3.csv",-0.007215004,-0.007195714,-0.007171245,0.4,NA,NA,7.5,NA,"16",1,3,7,"20230412",0.0160520011666667,6,"20230412",-0.00883699716666667 +"19","4/12/2023",7,"1","SDR_data","A2","SDR_979_resp_Plate3.csv",-0.01445337,-0.01458532,-0.015320367,0.4,NA,NA,8,NA,"14",1,3,4,"20230412",0.0160520011666667,6,"20230412",-0.00159863116666667 +"20","4/12/2023",7,"1","SDR_data","D3","SDR_799_resp_Plate1.csv",-0.008831966,-0.008831966,-0.00879605,0.4,NA,NA,7,NA,"26",1,1,7,"20230412",0.0160520011666667,6,"20230412",-0.00722003516666667 +"21","4/12/2023",7,"1","SDR_data","D3","SDR_979_resp_Plate3.csv",-0.005989703,-0.006080691,-0.006538441,0.4,NA,NA,8,NA,"13",2,3,4,"20230412",0.0160520011666667,6,"20230412",-0.0100622981666667 +"22","4/12/2023",7,"1","SDR_data","D4","SDR_799_resp_Plate1.csv",-0.010655061,-0.010655061,-0.009913779,0.4,NA,NA,7,NA,"26",2,1,7,"20230412",0.0160520011666667,6,"20230412",-0.00539694016666667 +"23","4/12/2023",7,"1","SDR_data","C6","SDR_979_resp_Plate3.csv",-0.010705594,-0.009834191,-0.009834191,0.4,NA,NA,7.5,NA,"16",2,3,7,"20230412",0.0160520011666667,6,"20230412",-0.00534640716666667 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filter(Parent %in% c("LOW")) + +leveneTest(Percent.deformed_trans ~ Run, data=df_low) +shapiro.test(df_low$Percent.deformed_trans) + +scheirerRayHare(Percent.deformed ~ Treatment*Run, + data = df_low) + + +dunnTest(Percent.deformed ~ Run, + data = df_low, + method="bh") +``` + +### Low larval exposure and Low parental exposure ("control") across generations +```{r} + +df_low_low <- df_low%>% + filter(Treatment %in% c("Low OA")) + +leveneTest(Percent.deformed_trans ~ Run, data=df_low_low) +shapiro.test(df_low_low$Percent.deformed_trans) + +mod <- aov(Percent.deformed_trans ~Run, data = df_low_low) +summary(mod) + +TukeyHSD(mod) +``` + + +################## + +# Broken down for each experiment + +### F1: Two runs + +```{r} + +df_2021 <- df%>% + filter(Year=="2021") + +ggplot(data=df_2021, aes(x=Treatment, y=Percent.deformed, fill=Treatment)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Deformed (2021: F1 Larvae) ", x ="Treatment", y = "Percent Deformed")+ + facet_wrap("Run") +``` + + +```{r} +df_run1 <- df%>% + filter(Run=="1") + +leveneTest(Percent.deformed_trans ~ Treatment, data=df_run1) +shapiro.test(df_run1$Percent.deformed_trans) + +df_run2 <- df%>% + filter(Run=="2") + +leveneTest(Percent.deformed_trans ~ Treatment, data=df_run2) +shapiro.test(df_run2$Percent.deformed_trans) +``` + + +```{r} +dunnTest(Percent.deformed ~ Treatment, + data = df_run1, + method="bh") +dunnTest(Percent.deformed ~ Treatment, + data = df_run2, + method="bh") +``` + + +```{r} +leveneTest(Percent.deformed_trans ~ Treatment, data=df_2021) +shapiro.test(df_2021$Percent.deformed_trans) +``` + +### F2 April 2022 + +```{r} +df_2022 <- df%>% + filter(Year=="2022") + +df_2022_3 <- df_2022%>% + filter(Run=="3") + +ggplot(data=df_2022_3, aes(x=Treatment, y=Percent.deformed, fill=Treatment)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Deformed, grouped by parentage (2022: F2 Larvae) ", x ="Treatment", y = "Percent Deformed")+ + facet_wrap("Parent") +``` + + +```{r} +leveneTest(Percent.deformed_trans ~ Treatment, data=df_2022_3) +shapiro.test(df_2022_3$Percent.deformed_trans) +``` + + +```{r} +scheirerRayHare(Percent.deformed ~ Treatment*Parent, + data = df_2022_3) + +dunnTest(Percent.deformed ~ Treatment, + data = df_2022_3, + method="bh") + +dunnTest(Percent.deformed ~ Parent, + data = df_2022_3, + method="bh") +``` + + +### F2 August 2022 + +```{r} +df_2022 <- df%>% + filter(Year=="2022") + +df_2022_4 <- df_2022%>% + filter(Run=="4") + +ggplot(data=df_2022_4, aes(x=Treatment, y=Percent.deformed, fill=Treatment)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Deformed (2022: F2 Larvae) ", x ="Treatment", y = "Percent Deformed") +``` + +```{r} + +leveneTest(Percent.deformed_trans ~ Treatment, data=df_2022_4) +shapiro.test(df_2022_4$Percent.deformed_trans) +``` + +```{r} + +res.kruskal <- kruskal.test(Percent.deformed ~ Treatment, data = df_2022_4) +res.kruskal + +``` + + +### F3 Larval April 2023 + +```{r} +df_6 <- df%>% + filter(Run=="6") + +ggplot(data=df_6, aes(x=Treatment, y=Percent.deformed, fill=Treatment)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Deformed, grouped by parentage (2023: F3 Larvae) ", x ="Treatment", y = "Percent Deformed")+ + facet_wrap("Parent") + + + +Run6_mean_deformaties <- df_6 %>% + dplyr::select(Treatment,Parent,Percent.deformed) %>% + na.omit() %>% + dplyr::group_by(Treatment,Parent) %>% + dplyr::summarise(mean_Perc_def = mean(Percent.deformed), + n = n(), + sd_Perc_def = sd(Percent.deformed), + se_Perc_def = sd_Perc_def/(sqrt(n))) + +library(forcats) + +ggplot(Run6_mean_deformaties) + + geom_errorbar(aes(x=Treatment, + ymin=mean_Perc_def-se_Perc_def, + ymax=mean_Perc_def+se_Perc_def), + width=0, # removes the horizontal line + colour="black", + size=1) + + geom_bar(aes(x=Treatment, y=mean_Perc_def,fill=factor(Treatment)), + stat="identity", + width = 0.75, + alpha = 0.5) + + labs(title="F3 Abnormalities- Full cross exposure", + x ="pCO2 Offspring Exposure", + y = "Percent Abnormalities") + + scale_fill_manual(breaks=c("Low OA", "Moderate OA", "High OA"), + values=c("forestgreen","orange", "purple")) + + theme_classic() + + theme(panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1), + axis.text=element_text(size=12), + legend.position="none") + + facet_wrap(~Parent) + + +Run6PLot_MeanSE_deformaties <- ggplot(data=Run6_mean_deformaties, + aes(x=fct_relevel(Treatment, c("Low OA", "Moderate OA", "High OA")), + y=Percent.deformed_trans, + colour=fct_relevel(Treatment, c("Low OA", "Moderate OA", "High OA")))) + + # scale_linetype(c("dotted","solid")) + + # scale_linetype_manual(breaks=c("Low", "High"), values=c("dashed","solid")) + + scale_colour_manual(breaks=c("Low OA", "Moderate OA", "High OA"), + values=c("forestgreen","orange", "purple")) + + geom_bar() + + stat_summary(fun.y="mean", size = 0.8, + position = position_dodge2(width = 1)) + + stat_summary(fun.min = function(x) mean(x) - sd(x)/sqrt(length(x)), + fun.max = function(x) mean(x) + sd(x)/sqrt(length(x)), + geom = 'errorbar', + width = 0, + position = position_dodge2(width = 1)) + + labs(title="F3 Abnormalities- Full cross exposure", + x ="pCO2 Offspring Exposure", + y = "Percent Abnormalities") + + theme_classic() + + theme(panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1), + axis.text=element_text(size=12), + legend.position="none") + + facet_wrap(~Parent) +Run6PLot_MeanSE_deformaties + +``` + + +```{r, F3 run 6 stats by history} + +df_6_HIGH <- df_6 %>% dplyr::filter(Parent %in% "HIGH") +df_6_MODERATE <- df_6 %>% dplyr::filter(Parent %in% "MODERATE") +df_6_LOW <- df_6 %>% dplyr::filter(Parent %in% "LOW") + + +anova_HIGH <- lm(Percent.deformed_trans ~ Treatment, data = df_6_HIGH) +shapiro.test(resid(anova_HIGH)) # 0.7455 +leveneTest(anova_HIGH) # 0.865 +summary(aov(anova_HIGH)) +# Df Sum Sq Mean Sq F value Pr(>F) +# Treatment 2 0.000305 0.000152 0.033 0.968 +# Residuals 6 0.027538 0.004590 + +anova_MODERATE <- lm(Percent.deformed_trans ~ Treatment, data = df_6_MODERATE) +shapiro.test(resid(anova_MODERATE)) # 0.5231 +leveneTest(anova_MODERATE) # 0.7784 +summary(aov(anova_MODERATE)) +# Df Sum Sq Mean Sq F value Pr(>F) +# Treatment 2 0.1244 0.06218 2.761 0.141 +# Residuals 6 0.1351 0.02252 + +anova_LOW <- lm(Percent.deformed_trans ~ Treatment, data = df_6_LOW) +shapiro.test(resid(anova_LOW)) # 0.9679 +leveneTest(anova_LOW) # 0.102 +summary(aov(anova_LOW)) +# Df Sum Sq Mean Sq F value Pr(>F) +# Treatment 2 0.2222 0.11108 5.188 0.0603 . +# Residuals 5 0.1071 0.02141 + +``` + + +```{r} +leveneTest(Percent.deformed_trans ~ Treatment, data=df_6) +shapiro.test(df_6$Percent.deformed_trans) +``` + +```{r} +mod <- aov(Percent.deformed_trans ~Treatment * Parent, data = df_6) +summary(mod) +``` + + +```{r} +scheirerRayHare(Percent.deformed ~ Treatment*Parent, + data = df_6) + +dunnTest(Percent.deformed ~ Treatment, + data = df_6, + method="bh") + +dunnTest(Percent.deformed ~ Parent, + data = df_6, + method="bh") +``` + + + +### Trimming the F3 to look at differences +```{r} + +df_6_trim <- df_6%>% + filter(Parent %in% c("MODERATE", "LOW")) + +ggplot(data=df_6_trim, aes(x=Treatment, y=Percent.deformed, fill=Treatment)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Deformed, grouped by parentage (2023: F3 Larvae) ", x ="Treatment", y = "Percent Deformed")+ + facet_wrap("Parent") +``` + +```{r} +scheirerRayHare(Percent.deformed ~ Treatment*Parent, + data = df_6_trim) + +#dunnTest(Percent.deformed ~ Treatment, +# data = df_6_trim, + # method="bh") + +#dunnTest(Percent.deformed ~ Parent, + # data = df_6_trim, + # method="bh") +``` + + + + + + + +Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot. diff --git a/RAnalysis/Scripts/LarvalGrowth.Rmd b/RAnalysis/Scripts/LarvalGrowth.Rmd new file mode 100644 index 0000000..56bd8a5 --- /dev/null +++ b/RAnalysis/Scripts/LarvalGrowth.Rmd @@ -0,0 +1,121 @@ +--- +title: "Larval Growth" +author: "Katie McFarland" +date: "9/29/2023" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + + +```{r, include=FALSE} +library("ggplot2") +library("tidyverse") +library(Rmisc) +library(rcompanion) +library(FSA) +``` + +```{r} +#Set Path +setwd("C:/Users/katherine.mcfarland/Documents/GitHub/EAD-ASEB-Airradians_multigen_OA/RAnalysis/Larvae") +``` + +# Larval Growth Data +```{r} +df<-read.csv("larval_growth.csv", header = T) + +df$Length<-as.numeric(df$Length) + +head(df) +str(df) +``` + + +```{r} +df$treatment <- factor(df$treatment,levels = c("Low OA", "Moderate OA", "High OA")) + +df$Parental_OA <- factor(df$Parental_OA,levels = c("Wild", "LOW", "MODERATE", "HIGH")) +``` + +### make data frames for each generation +```{r} +df_F1 <- df%>% + filter(Generation=="1") + +df_F2 <- df%>% + filter(Generation=="2") + +df_F3 <- df%>% + filter(Generation=="3") +``` + + +# F1 Larval Survival +```{r} + +stL <- summarySE(df_F1, measurevar="Length", groupvars=c("Age", "treatment")) +stL + +ggplot(stL, aes(x=Age, y=Length, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Length-se, ymax=Length+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) +``` + +# F2 Larval Survival +```{r} + +stL <- summarySE(df_F2, measurevar="Length", groupvars=c("Age", "treatment")) +stL + +ggplot(stL, aes(x=Age, y=Length, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Length-se, ymax=Length+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) + +``` +# F3 Larval Survival +```{r} + +stL <- summarySE(df_F3, measurevar="Length", groupvars=c("Age", "treatment")) +stL + +ggplot(stL, aes(x=Age, y=Length, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Length-se, ymax=Length+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black"))+ + facet_wrap("Parental_OA") + +``` + + +# Stats +Lenght data do not meet the assumptions of noramlity +```{r} +leveneTest(Length ~ treatment, data=df_F1) +shapiro.test(df_F1$Length) + +leveneTest(Length ~ treatment, data=df_F2) +shapiro.test(df_F2$Length) + +#leveneTest(Length ~ treatment, data=df_F3) +#shapiro.test(df_F3$Length) +``` + + + diff --git a/RAnalysis/Scripts/LarvalSurvival.Rmd b/RAnalysis/Scripts/LarvalSurvival.Rmd new file mode 100644 index 0000000..89ea2f0 --- /dev/null +++ b/RAnalysis/Scripts/LarvalSurvival.Rmd @@ -0,0 +1,154 @@ +--- +title: "Larval Growth and Survival" +author: "Katie McFarland" +date: "9/29/2023" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +```{r, include=FALSE} +library("ggplot2") +library("tidyverse") +library(Rmisc) +library(rcompanion) +library(FSA) +``` + +```{r} +#Set Path +setwd("C:/Users/katherine.mcfarland/Documents/GitHub/EAD-ASEB-Airradians_multigen_OA/RAnalysis/Larvae") +``` + + +#Larval Survival +```{r} +df<-read.csv("larval_survival.csv", header = T) + +df$Percent_Survival_trans <- asin(sqrt(df$Percent_Survival)) + +head(df) +str(df) +``` + +```{r} +df$treatment <- factor(df$treatment,levels = c("Low OA", "Moderate OA", "High OA")) + +df$Parental_OA <- factor(df$Parental_OA,levels = c("Wild", "LOW", "MODERATE", "HIGH")) +``` + +### make data frames for each generation +```{r} +df_F1 <- df%>% + filter(Generation=="1") + +df_F2 <- df%>% + filter(Generation=="2") + +df_F3 <- df%>% + filter(Generation=="3") +``` + +# F1 Larval Survival +```{r} + +stL <- summarySE(df_F1, measurevar="Percent_Survival", groupvars=c("Age", "treatment")) +stL + +ggplot(stL, aes(x=Age, y=Percent_Survival, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Percent_Survival-se, ymax=Percent_Survival+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) + +``` + +# F2 Larval Survival +```{r} + +stL <- summarySE(df_F2, measurevar="Percent_Survival", groupvars=c("Age", "treatment")) +stL + +ggplot(stL, aes(x=Age, y=Percent_Survival, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Percent_Survival-se, ymax=Percent_Survival+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) + +``` +# F3 Larval Survival +```{r} + +stL <- summarySE(df_F3, measurevar="Percent_Survival", groupvars=c("Age", "treatment", "Parental_OA")) +stL + +ggplot(stL, aes(x=Age, y=Percent_Survival, color=treatment))+ geom_line()+ + geom_point()+ + geom_errorbar(aes(ymin=Percent_Survival-se, ymax=Percent_Survival+se), width=.2, + position=position_dodge(.1)) + + scale_color_manual(values=c("green4", "darkorange1", "purple"))+ + theme(legend.position="right", legend.direction="vertical", legend.title = element_blank())+ theme_bw() + + labs(x="Age (days)", y="Percent Survival")+ #scale_y_continuous(breaks=seq(0,100,20))+ + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black"))+ + facet_wrap("Parental_OA") + +``` + +# Stats +Lenght data do not meet the assumptions of noramlity even with an asin(sqrt()) transformation +```{r} +leveneTest(Percent_Survival_trans ~ treatment, data=df_F1) +shapiro.test(df_F1$Percent_Survival_trans) + +leveneTest(Percent_Survival_trans ~ treatment, data=df_F2) +shapiro.test(df_F2$Percent_Survival_trans) + +leveneTest(Percent_Survival_trans ~ treatment, data=df_F3) +shapiro.test(df_F3$Percent_Survival_trans) +``` + +#Non parametric Stats +### F1 Survival +```{r} +scheirerRayHare(Percent_Survival ~ treatment*Age, + data = df_F1) + +dunnTest(Percent_Survival ~ treatment, + data = df_F1, + method="bh") + +``` + +### F2 Survival +```{r} +scheirerRayHare(Percent_Survival ~ treatment*Age, + data = df_F2) + +res.kruskal <- kruskal.test(Percent_Survival ~ treatment, data = df_F2) +res.kruskal + +``` + +### F3 Survival +```{r} + + +scheirerRayHare(Percent_Survival ~ treatment*Parental_OA, + data = df_F3) + +dunnTest(Percent_Survival ~ treatment, + data = df_F3, + method="bh") + +dunnTest(Percent_Survival ~ Parental_OA, + data = df_F3, + method="bh") +``` \ No newline at end of file diff --git a/RAnalysis/Scripts/Metamorphosis.Rmd b/RAnalysis/Scripts/Metamorphosis.Rmd new file mode 100644 index 0000000..222500c --- /dev/null +++ b/RAnalysis/Scripts/Metamorphosis.Rmd @@ -0,0 +1,141 @@ +--- +title: "Metamorphosis" +author: "Katie McFarland" +date: "4/24/2023" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + + +```{r} +library(ggplot2) +library(tidyr) +library(dplyr) + +library(rcompanion) +library(FSA) +``` + + +```{r} +#Set Path +setwd("C:/Users/katherine.mcfarland/Documents/Acidification/2020 OAP - scallops/R") +``` + +### Load Data +```{r} +#Here we are assing our data fram the name "df" so that we do not have to type out the full file name everytime we want to call it. +df<-read.csv("metamorphosis.csv", header = T) + +#df$Percent.deformed=as.numeric(df$Percent.deformed) + +dfParent=as.factor(df$Parent) +dfTtreatment=as.factor(df$Treatment) +dfExposure.OAt=as.factor(df$Exposure.OA) + +df$Generation=as.factor(df$Generation) + +df$Treatment <- factor(df$Treatment,levels = c("Low OA", "Moderate OA", "High OA")) + +df$Exposure.OA <- factor(df$Exposure.OA,levels = c("LOW", "MODERATE", "HIGH")) + +df$Parent <- factor(df$Parent,levels = c("LOW", "MODERATE", "HIGH")) + +#to look at columns names of your data frame +head(df) + +#Sturcture of the data - to check that variables are properly assigned to facotr or variable +str(df) +``` +```{r} + +df_F2_21 <- df%>% + filter(Age=="21") + +ggplot(data=df_F2_21, aes(x=Exposure.OA, y=sucessful.metamorphosis, fill=Exposure.OA)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Successful metamorphosis (2023: F2 Larvae - Age 21 days) ", x ="Treatment", y = "Percent sucessful metamorphosis") +#+ facet_wrap("Parent") +``` + + +```{r} + +df_F3_19 <- df%>% + filter(Age=="19") + +ggplot(data=df_F3_19, aes(x=Exposure.OA, y=sucessful.metamorphosis, fill=Exposure.OA)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent Successful metamorphosis, grouped by parentage (2023: F3 Larvae - Age 19 days) ", x ="Treatment", y = "Percent sucessful metamorphosis")+ + facet_wrap("Parent") +``` + +```{r} + +df_F3_19 <- df%>% + filter(Age=="19") + +ggplot(data=df_F3_19, aes(x=Exposure.OA, y=metamorphesed, fill=Exposure.OA)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent metamorphesed, grouped by parentage (2023: F3 Larvae - Age 19 days) ", x ="Treatment", y = "Percent sucessful metamorphosis")+ + facet_wrap("Parent") +``` +```{r} + +df_F3_19_trim <- df_F3_19%>% + filter(Parent %in% c("HIGH", "LOW")) + #filter(Parent=="HIGH, LOW") + +ggplot(data=df_F3_19_trim, aes(x=Exposure.OA, y=metamorphesed, fill=Exposure.OA)) + + geom_boxplot()+ scale_fill_manual(values=c("forestgreen","orange", "purple"))+ + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+ + #theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+ + labs(title="Percent metamorphesed, grouped by parentage (2023: F3 Larvae - Age 19 days) ", x ="Treatment", y = "Percent sucessful metamorphosis")+ + facet_wrap("Parent") +``` + +```{r} +leveneTest(sucessful.metamorphosis ~ Exposure.OA, data=df) +shapiro.test(df$sucessful.metamorphosis) + +df$sucessful.metamorphosis_trans <- asin(sqrt(df$sucessful.metamorphosis)) + +df_F2_21 <- df%>% + filter(Age=="21") + +leveneTest(sucessful.metamorphosis_trans ~ Exposure.OA, data=df_F2_21) +shapiro.test(df_F2_21$sucessful.metamorphosis_trans) + +df_F3_19 <- df%>% + filter(Age=="19") +leveneTest(sucessful.metamorphosis_trans ~ Exposure.OA, data=df_F3_19) +shapiro.test(df_F3_19$sucessful.metamorphosis_trans) +``` +```{r} +kruskal.test(sucessful.metamorphosis ~ Exposure.OA, data = df_F2_21) +``` + + + +```{r} +scheirerRayHare(sucessful.metamorphosis ~ Exposure.OA*Parent, + data = df_F3_19) + +dunnTest(sucessful.metamorphosis ~ Exposure.OA, + data = df_F3_19, + method="bh") + +dunnTest(sucessful.metamorphosis ~ Parent, + data = df_F3_19, + method="bh") +``` +