library(knitr)
library(readxl)
#detach(package:plyr)
library(dplyr)
library(ggplot2)
library(reshape2)
library(kableExtra)
set.seed(100)
files used
path <- "/Users/kylielanglois/SCCWRP/eDNA Sample Management - eDNA/ESTUARY_SAV"
#path to database files
inv <- read_excel(file.path(path, "eDNAmaster_inventory_ESTUARY_SAV.xlsx"),
sheet=1)
ex1 <- read_excel(file.path(path, "eDNAmaster_extraction_ESTUARY_SAV.xlsx"),
sheet=1)
seq <- read_excel(file.path(path, "eDNAmaster_extraction_ESTUARY_SAV.xlsx"),
sheet=3)
what has been processed?
SAMPLES
|
Project
|
rep/bl
|
year
|
# samples
|
# extracted
|
# sequenced
|
|
B23-R9
|
sample
|
23
|
102
|
99
|
95
|
|
B23-R9
|
sample
|
24
|
36
|
36
|
36
|
|
B23-SAV
|
sample
|
24
|
84
|
83
|
0
|
|
BAJA
|
sample
|
22
|
51
|
0
|
0
|
|
BAJA
|
sample
|
NR
|
5
|
0
|
0
|
|
Bight23
|
sample
|
23
|
125
|
35
|
0
|
|
EMPA
|
sample
|
24
|
228
|
109
|
0
|
|
EMPA
|
sample
|
25
|
174
|
0
|
0
|
|
EMPA
|
sample
|
SP
|
6
|
0
|
0
|
|
EMPA-Bight23
|
sample
|
23
|
245
|
10
|
0
|
|
EPA-SAV
|
sample
|
23
|
11
|
9
|
9
|
|
EPA-SAV
|
sample
|
24
|
11
|
11
|
11
|
|
PROP50
|
sample
|
23
|
25
|
12
|
0
|
|
PROP50
|
sample
|
24
|
45
|
45
|
45
|
|
Santa Ana River
|
sample
|
24
|
36
|
0
|
0
|
BLANKS
|
Project
|
rep/bl
|
year
|
# samples
|
# extracted
|
# sequenced
|
|
B23-R9
|
blank
|
23
|
14
|
11
|
4
|
|
B23-R9
|
blank
|
24
|
4
|
4
|
1
|
|
B23-SAV
|
blank
|
24
|
11
|
11
|
0
|
|
BAJA
|
blank
|
22
|
4
|
0
|
0
|
|
Bight23
|
blank
|
23
|
6
|
3
|
0
|
|
EMPA
|
blank
|
24
|
18
|
11
|
0
|
|
EMPA
|
blank
|
25
|
18
|
0
|
0
|
|
EPA-SAV
|
blank
|
23
|
4
|
3
|
3
|
|
EPA-SAV
|
blank
|
24
|
4
|
4
|
0
|
|
PROP50
|
blank
|
23
|
4
|
1
|
0
|
|
PROP50
|
blank
|
24
|
4
|
4
|
1
|
|
Santa Ana River
|
blank
|
24
|
2
|
0
|
0
|
exceptions
|
Project
|
StationCode
|
NOT extracted
|
|
B23-SAV
|
B23SAV-901
|
1
|
|
B23-R9
|
SC-AGH
|
FB
|
|
B23-R9
|
SC-BAT
|
FB
|
|
B23-R9
|
SC-KFR
|
2
|
|
B23-R9
|
SC-SEL
|
FB
|
|
B23-R9
|
SC-SDL
|
1
|
|
B23-R9
|
SC-SDL
|
2
|
|
EPA-SAV
|
UNB-PCH
|
1
|
|
EPA-SAV
|
UNB-PCH
|
FB
|
|
EPA-SAV
|
UNB-PCH
|
2
|
filter type
|
Sample type
|
total samples
|
|
Smith-Root
|
538
|
|
coffee filter
|
267
|
|
sterivex
|
265
|
|
FLAT
|
193
|
|
sediment
|
14
|
DNA concentration
BLANKS
|
Project
|
min
|
mean
|
max
|
|
B23-R9
|
0.00
|
0.02
|
0.06
|
|
Bight23
|
0.03
|
0.03
|
0.03
|
|
EPA-SAV
|
0.00
|
9.55
|
62.80
|
|
PROP50
|
0.00
|
1.15
|
1.76
|
## [1] "blanks with > 2 ng/ul DNA: EPA-SAV_PCH-E BL_0.45CN E2 & EPA-SAV_PCH-E BL_0.45CN E1"