r code :to find the number of bacteria that are resistant to each type of drug by type of aquaculture and by year data a
Posted: Fri Nov 26, 2021 8:26 am
r code :to find the number of bacteria that are resistant
to each type of drug by type of aquaculture and by year data as
below
- Antibiotics was
antimicrobial : Amoxicillin (AMX), Ceftazidime (CAZ), Cefotaxime
(CTX), Ciprofloxacin (CIP), Enrofloxacin (ENR),
Trimethoprim/Sulfamethoxazole (SXT), Colistin (COL),
Oxytetracycline (OXY)
- Value is the
laboratory-measured resistance analysis (MIC breakpoints), where
each antimicrobial drug has a different level of resistance
AMX >= 32 CAZ >=16 CTX >=4 CIP
>= 4 ENR >= 2 SXT >= 4 COL
>=4 OXY >= 4
- Resistance is
the level of MIC breakpoints. There are three levels: susceptible
(S), intermediate (I) and resistant (R), where R indicates
bacterial resistance.
- AquaEnvi is two
types of aquaculture: freshwater aquaculture and coastal
aquaculture.
r code :Use MasterFileLong.csv to find the number of
bacteria that are resistant to each type of drug by type of
aquaculture and by year and calculate the % of drug-resistant
bacteria per total number of samples within the drug group data as
below
- Antibiotics was
antimicrobial : Amoxicillin (AMX), Ceftazidime (CAZ), Cefotaxime
(CTX), Ciprofloxacin (CIP), Enrofloxacin (ENR),
Trimethoprim/Sulfamethoxazole (SXT), Colistin (COL),
Oxytetracycline (OXY)
- Value is the
laboratory-measured resistance analysis (MIC breakpoints), where
each antimicrobial drug has a different level of resistance
AMX >= 32 CAZ >=16 CTX >=4 CIP
>= 4 ENR >= 2 SXT >= 4 COL
>=4 OXY >= 4
- Resistance is
the level of MIC breakpoints. There are three levels: susceptible
(S), intermediate (I) and resistant (R), where R indicates
bacterial resistance.
- AquaEnvi is two
types of aquaculture: freshwater aquaculture and coastal
aquaculture.
ID
AquaEnvi
Bact.Code
Year
Antibiotics
Value
Status
1
Freshwater
BEC60/01
2560
AMX
1024
R
2
Freshwater
BEC60/02
2560
AMX
256
R
4
Freshwater
BEC60/04
2560
AMX
8
S
51
Coastal
SEC 62/11
2562
COL
0.25
I
52
Coastal
SEC 62/12
2562
COL
2
I
56
Coastal
SEC 62/16
2562
COL
0.5
I
60
Coastal
SEC 62/20
2562
COL
12
Freshwater
EC63/12
2563
ENR
4
R
13
Freshwater
EC63/13
2563
ENR
4
R
14
Freshwater
EC63/14
2563
ENR
4
R
16
Freshwater
EC63/16
2563
ENR
128
R
4
Freshwater
BEC60/04
2560
OXY
1
S
5
Freshwater
BEC60/05
2560
OXY
1
S
9
Freshwater
BEC60/09
2560
OXY
2
S
to each type of drug by type of aquaculture and by year data as
below
- Antibiotics was
antimicrobial : Amoxicillin (AMX), Ceftazidime (CAZ), Cefotaxime
(CTX), Ciprofloxacin (CIP), Enrofloxacin (ENR),
Trimethoprim/Sulfamethoxazole (SXT), Colistin (COL),
Oxytetracycline (OXY)
- Value is the
laboratory-measured resistance analysis (MIC breakpoints), where
each antimicrobial drug has a different level of resistance
AMX >= 32 CAZ >=16 CTX >=4 CIP
>= 4 ENR >= 2 SXT >= 4 COL
>=4 OXY >= 4
- Resistance is
the level of MIC breakpoints. There are three levels: susceptible
(S), intermediate (I) and resistant (R), where R indicates
bacterial resistance.
- AquaEnvi is two
types of aquaculture: freshwater aquaculture and coastal
aquaculture.
r code :Use MasterFileLong.csv to find the number of
bacteria that are resistant to each type of drug by type of
aquaculture and by year and calculate the % of drug-resistant
bacteria per total number of samples within the drug group data as
below
- Antibiotics was
antimicrobial : Amoxicillin (AMX), Ceftazidime (CAZ), Cefotaxime
(CTX), Ciprofloxacin (CIP), Enrofloxacin (ENR),
Trimethoprim/Sulfamethoxazole (SXT), Colistin (COL),
Oxytetracycline (OXY)
- Value is the
laboratory-measured resistance analysis (MIC breakpoints), where
each antimicrobial drug has a different level of resistance
AMX >= 32 CAZ >=16 CTX >=4 CIP
>= 4 ENR >= 2 SXT >= 4 COL
>=4 OXY >= 4
- Resistance is
the level of MIC breakpoints. There are three levels: susceptible
(S), intermediate (I) and resistant (R), where R indicates
bacterial resistance.
- AquaEnvi is two
types of aquaculture: freshwater aquaculture and coastal
aquaculture.
ID
AquaEnvi
Bact.Code
Year
Antibiotics
Value
Status
1
Freshwater
BEC60/01
2560
AMX
1024
R
2
Freshwater
BEC60/02
2560
AMX
256
R
4
Freshwater
BEC60/04
2560
AMX
8
S
51
Coastal
SEC 62/11
2562
COL
0.25
I
52
Coastal
SEC 62/12
2562
COL
2
I
56
Coastal
SEC 62/16
2562
COL
0.5
I
60
Coastal
SEC 62/20
2562
COL
12
Freshwater
EC63/12
2563
ENR
4
R
13
Freshwater
EC63/13
2563
ENR
4
R
14
Freshwater
EC63/14
2563
ENR
4
R
16
Freshwater
EC63/16
2563
ENR
128
R
4
Freshwater
BEC60/04
2560
OXY
1
S
5
Freshwater
BEC60/05
2560
OXY
1
S
9
Freshwater
BEC60/09
2560
OXY
2
S