AMR 2.1.1.9126__tar.gz → 2.1.1.9127__tar.gz

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Files changed (12) hide show
  1. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/datasets.py +6 -0
  2. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/PKG-INFO +42 -43
  3. {amr-2.1.1.9126 → amr-2.1.1.9127}/PKG-INFO +42 -43
  4. {amr-2.1.1.9126 → amr-2.1.1.9127}/README.md +41 -42
  5. {amr-2.1.1.9126 → amr-2.1.1.9127}/setup.py +1 -1
  6. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/__init__.py +0 -0
  7. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/functions.py +0 -0
  8. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/SOURCES.txt +0 -0
  9. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/dependency_links.txt +0 -0
  10. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/requires.txt +0 -0
  11. {amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/top_level.txt +0 -0
  12. {amr-2.1.1.9126 → amr-2.1.1.9127}/setup.cfg +0 -0
{amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/datasets.py RENAMED
@@ -19,6 +19,9 @@ r_lib_path = os.path.join(venv_path, "R_libs")
19
19
  os.makedirs(r_lib_path, exist_ok=True)
20
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  # Set the R library path in .libPaths
21
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  base = importr('base')
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+ # Turn off warnings
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+ base.options(warn = -1)
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+
22
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  base._libPaths(r_lib_path)
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  r_amr_lib_path = base._libPaths()[0]
24
27
 
@@ -46,6 +49,9 @@ if r_amr_version != python_amr_version:
46
49
  except Exception as e:
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  print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
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+ # Restore warnings to default
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+ base.options(warn = 0)
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+
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  print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
50
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  # Activate the automatic conversion between R and pandas DataFrames
{amr-2.1.1.9126 → amr-2.1.1.9127}/AMR.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: AMR
3
- Version: 2.1.1.9126
3
+ Version: 2.1.1.9127
4
4
  Summary: A Python wrapper for the AMR R package
5
5
  Home-page: https://github.com/msberends/AMR
6
6
  Author: Matthijs Berends
@@ -98,48 +98,6 @@ print(df)
98
98
 
99
99
  * **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
100
100
 
101
-
102
- ## Taxonomic Data Sets Now in Python!
103
-
104
- As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
105
-
106
- ```python
107
- AMR.microorganisms
108
- ```
109
-
110
- | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
111
- |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
112
- | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
113
- | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
114
- | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
115
- | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
116
- | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
117
- | ... | ... | ... | ... | ... | ... | ... | ... |
118
- | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
119
- | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
120
- | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
121
- | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
122
- | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
123
-
124
- ```python
125
- AMR.antibiotics
126
- ```
127
-
128
- | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
129
- |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
130
- | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
131
- | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
132
- | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
133
- | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
134
- | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
135
- | ... | ... | ... | ... | ... | ... | ... | ... |
136
- | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
137
- | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
138
- | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
139
- | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
140
- | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
141
-
142
-
143
101
  ## Calculating AMR
144
102
 
145
103
  ```python
@@ -190,6 +148,47 @@ print(result2b)
190
148
 
191
149
  In this example, we generate an antibiogram by selecting various antibiotics.
192
150
 
151
+ ## Taxonomic Data Sets Now in Python!
152
+
153
+ As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
154
+
155
+ ```python
156
+ AMR.microorganisms
157
+ ```
158
+
159
+ | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
160
+ |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
161
+ | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
162
+ | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
163
+ | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
164
+ | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
165
+ | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
166
+ | ... | ... | ... | ... | ... | ... | ... | ... |
167
+ | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
168
+ | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
169
+ | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
170
+ | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
171
+ | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
172
+
173
+ ```python
174
+ AMR.antibiotics
175
+ ```
176
+
177
+ | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
178
+ |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
179
+ | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
180
+ | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
181
+ | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
182
+ | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
183
+ | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
184
+ | ... | ... | ... | ... | ... | ... | ... | ... |
185
+ | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
186
+ | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
187
+ | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
188
+ | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
189
+ | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
190
+
191
+
193
192
  # Conclusion
194
193
 
195
194
  With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.
{amr-2.1.1.9126 → amr-2.1.1.9127}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: AMR
3
- Version: 2.1.1.9126
3
+ Version: 2.1.1.9127
4
4
  Summary: A Python wrapper for the AMR R package
5
5
  Home-page: https://github.com/msberends/AMR
6
6
  Author: Matthijs Berends
@@ -98,48 +98,6 @@ print(df)
98
98
 
99
99
  * **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
100
100
 
101
-
102
- ## Taxonomic Data Sets Now in Python!
103
-
104
- As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
105
-
106
- ```python
107
- AMR.microorganisms
108
- ```
109
-
110
- | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
111
- |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
112
- | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
113
- | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
114
- | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
115
- | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
116
- | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
117
- | ... | ... | ... | ... | ... | ... | ... | ... |
118
- | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
119
- | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
120
- | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
121
- | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
122
- | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
123
-
124
- ```python
125
- AMR.antibiotics
126
- ```
127
-
128
- | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
129
- |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
130
- | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
131
- | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
132
- | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
133
- | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
134
- | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
135
- | ... | ... | ... | ... | ... | ... | ... | ... |
136
- | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
137
- | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
138
- | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
139
- | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
140
- | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
141
-
142
-
143
101
  ## Calculating AMR
144
102
 
145
103
  ```python
@@ -190,6 +148,47 @@ print(result2b)
190
148
 
191
149
  In this example, we generate an antibiogram by selecting various antibiotics.
192
150
 
151
+ ## Taxonomic Data Sets Now in Python!
152
+
153
+ As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
154
+
155
+ ```python
156
+ AMR.microorganisms
157
+ ```
158
+
159
+ | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
160
+ |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
161
+ | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
162
+ | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
163
+ | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
164
+ | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
165
+ | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
166
+ | ... | ... | ... | ... | ... | ... | ... | ... |
167
+ | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
168
+ | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
169
+ | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
170
+ | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
171
+ | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
172
+
173
+ ```python
174
+ AMR.antibiotics
175
+ ```
176
+
177
+ | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
178
+ |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
179
+ | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
180
+ | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
181
+ | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
182
+ | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
183
+ | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
184
+ | ... | ... | ... | ... | ... | ... | ... | ... |
185
+ | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
186
+ | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
187
+ | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
188
+ | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
189
+ | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
190
+
191
+
193
192
  # Conclusion
194
193
 
195
194
  With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.
{amr-2.1.1.9126 → amr-2.1.1.9127}/README.md RENAMED
@@ -70,48 +70,6 @@ print(df)
70
70
 
71
71
  * **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
72
72
 
73
-
74
- ## Taxonomic Data Sets Now in Python!
75
-
76
- As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
77
-
78
- ```python
79
- AMR.microorganisms
80
- ```
81
-
82
- | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
83
- |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
84
- | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
85
- | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
86
- | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
87
- | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
88
- | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
89
- | ... | ... | ... | ... | ... | ... | ... | ... |
90
- | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
91
- | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
92
- | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
93
- | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
94
- | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
95
-
96
- ```python
97
- AMR.antibiotics
98
- ```
99
-
100
- | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
101
- |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
102
- | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
103
- | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
104
- | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
105
- | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
106
- | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
107
- | ... | ... | ... | ... | ... | ... | ... | ... |
108
- | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
109
- | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
110
- | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
111
- | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
112
- | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
113
-
114
-
115
73
  ## Calculating AMR
116
74
 
117
75
  ```python
@@ -162,6 +120,47 @@ print(result2b)
162
120
 
163
121
  In this example, we generate an antibiogram by selecting various antibiotics.
164
122
 
123
+ ## Taxonomic Data Sets Now in Python!
124
+
125
+ As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antibiotics`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
126
+
127
+ ```python
128
+ AMR.microorganisms
129
+ ```
130
+
131
+ | mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
132
+ |--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
133
+ | B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
134
+ | B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
135
+ | B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
136
+ | B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
137
+ | B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
138
+ | ... | ... | ... | ... | ... | ... | ... | ... |
139
+ | B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
140
+ | B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
141
+ | B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
142
+ | B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
143
+ | F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
144
+
145
+ ```python
146
+ AMR.antibiotics
147
+ ```
148
+
149
+ | ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
150
+ |-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
151
+ | AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
152
+ | ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
153
+ | ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
154
+ | ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
155
+ | AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
156
+ | ... | ... | ... | ... | ... | ... | ... | ... |
157
+ | VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
158
+ | VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
159
+ | XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
160
+ | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
161
+ | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
162
+
163
+
165
164
  # Conclusion
166
165
 
167
166
  With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.
{amr-2.1.1.9126 → amr-2.1.1.9127}/setup.py RENAMED
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
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2
 
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  setup(
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  name='AMR',
5
- version='2.1.1.9126',
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+ version='2.1.1.9127',
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  packages=find_packages(),
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  install_requires=[
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  'rpy2',
{amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/__init__.py RENAMED
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{amr-2.1.1.9126 → amr-2.1.1.9127}/AMR/functions.py RENAMED
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{amr-2.1.1.9126 → amr-2.1.1.9127}/setup.cfg RENAMED
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