AMR 2.1.1.9234__tar.gz → 2.1.1.9236__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (12) hide show
  1. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/datasets.py +2 -2
  2. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/functions.py +209 -209
  3. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/PKG-INFO +1 -1
  4. {amr-2.1.1.9234 → amr-2.1.1.9236}/PKG-INFO +1 -1
  5. {amr-2.1.1.9234 → amr-2.1.1.9236}/setup.py +1 -1
  6. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/__init__.py +0 -0
  7. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/SOURCES.txt +0 -0
  8. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/dependency_links.txt +0 -0
  9. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/requires.txt +0 -0
  10. {amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/top_level.txt +0 -0
  11. {amr-2.1.1.9234 → amr-2.1.1.9236}/README.md +0 -0
  12. {amr-2.1.1.9234 → amr-2.1.1.9236}/setup.cfg +0 -0
{amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/datasets.py RENAMED
@@ -27,7 +27,7 @@ base._libPaths(r_lib_path)
27
27
  # Check if the AMR package is installed in R
28
28
  if not isinstalled('AMR', lib_loc=r_lib_path):
29
29
  print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True)
30
- utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
30
+ utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True)
31
31
 
32
32
  # # Retrieve Python AMR version
33
33
  # try:
@@ -43,7 +43,7 @@ if not isinstalled('AMR', lib_loc=r_lib_path):
43
43
  # if r_amr_version != python_amr_version:
44
44
  # try:
45
45
  # print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
46
- # utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
46
+ # utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True)
47
47
  # except Exception as e:
48
48
  # print(f"AMR: Could not update: {e}", flush=True)
49
49
 
{amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/functions.py RENAMED
@@ -37,629 +37,629 @@ def convert_to_python(r_output):
37
37
  # Fall-back
38
38
  return r_output
39
39
  def ab_class(*args, **kwargs):
40
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
40
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
41
41
  return convert_to_python(amr_r.ab_class(*args, **kwargs))
42
42
  def ab_selector(*args, **kwargs):
43
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
43
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
44
44
  return convert_to_python(amr_r.ab_selector(*args, **kwargs))
45
45
  def ab_from_text(text, *args, **kwargs):
46
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
46
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
47
47
  return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
48
48
  def ab_name(x, *args, **kwargs):
49
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
49
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
50
50
  return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
51
51
  def ab_cid(x, *args, **kwargs):
52
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
52
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
53
53
  return convert_to_python(amr_r.ab_cid(x, *args, **kwargs))
54
54
  def ab_synonyms(x, *args, **kwargs):
55
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
55
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
56
56
  return convert_to_python(amr_r.ab_synonyms(x, *args, **kwargs))
57
57
  def ab_tradenames(x, *args, **kwargs):
58
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
58
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
59
59
  return convert_to_python(amr_r.ab_tradenames(x, *args, **kwargs))
60
60
  def ab_group(x, *args, **kwargs):
61
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
61
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
62
62
  return convert_to_python(amr_r.ab_group(x, *args, **kwargs))
63
63
  def ab_atc(x, *args, **kwargs):
64
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
64
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
65
65
  return convert_to_python(amr_r.ab_atc(x, *args, **kwargs))
66
66
  def ab_atc_group1(x, *args, **kwargs):
67
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
67
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
68
68
  return convert_to_python(amr_r.ab_atc_group1(x, *args, **kwargs))
69
69
  def ab_atc_group2(x, *args, **kwargs):
70
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
70
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
71
71
  return convert_to_python(amr_r.ab_atc_group2(x, *args, **kwargs))
72
72
  def ab_loinc(x, *args, **kwargs):
73
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
73
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
74
74
  return convert_to_python(amr_r.ab_loinc(x, *args, **kwargs))
75
75
  def ab_ddd(x, *args, **kwargs):
76
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
76
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
77
77
  return convert_to_python(amr_r.ab_ddd(x, *args, **kwargs))
78
78
  def ab_ddd_units(x, *args, **kwargs):
79
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
79
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
80
80
  return convert_to_python(amr_r.ab_ddd_units(x, *args, **kwargs))
81
81
  def ab_info(x, *args, **kwargs):
82
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
82
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
83
83
  return convert_to_python(amr_r.ab_info(x, *args, **kwargs))
84
84
  def ab_url(x, *args, **kwargs):
85
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
85
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
86
86
  return convert_to_python(amr_r.ab_url(x, *args, **kwargs))
87
87
  def ab_property(x, *args, **kwargs):
88
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
88
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
89
89
  return convert_to_python(amr_r.ab_property(x, *args, **kwargs))
90
90
  def add_custom_antimicrobials(x):
91
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
91
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
92
92
  return convert_to_python(amr_r.add_custom_antimicrobials(x))
93
93
  def clear_custom_antimicrobials(*args, **kwargs):
94
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
94
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
95
95
  return convert_to_python(amr_r.clear_custom_antimicrobials(*args, **kwargs))
96
96
  def add_custom_microorganisms(x):
97
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
97
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
98
98
  return convert_to_python(amr_r.add_custom_microorganisms(x))
99
99
  def clear_custom_microorganisms(*args, **kwargs):
100
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
100
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
101
101
  return convert_to_python(amr_r.clear_custom_microorganisms(*args, **kwargs))
102
102
  def age(x, *args, **kwargs):
103
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
103
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
104
104
  return convert_to_python(amr_r.age(x, *args, **kwargs))
105
105
  def age_groups(x, *args, **kwargs):
106
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
106
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
107
107
  return convert_to_python(amr_r.age_groups(x, *args, **kwargs))
108
108
  def antibiogram(x, *args, **kwargs):
109
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
109
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
110
110
  return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
111
111
  def wisca(x, *args, **kwargs):
112
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
112
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
113
113
  return convert_to_python(amr_r.wisca(x, *args, **kwargs))
114
114
  def retrieve_wisca_parameters(wisca_model, *args, **kwargs):
115
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
115
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
116
116
  return convert_to_python(amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs))
117
117
  def aminoglycosides(only_sir_columns = False, *args, **kwargs):
118
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
118
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
119
119
  return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
120
120
  def aminopenicillins(only_sir_columns = False, *args, **kwargs):
121
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
121
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
122
122
  return convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
123
123
  def antifungals(only_sir_columns = False, *args, **kwargs):
124
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
124
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
125
125
  return convert_to_python(amr_r.antifungals(only_sir_columns = False, *args, **kwargs))
126
126
  def antimycobacterials(only_sir_columns = False, *args, **kwargs):
127
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
127
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
128
128
  return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
129
129
  def betalactams(only_sir_columns = False, *args, **kwargs):
130
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
130
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
131
131
  return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
132
132
  def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
133
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
133
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
134
134
  return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
135
135
  def carbapenems(only_sir_columns = False, *args, **kwargs):
136
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
136
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
137
137
  return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
138
138
  def cephalosporins(only_sir_columns = False, *args, **kwargs):
139
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
139
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
140
140
  return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
141
141
  def cephalosporins_1st(only_sir_columns = False, *args, **kwargs):
142
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
142
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
143
143
  return convert_to_python(amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs))
144
144
  def cephalosporins_2nd(only_sir_columns = False, *args, **kwargs):
145
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
145
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
146
146
  return convert_to_python(amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs))
147
147
  def cephalosporins_3rd(only_sir_columns = False, *args, **kwargs):
148
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
148
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
149
149
  return convert_to_python(amr_r.cephalosporins_3rd(only_sir_columns = False, *args, **kwargs))
150
150
  def cephalosporins_4th(only_sir_columns = False, *args, **kwargs):
151
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
151
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
152
152
  return convert_to_python(amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs))
153
153
  def cephalosporins_5th(only_sir_columns = False, *args, **kwargs):
154
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
154
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
155
155
  return convert_to_python(amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs))
156
156
  def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
157
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
157
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
158
158
  return convert_to_python(amr_r.fluoroquinolones(only_sir_columns = False, *args, **kwargs))
159
159
  def glycopeptides(only_sir_columns = False, *args, **kwargs):
160
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
160
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
161
161
  return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
162
162
  def isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs):
163
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
163
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
164
164
  return convert_to_python(amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs))
165
165
  def lincosamides(only_sir_columns = False, *args, **kwargs):
166
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
166
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
167
167
  return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
168
168
  def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
169
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
169
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
170
170
  return convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
171
171
  def macrolides(only_sir_columns = False, *args, **kwargs):
172
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
172
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
173
173
  return convert_to_python(amr_r.macrolides(only_sir_columns = False, *args, **kwargs))
174
174
  def monobactams(only_sir_columns = False, *args, **kwargs):
175
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
175
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
176
176
  return convert_to_python(amr_r.monobactams(only_sir_columns = False, *args, **kwargs))
177
177
  def nitrofurans(only_sir_columns = False, *args, **kwargs):
178
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
178
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
179
179
  return convert_to_python(amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs))
180
180
  def oxazolidinones(only_sir_columns = False, *args, **kwargs):
181
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
181
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
182
182
  return convert_to_python(amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs))
183
183
  def penicillins(only_sir_columns = False, *args, **kwargs):
184
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
184
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
185
185
  return convert_to_python(amr_r.penicillins(only_sir_columns = False, *args, **kwargs))
186
186
  def phenicols(only_sir_columns = False, *args, **kwargs):
187
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
187
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
188
188
  return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
189
189
  def polymyxins(only_sir_columns = False, *args, **kwargs):
190
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
190
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
191
191
  return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
192
192
  def quinolones(only_sir_columns = False, *args, **kwargs):
193
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
193
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
194
194
  return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
195
195
  def rifamycins(only_sir_columns = False, *args, **kwargs):
196
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
196
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
197
197
  return convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
198
198
  def streptogramins(only_sir_columns = False, *args, **kwargs):
199
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
199
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
200
200
  return convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
201
201
  def sulfonamides(only_sir_columns = False, *args, **kwargs):
202
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
202
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
203
203
  return convert_to_python(amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs))
204
204
  def tetracyclines(only_sir_columns = False, *args, **kwargs):
205
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
205
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
206
206
  return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
207
207
  def trimethoprims(only_sir_columns = False, *args, **kwargs):
208
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
208
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
209
209
  return convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
210
210
  def ureidopenicillins(only_sir_columns = False, *args, **kwargs):
211
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
211
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
212
212
  return convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
213
213
  def amr_class(amr_class, *args, **kwargs):
214
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
214
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
215
215
  return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
216
216
  def amr_selector(filter, *args, **kwargs):
217
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
217
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
218
218
  return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
219
219
  def administrable_per_os(only_sir_columns = False, *args, **kwargs):
220
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
220
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
221
221
  return convert_to_python(amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs))
222
222
  def administrable_iv(only_sir_columns = False, *args, **kwargs):
223
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
223
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
224
224
  return convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
225
225
  def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
226
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
226
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
227
227
  return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
228
228
  def as_ab(x, *args, **kwargs):
229
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
229
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
230
230
  return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
231
231
  def is_ab(x):
232
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
232
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
233
233
  return convert_to_python(amr_r.is_ab(x))
234
234
  def ab_reset_session(*args, **kwargs):
235
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
235
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
236
236
  return convert_to_python(amr_r.ab_reset_session(*args, **kwargs))
237
237
  def as_av(x, *args, **kwargs):
238
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
238
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
239
239
  return convert_to_python(amr_r.as_av(x, *args, **kwargs))
240
240
  def is_av(x):
241
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
241
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
242
242
  return convert_to_python(amr_r.is_av(x))
243
243
  def as_disk(x, *args, **kwargs):
244
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
244
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
245
245
  return convert_to_python(amr_r.as_disk(x, *args, **kwargs))
246
246
  def is_disk(x):
247
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
247
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
248
248
  return convert_to_python(amr_r.is_disk(x))
249
249
  def as_mic(x, *args, **kwargs):
250
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
250
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
251
251
  return convert_to_python(amr_r.as_mic(x, *args, **kwargs))
252
252
  def is_mic(x):
253
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
253
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
254
254
  return convert_to_python(amr_r.is_mic(x))
255
255
  def rescale_mic(x, *args, **kwargs):
256
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
256
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
257
257
  return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
258
258
  def mic_p50(x, *args, **kwargs):
259
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
259
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
260
260
  return convert_to_python(amr_r.mic_p50(x, *args, **kwargs))
261
261
  def mic_p90(x, *args, **kwargs):
262
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
262
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
263
263
  return convert_to_python(amr_r.mic_p90(x, *args, **kwargs))
264
264
  def as_mo(x, *args, **kwargs):
265
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
265
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
266
266
  return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
267
267
  def is_mo(x):
268
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
268
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
269
269
  return convert_to_python(amr_r.is_mo(x))
270
270
  def mo_uncertainties(*args, **kwargs):
271
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
271
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
272
272
  return convert_to_python(amr_r.mo_uncertainties(*args, **kwargs))
273
273
  def mo_renamed(*args, **kwargs):
274
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
274
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
275
275
  return convert_to_python(amr_r.mo_renamed(*args, **kwargs))
276
276
  def mo_failures(*args, **kwargs):
277
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
277
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
278
278
  return convert_to_python(amr_r.mo_failures(*args, **kwargs))
279
279
  def mo_reset_session(*args, **kwargs):
280
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
280
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
281
281
  return convert_to_python(amr_r.mo_reset_session(*args, **kwargs))
282
282
  def mo_cleaning_regex(*args, **kwargs):
283
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
283
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
284
284
  return convert_to_python(amr_r.mo_cleaning_regex(*args, **kwargs))
285
285
  def as_sir(x, *args, **kwargs):
286
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
286
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
287
287
  return convert_to_python(amr_r.as_sir(x, *args, **kwargs))
288
288
  def is_sir(x):
289
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
289
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
290
290
  return convert_to_python(amr_r.is_sir(x))
291
291
  def is_sir_eligible(x, *args, **kwargs):
292
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
292
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
293
293
  return convert_to_python(amr_r.is_sir_eligible(x, *args, **kwargs))
294
294
  def sir_interpretation_history(clean):
295
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
295
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
296
296
  return convert_to_python(amr_r.sir_interpretation_history(clean))
297
297
  def atc_online_property(atc_code, *args, **kwargs):
298
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
298
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
299
299
  return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
300
300
  def atc_online_groups(atc_code, *args, **kwargs):
301
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
301
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
302
302
  return convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
303
303
  def atc_online_ddd(atc_code, *args, **kwargs):
304
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
304
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
305
305
  return convert_to_python(amr_r.atc_online_ddd(atc_code, *args, **kwargs))
306
306
  def atc_online_ddd_units(atc_code, *args, **kwargs):
307
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
307
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
308
308
  return convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
309
309
  def av_from_text(text, *args, **kwargs):
310
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
310
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
311
311
  return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
312
312
  def av_name(x, *args, **kwargs):
313
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
313
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
314
314
  return convert_to_python(amr_r.av_name(x, *args, **kwargs))
315
315
  def av_cid(x, *args, **kwargs):
316
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
316
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
317
317
  return convert_to_python(amr_r.av_cid(x, *args, **kwargs))
318
318
  def av_synonyms(x, *args, **kwargs):
319
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
319
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
320
320
  return convert_to_python(amr_r.av_synonyms(x, *args, **kwargs))
321
321
  def av_tradenames(x, *args, **kwargs):
322
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
322
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
323
323
  return convert_to_python(amr_r.av_tradenames(x, *args, **kwargs))
324
324
  def av_group(x, *args, **kwargs):
325
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
325
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
326
326
  return convert_to_python(amr_r.av_group(x, *args, **kwargs))
327
327
  def av_atc(x, *args, **kwargs):
328
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
328
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
329
329
  return convert_to_python(amr_r.av_atc(x, *args, **kwargs))
330
330
  def av_loinc(x, *args, **kwargs):
331
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
331
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
332
332
  return convert_to_python(amr_r.av_loinc(x, *args, **kwargs))
333
333
  def av_ddd(x, *args, **kwargs):
334
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
334
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
335
335
  return convert_to_python(amr_r.av_ddd(x, *args, **kwargs))
336
336
  def av_ddd_units(x, *args, **kwargs):
337
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
337
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
338
338
  return convert_to_python(amr_r.av_ddd_units(x, *args, **kwargs))
339
339
  def av_info(x, *args, **kwargs):
340
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
340
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
341
341
  return convert_to_python(amr_r.av_info(x, *args, **kwargs))
342
342
  def av_url(x, *args, **kwargs):
343
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
343
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
344
344
  return convert_to_python(amr_r.av_url(x, *args, **kwargs))
345
345
  def av_property(x, *args, **kwargs):
346
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
346
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
347
347
  return convert_to_python(amr_r.av_property(x, *args, **kwargs))
348
348
  def availability(tbl, *args, **kwargs):
349
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
349
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
350
350
  return convert_to_python(amr_r.availability(tbl, *args, **kwargs))
351
351
  def bug_drug_combinations(x, *args, **kwargs):
352
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
352
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
353
353
  return convert_to_python(amr_r.bug_drug_combinations(x, *args, **kwargs))
354
354
  def count_resistant(*args, **kwargs):
355
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
355
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
356
356
  return convert_to_python(amr_r.count_resistant(*args, **kwargs))
357
357
  def count_susceptible(*args, **kwargs):
358
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
358
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
359
359
  return convert_to_python(amr_r.count_susceptible(*args, **kwargs))
360
360
  def count_S(*args, **kwargs):
361
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
361
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
362
362
  return convert_to_python(amr_r.count_S(*args, **kwargs))
363
363
  def count_SI(*args, **kwargs):
364
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
364
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
365
365
  return convert_to_python(amr_r.count_SI(*args, **kwargs))
366
366
  def count_I(*args, **kwargs):
367
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
367
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
368
368
  return convert_to_python(amr_r.count_I(*args, **kwargs))
369
369
  def count_IR(*args, **kwargs):
370
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
370
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
371
371
  return convert_to_python(amr_r.count_IR(*args, **kwargs))
372
372
  def count_R(*args, **kwargs):
373
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
373
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
374
374
  return convert_to_python(amr_r.count_R(*args, **kwargs))
375
375
  def count_all(*args, **kwargs):
376
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
376
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
377
377
  return convert_to_python(amr_r.count_all(*args, **kwargs))
378
378
  def n_sir(*args, **kwargs):
379
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
379
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
380
380
  return convert_to_python(amr_r.n_sir(*args, **kwargs))
381
381
  def count_df(data, *args, **kwargs):
382
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
382
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
383
383
  return convert_to_python(amr_r.count_df(data, *args, **kwargs))
384
384
  def custom_eucast_rules(*args, **kwargs):
385
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
385
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
386
386
  return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
387
387
  def eucast_rules(x, *args, **kwargs):
388
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
388
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
389
389
  return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
390
390
  def eucast_dosage(ab, *args, **kwargs):
391
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
391
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
392
392
  return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
393
393
  def export_ncbi_biosample(x, *args, **kwargs):
394
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
394
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
395
395
  return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
396
396
  def first_isolate(x = None, *args, **kwargs):
397
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
397
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
398
398
  return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
399
399
  def filter_first_isolate(x = None, *args, **kwargs):
400
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
400
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
401
401
  return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
402
402
  def g_test(x, *args, **kwargs):
403
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
403
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
404
404
  return convert_to_python(amr_r.g_test(x, *args, **kwargs))
405
405
  def is_new_episode(x, *args, **kwargs):
406
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
406
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
407
407
  return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
408
408
  def ggplot_pca(x, *args, **kwargs):
409
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
409
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
410
410
  return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
411
411
  def ggplot_sir(data, *args, **kwargs):
412
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
412
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
413
413
  return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
414
414
  def geom_sir(position = None, *args, **kwargs):
415
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
415
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
416
416
  return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
417
417
  def guess_ab_col(x = None, *args, **kwargs):
418
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
418
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
419
419
  return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
420
420
  def italicise_taxonomy(string, *args, **kwargs):
421
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
421
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
422
422
  return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
423
423
  def italicize_taxonomy(string, *args, **kwargs):
424
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
424
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
425
425
  return convert_to_python(amr_r.italicize_taxonomy(string, *args, **kwargs))
426
426
  def inner_join_microorganisms(x, *args, **kwargs):
427
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
427
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
428
428
  return convert_to_python(amr_r.inner_join_microorganisms(x, *args, **kwargs))
429
429
  def left_join_microorganisms(x, *args, **kwargs):
430
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
430
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
431
431
  return convert_to_python(amr_r.left_join_microorganisms(x, *args, **kwargs))
432
432
  def right_join_microorganisms(x, *args, **kwargs):
433
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
433
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
434
434
  return convert_to_python(amr_r.right_join_microorganisms(x, *args, **kwargs))
435
435
  def full_join_microorganisms(x, *args, **kwargs):
436
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
436
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
437
437
  return convert_to_python(amr_r.full_join_microorganisms(x, *args, **kwargs))
438
438
  def semi_join_microorganisms(x, *args, **kwargs):
439
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
439
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
440
440
  return convert_to_python(amr_r.semi_join_microorganisms(x, *args, **kwargs))
441
441
  def anti_join_microorganisms(x, *args, **kwargs):
442
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
442
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
443
443
  return convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
444
444
  def key_antimicrobials(x = None, *args, **kwargs):
445
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
445
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
446
446
  return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
447
447
  def all_antimicrobials(x = None, *args, **kwargs):
448
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
448
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
449
449
  return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
450
450
  def kurtosis(x, *args, **kwargs):
451
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
451
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
452
452
  return convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
453
453
  def like(x, *args, **kwargs):
454
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
454
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
455
455
  return convert_to_python(amr_r.like(x, *args, **kwargs))
456
456
  def mdro(x = None, *args, **kwargs):
457
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
457
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
458
458
  return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
459
459
  def custom_mdro_guideline(*args, **kwargs):
460
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
460
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
461
461
  return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
462
462
  def brmo(x = None, *args, **kwargs):
463
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
463
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
464
464
  return convert_to_python(amr_r.brmo(x = None, *args, **kwargs))
465
465
  def mrgn(x = None, *args, **kwargs):
466
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
466
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
467
467
  return convert_to_python(amr_r.mrgn(x = None, *args, **kwargs))
468
468
  def mdr_tb(x = None, *args, **kwargs):
469
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
469
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
470
470
  return convert_to_python(amr_r.mdr_tb(x = None, *args, **kwargs))
471
471
  def mdr_cmi2012(x = None, *args, **kwargs):
472
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
472
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
473
473
  return convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
474
474
  def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
475
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
475
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
476
476
  return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
477
477
  def mean_amr_distance(x, *args, **kwargs):
478
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
478
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
479
479
  return convert_to_python(amr_r.mean_amr_distance(x, *args, **kwargs))
480
480
  def amr_distance_from_row(amr_distance, *args, **kwargs):
481
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
481
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
482
482
  return convert_to_python(amr_r.amr_distance_from_row(amr_distance, *args, **kwargs))
483
483
  def mo_matching_score(x, *args, **kwargs):
484
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
484
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
485
485
  return convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
486
486
  def mo_name(x, *args, **kwargs):
487
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
487
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
488
488
  return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
489
489
  def mo_fullname(x, *args, **kwargs):
490
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
490
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
491
491
  return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
492
492
  def mo_shortname(x, *args, **kwargs):
493
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
493
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
494
494
  return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
495
495
  def mo_subspecies(x, *args, **kwargs):
496
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
496
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
497
497
  return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
498
498
  def mo_species(x, *args, **kwargs):
499
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
499
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
500
500
  return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
501
501
  def mo_genus(x, *args, **kwargs):
502
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
502
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
503
503
  return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
504
504
  def mo_family(x, *args, **kwargs):
505
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
505
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
506
506
  return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
507
507
  def mo_order(x, *args, **kwargs):
508
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
508
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
509
509
  return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
510
510
  def mo_class(x, *args, **kwargs):
511
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
511
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
512
512
  return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
513
513
  def mo_phylum(x, *args, **kwargs):
514
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
514
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
515
515
  return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
516
516
  def mo_kingdom(x, *args, **kwargs):
517
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
517
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
518
518
  return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
519
519
  def mo_domain(x, *args, **kwargs):
520
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
520
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
521
521
  return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
522
522
  def mo_type(x, *args, **kwargs):
523
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
523
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
524
524
  return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
525
525
  def mo_status(x, *args, **kwargs):
526
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
526
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
527
527
  return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
528
528
  def mo_pathogenicity(x, *args, **kwargs):
529
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
529
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
530
530
  return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
531
531
  def mo_gramstain(x, *args, **kwargs):
532
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
532
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
533
533
  return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
534
534
  def mo_is_gram_negative(x, *args, **kwargs):
535
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
535
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
536
536
  return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
537
537
  def mo_is_gram_positive(x, *args, **kwargs):
538
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
538
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
539
539
  return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
540
540
  def mo_is_yeast(x, *args, **kwargs):
541
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
541
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
542
542
  return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
543
543
  def mo_is_intrinsic_resistant(x, *args, **kwargs):
544
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
544
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
545
545
  return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
546
546
  def mo_oxygen_tolerance(x, *args, **kwargs):
547
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
547
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
548
548
  return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
549
549
  def mo_is_anaerobic(x, *args, **kwargs):
550
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
550
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
551
551
  return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
552
552
  def mo_snomed(x, *args, **kwargs):
553
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
553
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
554
554
  return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
555
555
  def mo_ref(x, *args, **kwargs):
556
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
556
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
557
557
  return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
558
558
  def mo_authors(x, *args, **kwargs):
559
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
559
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
560
560
  return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
561
561
  def mo_year(x, *args, **kwargs):
562
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
562
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
563
563
  return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
564
564
  def mo_lpsn(x, *args, **kwargs):
565
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
565
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
566
566
  return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
567
567
  def mo_mycobank(x, *args, **kwargs):
568
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
568
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
569
569
  return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
570
570
  def mo_gbif(x, *args, **kwargs):
571
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
571
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
572
572
  return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
573
573
  def mo_rank(x, *args, **kwargs):
574
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
574
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
575
575
  return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
576
576
  def mo_taxonomy(x, *args, **kwargs):
577
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
577
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
578
578
  return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
579
579
  def mo_synonyms(x, *args, **kwargs):
580
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
580
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
581
581
  return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
582
582
  def mo_current(x, *args, **kwargs):
583
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
583
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
584
584
  return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
585
585
  def mo_group_members(x, *args, **kwargs):
586
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
586
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
587
587
  return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
588
588
  def mo_info(x, *args, **kwargs):
589
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
589
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
590
590
  return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
591
591
  def mo_url(x, *args, **kwargs):
592
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
592
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
593
593
  return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
594
594
  def mo_property(x, *args, **kwargs):
595
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
595
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
596
596
  return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
597
597
  def pca(x, *args, **kwargs):
598
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
598
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
599
599
  return convert_to_python(amr_r.pca(x, *args, **kwargs))
600
600
  def theme_sir(*args, **kwargs):
601
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
601
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
602
602
  return convert_to_python(amr_r.theme_sir(*args, **kwargs))
603
603
  def labels_sir_count(position = None, *args, **kwargs):
604
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
604
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
605
605
  return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
606
606
  def resistance(*args, **kwargs):
607
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
607
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
608
608
  return convert_to_python(amr_r.resistance(*args, **kwargs))
609
609
  def susceptibility(*args, **kwargs):
610
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
610
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
611
611
  return convert_to_python(amr_r.susceptibility(*args, **kwargs))
612
612
  def sir_confidence_interval(*args, **kwargs):
613
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
613
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
614
614
  return convert_to_python(amr_r.sir_confidence_interval(*args, **kwargs))
615
615
  def proportion_R(*args, **kwargs):
616
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
616
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
617
617
  return convert_to_python(amr_r.proportion_R(*args, **kwargs))
618
618
  def proportion_IR(*args, **kwargs):
619
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
619
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
620
620
  return convert_to_python(amr_r.proportion_IR(*args, **kwargs))
621
621
  def proportion_I(*args, **kwargs):
622
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
622
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
623
623
  return convert_to_python(amr_r.proportion_I(*args, **kwargs))
624
624
  def proportion_SI(*args, **kwargs):
625
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
625
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
626
626
  return convert_to_python(amr_r.proportion_SI(*args, **kwargs))
627
627
  def proportion_S(*args, **kwargs):
628
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
628
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
629
629
  return convert_to_python(amr_r.proportion_S(*args, **kwargs))
630
630
  def proportion_df(data, *args, **kwargs):
631
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
631
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
632
632
  return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
633
633
  def sir_df(data, *args, **kwargs):
634
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
634
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
635
635
  return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
636
636
  def random_mic(size = None, *args, **kwargs):
637
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
637
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
638
638
  return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
639
639
  def random_disk(size = None, *args, **kwargs):
640
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
640
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
641
641
  return convert_to_python(amr_r.random_disk(size = None, *args, **kwargs))
642
642
  def random_sir(size = None, *args, **kwargs):
643
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
643
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
644
644
  return convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
645
645
  def resistance_predict(x, *args, **kwargs):
646
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
646
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
647
647
  return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
648
648
  def sir_predict(x, *args, **kwargs):
649
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
649
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
650
650
  return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
651
651
  def ggplot_sir_predict(x, *args, **kwargs):
652
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
652
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
653
653
  return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
654
654
  def skewness(x, *args, **kwargs):
655
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
655
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
656
656
  return convert_to_python(amr_r.skewness(x, *args, **kwargs))
657
657
  def top_n_microorganisms(x, *args, **kwargs):
658
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
658
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
659
659
  return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
660
660
  def reset_AMR_locale(*args, **kwargs):
661
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
661
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
662
662
  return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
663
663
  def translate_AMR(x, *args, **kwargs):
664
- """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
664
+ """See our website of the R package for the manual: https://amr-for-r.org/index.html"""
665
665
  return convert_to_python(amr_r.translate_AMR(x, *args, **kwargs))
{amr-2.1.1.9234 → amr-2.1.1.9236}/AMR.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: AMR
3
- Version: 2.1.1.9234
3
+ Version: 2.1.1.9236
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
{amr-2.1.1.9234 → amr-2.1.1.9236}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: AMR
3
- Version: 2.1.1.9234
3
+ Version: 2.1.1.9236
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
{amr-2.1.1.9234 → amr-2.1.1.9236}/setup.py RENAMED
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
2
2
 
3
3
  setup(
4
4
  name='AMR',
5
- version='2.1.1.9234',
5
+ version='2.1.1.9236',
6
6
  packages=find_packages(),
7
7
  install_requires=[
8
8
  'rpy2',
{amr-2.1.1.9234 → amr-2.1.1.9236}/AMR/__init__.py RENAMED
File without changes
{amr-2.1.1.9234 → amr-2.1.1.9236}/README.md RENAMED
File without changes
{amr-2.1.1.9234 → amr-2.1.1.9236}/setup.cfg RENAMED
File without changes