@ -31,7 +31,7 @@
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9215 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9216 < / small >
< button class = "navbar-toggler" type = "button" data-bs-toggle = "collapse" data-bs-target = "#navbar" aria-controls = "navbar" aria-expanded = "false" aria-label = "Toggle navigation" >
@ -104,27 +104,40 @@ need to have R installed, Python users can now easily work with AMR data
directly through Python code.< / p >
< / div >
< div class = "section level2" >
< h2 id = "install" > Install < a class = "anchor" aria-label = "anchor" href = "#install " > < / a >
< h2 id = "prerequisites" > Prerequisites < a class = "anchor" aria-label = "anchor" href = "#prerequisites " > < / a >
< / h2 >
< p > This package was only tested with < a href = "https://docs.python.org/3/library/venv.html" class = "external-link" > < code > venv< / code > < / a > .
You can set up such a virtual environment by running:< / p >
< div class = "sourceCode" id = "cb1" > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb1-1" > < a href = "#cb1-1" tabindex = "-1" > < / a > < span class = "co" > # for linux and macOS:< / span > < / span >
< span id = "cb1-2" > < a href = "#cb1-2" tabindex = "-1" > < / a > python < span class = "op" > -< / span > m venv < span class = "op" > /< / span > path< span class = "op" > /< / span > to< span class = "op" > /< / span > new< span class = "op" > /< / span > virtual< span class = "op" > /< / span > environment< / span >
< span id = "cb1-3" > < a href = "#cb1-3" tabindex = "-1" > < / a > < span class = "co" > # for Windows:< / span > < / span >
< span id = "cb1-4" > < a href = "#cb1-4" tabindex = "-1" > < / a > python < span class = "op" > -< / span > m venv C:\path\to\new\virtual\environment< / span > < / code > < / pre > < / div >
< p > Then you can < a href = "https://docs.python.org/3/library/venv.html#how-venvs-work" class = "external-link" > activate
the environment< / a > , after the which the virtual environment is ready to
work with.< / p >
< / div >
< div class = "section level2" >
< h2 id = "install-amr" > Install AMR< a class = "anchor" aria-label = "anchor" href = "#install-amr" > < / a >
< / h2 >
< ol style = "list-style-type: decimal" >
< li >
< p > Since the Python package is available on the official < a href = "https://pypi.org/project/AMR/" class = "external-link" > Python Package Index< / a > , you can
just run:< / p >
< div class = "sourceCode" id = "cb1 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb1 -1" > < a href = "#cb1 -1" tabindex = "-1" > < / a > < span class = "ex" > pip< / span > install AMR< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb2 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb2 -1" > < a href = "#cb2 -1" tabindex = "-1" > < / a > < span class = "ex" > pip< / span > install AMR< / span > < / code > < / pre > < / div >
< / li >
< li >
< p > Make sure you have R installed. There is < strong > no need to
install the < code > AMR< / code > R package< / strong > , as it will be installed
automatically.< / p >
< p > For Linux:< / p >
< div class = "sourceCode" id = "cb2 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb2 -1" > < a href = "#cb2 -1" tabindex = "-1" > < / a > < span class = "co" > # Ubuntu / Debian< / span > < / span >
< span id = "cb2 -2" > < a href = "#cb2 -2" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > apt install r-base< / span >
< span id = "cb2 -3" > < a href = "#cb2 -3" tabindex = "-1" > < / a > < span class = "co" > # Fedora:< / span > < / span >
< span id = "cb2 -4" > < a href = "#cb2 -4" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > dnf install R< / span >
< span id = "cb2 -5" > < a href = "#cb2 -5" tabindex = "-1" > < / a > < span class = "co" > # CentOS/RHEL< / span > < / span >
< span id = "cb2 -6" > < a href = "#cb2 -6" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > yum install R< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb3 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb3 -1" > < a href = "#cb3 -1" tabindex = "-1" > < / a > < span class = "co" > # Ubuntu / Debian< / span > < / span >
< span id = "cb3 -2" > < a href = "#cb3 -2" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > apt install r-base< / span >
< span id = "cb3 -3" > < a href = "#cb3 -3" tabindex = "-1" > < / a > < span class = "co" > # Fedora:< / span > < / span >
< span id = "cb3 -4" > < a href = "#cb3 -4" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > dnf install R< / span >
< span id = "cb3 -5" > < a href = "#cb3 -5" tabindex = "-1" > < / a > < span class = "co" > # CentOS/RHEL< / span > < / span >
< span id = "cb3 -6" > < a href = "#cb3 -6" tabindex = "-1" > < / a > < span class = "fu" > sudo< / span > yum install R< / span > < / code > < / pre > < / div >
< p > For macOS (using < a href = "https://brew.sh" class = "external-link" > Homebrew< / a > ):< / p >
< div class = "sourceCode" id = "cb3 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb3 -1" > < a href = "#cb3 -1" tabindex = "-1" > < / a > < span class = "ex" > brew< / span > install r< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb4 " > < pre class = "sourceCode bash" > < code class = "sourceCode bash" > < span id = "cb4 -1" > < a href = "#cb4 -1" tabindex = "-1" > < / a > < span class = "ex" > brew< / span > install r< / span > < / code > < / pre > < / div >
< p > For Windows, visit the < a href = "https://cran.r-project.org" class = "external-link" > CRAN
download page< / a > to download and install R.< / p >
< / li >
@ -138,22 +151,22 @@ download page</a> to download and install R.</p>
< / h3 >
< p > Here’
drug names using the < code > AMR< / code > Python package:< / p >
< div class = "sourceCode" id = "cb4 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb4 -1" > < a href = "#cb4 -1" tabindex = "-1" > < / a > < span class = "im" > import< / span > pandas < span class = "im" > as< / span > pd< / span >
< span id = "cb4 -2" > < a href = "#cb4 -2" tabindex = "-1" > < / a > < span class = "im" > import< / span > AMR< / span >
< span id = "cb4 -3" > < a href = "#cb4 -3" tabindex = "-1" > < / a > < / span >
< span id = "cb4 -4" > < a href = "#cb4 -4" tabindex = "-1" > < / a > < span class = "co" > # Sample data< / span > < / span >
< span id = "cb4 -5" > < a href = "#cb4 -5" tabindex = "-1" > < / a > data < span class = "op" > =< / span > {< / span >
< span id = "cb4 -6" > < a href = "#cb4 -6" tabindex = "-1" > < / a > < span class = "st" > "MOs"< / span > : [< span class = "st" > 'E. coli'< / span > , < span class = "st" > 'ESCCOL'< / span > , < span class = "st" > 'esco'< / span > , < span class = "st" > 'Esche coli'< / span > ],< / span >
< span id = "cb4 -7" > < a href = "#cb4 -7" tabindex = "-1" > < / a > < span class = "st" > "Drug"< / span > : [< span class = "st" > 'Cipro'< / span > , < span class = "st" > 'CIP'< / span > , < span class = "st" > 'J01MA02'< / span > , < span class = "st" > 'Ciproxin'< / span > ]< / span >
< span id = "cb4 -8" > < a href = "#cb4 -8" tabindex = "-1" > < / a > }< / span >
< span id = "cb4 -9" > < a href = "#cb4 -9" tabindex = "-1" > < / a > df < span class = "op" > =< / span > pd.DataFrame(data)< / span >
< span id = "cb4 -10" > < a href = "#cb4 -10" tabindex = "-1" > < / a > < / span >
< span id = "cb4 -11" > < a href = "#cb4 -11" tabindex = "-1" > < / a > < span class = "co" > # Use AMR functions to clean microorganism and drug names< / span > < / span >
< span id = "cb4 -12" > < a href = "#cb4 -12" tabindex = "-1" > < / a > df[< span class = "st" > 'MO_clean'< / span > ] < span class = "op" > =< / span > AMR.mo_name(df[< span class = "st" > 'MOs'< / span > ])< / span >
< span id = "cb4 -13" > < a href = "#cb4 -13" tabindex = "-1" > < / a > df[< span class = "st" > 'Drug_clean'< / span > ] < span class = "op" > =< / span > AMR.ab_name(df[< span class = "st" > 'Drug'< / span > ])< / span >
< span id = "cb4 -14" > < a href = "#cb4 -14" tabindex = "-1" > < / a > < / span >
< span id = "cb4 -15" > < a href = "#cb4 -15" tabindex = "-1" > < / a > < span class = "co" > # Display the results< / span > < / span >
< span id = "cb4 -16" > < a href = "#cb4 -16" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (df)< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb5 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb5 -1" > < a href = "#cb5 -1" tabindex = "-1" > < / a > < span class = "im" > import< / span > pandas < span class = "im" > as< / span > pd< / span >
< span id = "cb5 -2" > < a href = "#cb5 -2" tabindex = "-1" > < / a > < span class = "im" > import< / span > AMR< / span >
< span id = "cb5 -3" > < a href = "#cb5 -3" tabindex = "-1" > < / a > < / span >
< span id = "cb5 -4" > < a href = "#cb5 -4" tabindex = "-1" > < / a > < span class = "co" > # Sample data< / span > < / span >
< span id = "cb5 -5" > < a href = "#cb5 -5" tabindex = "-1" > < / a > data < span class = "op" > =< / span > {< / span >
< span id = "cb5 -6" > < a href = "#cb5 -6" tabindex = "-1" > < / a > < span class = "st" > "MOs"< / span > : [< span class = "st" > 'E. coli'< / span > , < span class = "st" > 'ESCCOL'< / span > , < span class = "st" > 'esco'< / span > , < span class = "st" > 'Esche coli'< / span > ],< / span >
< span id = "cb5 -7" > < a href = "#cb5 -7" tabindex = "-1" > < / a > < span class = "st" > "Drug"< / span > : [< span class = "st" > 'Cipro'< / span > , < span class = "st" > 'CIP'< / span > , < span class = "st" > 'J01MA02'< / span > , < span class = "st" > 'Ciproxin'< / span > ]< / span >
< span id = "cb5 -8" > < a href = "#cb5 -8" tabindex = "-1" > < / a > }< / span >
< span id = "cb5 -9" > < a href = "#cb5 -9" tabindex = "-1" > < / a > df < span class = "op" > =< / span > pd.DataFrame(data)< / span >
< span id = "cb5 -10" > < a href = "#cb5 -10" tabindex = "-1" > < / a > < / span >
< span id = "cb5 -11" > < a href = "#cb5 -11" tabindex = "-1" > < / a > < span class = "co" > # Use AMR functions to clean microorganism and drug names< / span > < / span >
< span id = "cb5 -12" > < a href = "#cb5 -12" tabindex = "-1" > < / a > df[< span class = "st" > 'MO_clean'< / span > ] < span class = "op" > =< / span > AMR.mo_name(df[< span class = "st" > 'MOs'< / span > ])< / span >
< span id = "cb5 -13" > < a href = "#cb5 -13" tabindex = "-1" > < / a > df[< span class = "st" > 'Drug_clean'< / span > ] < span class = "op" > =< / span > AMR.ab_name(df[< span class = "st" > 'Drug'< / span > ])< / span >
< span id = "cb5 -14" > < a href = "#cb5 -14" tabindex = "-1" > < / a > < / span >
< span id = "cb5 -15" > < a href = "#cb5 -15" tabindex = "-1" > < / a > < span class = "co" > # Display the results< / span > < / span >
< span id = "cb5 -16" > < a href = "#cb5 -16" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (df)< / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th > MOs< / th >
@ -207,12 +220,12 @@ the standard name, “Ciprofloxacin”.</p></li>
< div class = "section level3" >
< h3 id = "calculating-amr" > Calculating AMR< a class = "anchor" aria-label = "anchor" href = "#calculating-amr" > < / a >
< / h3 >
< div class = "sourceCode" id = "cb5 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb5 -1" > < a href = "#cb5 -1" tabindex = "-1" > < / a > < span class = "im" > import< / span > AMR< / span >
< span id = "cb5 -2" > < a href = "#cb5 -2" tabindex = "-1" > < / a > < span class = "im" > import< / span > pandas < span class = "im" > as< / span > pd< / span >
< span id = "cb5 -3" > < a href = "#cb5 -3" tabindex = "-1" > < / a > < / span >
< span id = "cb5 -4" > < a href = "#cb5 -4" tabindex = "-1" > < / a > df < span class = "op" > =< / span > AMR.example_isolates< / span >
< span id = "cb5 -5" > < a href = "#cb5 -5" tabindex = "-1" > < / a > result < span class = "op" > =< / span > AMR.resistance(df[< span class = "st" > "AMX"< / span > ])< / span >
< span id = "cb5 -6" > < a href = "#cb5 -6" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result)< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb6 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb6 -1" > < a href = "#cb6 -1" tabindex = "-1" > < / a > < span class = "im" > import< / span > AMR< / span >
< span id = "cb6 -2" > < a href = "#cb6 -2" tabindex = "-1" > < / a > < span class = "im" > import< / span > pandas < span class = "im" > as< / span > pd< / span >
< span id = "cb6 -3" > < a href = "#cb6 -3" tabindex = "-1" > < / a > < / span >
< span id = "cb6 -4" > < a href = "#cb6 -4" tabindex = "-1" > < / a > df < span class = "op" > =< / span > AMR.example_isolates< / span >
< span id = "cb6 -5" > < a href = "#cb6 -5" tabindex = "-1" > < / a > result < span class = "op" > =< / span > AMR.resistance(df[< span class = "st" > "AMX"< / span > ])< / span >
< span id = "cb6 -6" > < a href = "#cb6 -6" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result)< / span > < / code > < / pre > < / div >
< pre > < code > [0.59555556]< / code > < / pre >
< / div >
< div class = "section level3" >
@ -222,8 +235,8 @@ the standard name, “Ciprofloxacin”.</p></li>
generating an antibiogram, a table that summarises the antimicrobial
susceptibility of bacterial isolates. Here’
antibiogram from Python:< / p >
< div class = "sourceCode" id = "cb7 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb7 -1" > < a href = "#cb7 -1" tabindex = "-1" > < / a > result2a < span class = "op" > =< / span > AMR.antibiogram(df[[< span class = "st" > "mo"< / span > , < span class = "st" > "AMX"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > ]])< / span >
< span id = "cb7 -2" > < a href = "#cb7 -2" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result2a)< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb8 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb8 -1" > < a href = "#cb8 -1" tabindex = "-1" > < / a > result2a < span class = "op" > =< / span > AMR.antibiogram(df[[< span class = "st" > "mo"< / span > , < span class = "st" > "AMX"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > ]])< / span >
< span id = "cb8 -2" > < a href = "#cb8 -2" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result2a)< / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "22%" >
@ -294,8 +307,8 @@ antibiogram from Python:</p>
< / tr >
< / tbody >
< / table >
< div class = "sourceCode" id = "cb8 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb8 -1" > < a href = "#cb8 -1" tabindex = "-1" > < / a > result2b < span class = "op" > =< / span > AMR.antibiogram(df[[< span class = "st" > "mo"< / span > , < span class = "st" > "AMX"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > ]], mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > )< / span >
< span id = "cb8 -2" > < a href = "#cb8 -2" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result2b)< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb9 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb9 -1" > < a href = "#cb9 -1" tabindex = "-1" > < / a > result2b < span class = "op" > =< / span > AMR.antibiogram(df[[< span class = "st" > "mo"< / span > , < span class = "st" > "AMX"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > ]], mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > )< / span >
< span id = "cb9 -2" > < a href = "#cb9 -2" tabindex = "-1" > < / a > < span class = "bu" > print< / span > (result2b)< / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "20%" >
@ -335,7 +348,7 @@ the <code>AMR</code> R package, <code>microorganisms</code>,
< code > antimicrobials< / code > , < code > clinical_breakpoints< / code > , and
< code > example_isolates< / code > , are now available as regular Python data
frames:< / p >
< div class = "sourceCode" id = "cb9 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb9 -1" > < a href = "#cb9 -1" tabindex = "-1" > < / a > AMR.microorganisms< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb10 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb10 -1" > < a href = "#cb10 -1" tabindex = "-1" > < / a > AMR.microorganisms< / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "11%" >
@ -470,7 +483,7 @@ frames:</p>
< / tr >
< / tbody >
< / table >
< div class = "sourceCode" id = "cb10 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb10 -1" > < a href = "#cb10 -1" tabindex = "-1" > < / a > AMR.antimicrobials< / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb11 " > < pre class = "sourceCode python" > < code class = "sourceCode python" > < span id = "cb11 -1" > < a href = "#cb11 -1" tabindex = "-1" > < / a > AMR.antimicrobials< / span > < / code > < / pre > < / div >
< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "4%" >
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