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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Check Availability of Columns< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/availability.R" class = "external-link" > < code > R/availability.R< / code > < / a > < / small >
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< div class = "ref-description section level2" >
< p > Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. < code > < a href = "proportion.html" > susceptibility()< / a > < / code > and < code > < a href = "proportion.html" > resistance()< / a > < / code > .< / p >
< / div >
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< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > availability< / span > < span class = "op" > (< / span > < span class = "va" > tbl< / span > , width < span class = "op" > =< / span > < span class = "cn" > NULL< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > tbl< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > or < a href = "https://rdrr.io/r/base/list.html" class = "external-link" > list< / a > < / p > < / dd >
< dt > width< / dt >
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< dd > < p > number of characters to present the visual availability - the default is filling the width of the console< / p > < / dd >
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< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
< p > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > with column names of < code > tbl< / code > as row names< / p >
< / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > The function returns a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > with columns < code > "resistant"< / code > and < code > "visual_resistance"< / code > . The values in that columns are calculated with < code > < a href = "proportion.html" > resistance()< / a > < / code > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "fu" > availability< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > count available visual_availabilty resistant visual_resistance< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > date 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > patient 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > age 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > gender 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ward 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo 2000 100.0% |####################| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > PEN 1629 81.5% |################----| 73.7% |##############------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > OXA 365 18.3% |###-----------------| 31.2% |######--------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FLC 943 47.2% |#########-----------| 29.5% |#####---------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMX 1350 67.5% |#############-------| 59.6% |###########---------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMC 1879 94.0% |##################--| 23.7% |####----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMP 1350 67.5% |#############-------| 59.6% |###########---------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TZP 1001 50.0% |##########----------| 12.6% |##------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CZO 446 22.3% |####----------------| 44.6% |########------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FEP 724 36.2% |#######-------------| 14.2% |##------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CXM 1789 89.5% |#################---| 26.3% |#####---------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FOX 818 40.9% |########------------| 27.4% |#####---------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CTX 943 47.2% |#########-----------| 15.5% |###-----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CAZ 1811 90.6% |##################--| 66.5% |#############-------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CRO 943 47.2% |#########-----------| 15.5% |###-----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > GEN 1855 92.8% |##################--| 24.6% |####----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TOB 1351 67.6% |#############-------| 34.4% |######--------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMK 692 34.6% |######--------------| 63.7% |############--------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > KAN 471 23.6% |####----------------| 100.0% |####################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TMP 1499 75.0% |###############-----| 38.1% |#######-------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > SXT 1759 88.0% |#################---| 20.5% |####----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NIT 743 37.2% |#######-------------| 17.1% |###-----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FOS 351 17.6% |###-----------------| 42.2% |########------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > LNZ 1023 51.2% |##########----------| 69.3% |#############-------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CIP 1409 70.5% |#############-------| 16.2% |###-----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MFX 211 10.6% |##------------------| 33.6% |######--------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > VAN 1861 93.1% |##################--| 38.3% |#######-------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TEC 976 48.8% |#########-----------| 75.7% |###############-----|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TCY 1200 60.0% |###########---------| 29.8% |#####---------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TGC 798 39.9% |########------------| 12.7% |##------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > DOX 1136 56.8% |###########---------| 27.7% |#####---------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ERY 1894 94.7% |##################--| 57.2% |###########---------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CLI 1520 76.0% |###############-----| 61.2% |############--------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AZM 1894 94.7% |##################--| 57.2% |###########---------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > IPM 889 44.5% |########------------| 6.2% |#-------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MEM 829 41.5% |########------------| 5.9% |#-------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MTR 34 1.7% |--------------------| 14.7% |##------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CHL 154 7.7% |#-------------------| 21.4% |####----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > COL 1640 82.0% |################----| 81.2% |################----|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MUP 270 13.5% |##------------------| 5.9% |#-------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > RIF 1003 50.2% |##########----------| 69.6% |#############-------|< / span >
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< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > < span class = "op" > ==< / span > < span class = "fu" > < a href = "as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Escherichia coli"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select_all.html" class = "external-link" > select_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > availability< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > count available visual_availabilty resistant visual_resistance< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > PEN 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > OXA 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FLC 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMX 392 83.9% |##################----| 50.0% |###########-----------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMC 467 100.0% |######################| 13.1% |##--------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMP 392 83.9% |##################----| 50.0% |###########-----------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TZP 416 89.1% |###################---| 5.5% |#---------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CZO 82 17.6% |###-------------------| 2.4% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FEP 317 67.9% |##############--------| 2.8% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CXM 465 99.6% |######################| 5.4% |#---------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FOX 377 80.7% |#################-----| 6.9% |#---------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CTX 459 98.3% |#####################-| 2.4% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CAZ 460 98.5% |#####################-| 2.4% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CRO 459 98.3% |#####################-| 2.4% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > GEN 460 98.5% |#####################-| 2.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TOB 462 98.9% |#####################-| 2.6% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AMK 171 36.6% |########--------------| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > KAN 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TMP 396 84.8% |##################----| 39.1% |########--------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > SXT 465 99.6% |######################| 31.6% |######----------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NIT 458 98.1% |#####################-| 2.8% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > FOS 61 13.1% |##--------------------| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > LNZ 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CIP 456 97.6% |#####################-| 12.5% |##--------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MFX 57 12.2% |##--------------------| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > VAN 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TEC 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TCY 3 0.6% |----------------------| 66.7% |##############--------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > TGC 68 14.6% |###-------------------| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > DOX 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ERY 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CLI 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > AZM 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > IPM 422 90.4% |###################---| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MEM 418 89.5% |###################---| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MTR 2 0.4% |----------------------| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CHL 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > COL 240 51.4% |###########-----------| 0.0% |----------------------|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > MUP 0 0.0% |----------------------| < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > RIF 467 100.0% |######################| 100.0% |######################|< / span >
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
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