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