Trying different groupings
## # A tibble: 28 x 9
## # Groups: pna_type, binned_outcome, ethnicity, gender, races, smoking_status,
## # pathogen [28]
## pna_type binned_outcome ethnicity gender races smoking_status pathogen
## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 Other Pneumonia Deceased Not Hisp~ Male White Never Smoker NA
## 2 COVID-19 Deceased Not Hisp~ Male White NA SARS-Co~
## 3 COVID-19 Deceased Not Hisp~ Male White Past Smoker SARS-Co~
## 4 COVID-19 Home Hispanic~ Female Unkn~ Never Smoker SARS-Co~
## 5 COVID-19 Home Hispanic~ Male Unkn~ NA SARS-Co~
## 6 COVID-19 Home Hispanic~ Male White NA SARS-Co~
## 7 COVID-19 Home Hispanic~ Male White Never Smoker SARS-Co~
## 8 COVID-19 Home Hispanic~ Male White Past Smoker SARS-Co~
## 9 COVID-19 Home Not Hisp~ Female Blac~ NA SARS-Co~
## 10 COVID-19 Home Not Hisp~ Male White Never Smoker SARS-Co~
## # ... with 18 more rows, and 2 more variables: Superinfection <chr>, Freq <int>
## # A tibble: 17 x 5
## # Groups: gender, pna_type, Superinfection [9]
## gender pna_type Superinfection binned_outcome Freq
## <chr> <chr> <chr> <chr> <int>
## 1 Male COVID-19 Primary Only Home 5
## 2 Male Other Pneumonia NA Deceased 3
## 3 Female COVID-19 Primary Only Home 2
## 4 Female Other Pneumonia NA LTAC 2
## 5 Female Other Viral Pneumonia Primary Only Deceased 2
## 6 Male COVID-19 Primary Only LTAC 2
## 7 Male Other Viral Pneumonia Primary Only Deceased 2
## 8 Male Other Viral Pneumonia Primary Only Inpatient Facility 2
## 9 Female COVID-19 Superinfection LTAC 1
## 10 Female Other Pneumonia NA Deceased 1
## 11 Female Other Viral Pneumonia Primary Only Inpatient Facility 1
## 12 Male COVID-19 Primary Only Deceased 1
## 13 Male COVID-19 Primary Only Inpatient Facility 1
## 14 Male COVID-19 Superinfection Deceased 1
## 15 Male COVID-19 Superinfection Inpatient Facility 1
## 16 Male Other Pneumonia NA LTAC 1
## 17 Male Other Viral Pneumonia Superinfection Home 1
## # A tibble: 9 x 4
## # Groups: gender, pna_type [6]
## gender pna_type Superinfection Freq
## <chr> <chr> <chr> <int>
## 1 Male COVID-19 Primary Only 9
## 2 Male Other Pneumonia NA 4
## 3 Male Other Viral Pneumonia Primary Only 4
## 4 Female Other Pneumonia NA 3
## 5 Female Other Viral Pneumonia Primary Only 3
## 6 Female COVID-19 Primary Only 2
## 7 Male COVID-19 Superinfection 2
## 8 Female COVID-19 Superinfection 1
## 9 Male Other Viral Pneumonia Superinfection 1
## # A tibble: 19 x 5
## # Groups: pna_type, GRAM_STAIN_REPORT_Organisms, GRAM_STAIN_REPORT_RBC [13]
## pna_type GRAM_STAIN_REPO~ GRAM_STAIN_REPO~ GRAM_STAIN_REPO~ Freq
## <chr> <chr> <chr> <chr> <int>
## 1 COVID-19 No Organisms Se~ NA White Blood Cel~ 7
## 2 Other Viral Pneumon~ No Organisms Se~ NA White Blood Cel~ 3
## 3 COVID-19 No Organisms Se~ Many Red Blood ~ Many White Bloo~ 2
## 4 COVID-19 No Organisms Se~ Red Blood Cells~ White Blood Cel~ 2
## 5 COVID-19 Gram Positive R~ Red Blood Cells~ White Blood Cel~ 1
## 6 COVID-19 No Organisms Se~ Many Red Blood ~ Few White Blood~ 1
## 7 COVID-19 No Organisms Se~ NA Moderate White ~ 1
## 8 Other Pneumonia Few Gram Positi~ NA Many White Bloo~ 1
## 9 Other Pneumonia Gram Positive C~ NA White Blood Cel~ 1
## 10 Other Pneumonia Gram Positive R~ NA White Blood Cel~ 1
## 11 Other Pneumonia No Organisms Se~ NA Few White Blood~ 1
## 12 Other Pneumonia No Organisms Se~ NA Rare White Bloo~ 1
## 13 Other Pneumonia No Organisms Se~ NA White Blood Cel~ 1
## 14 Other Pneumonia Rare Gram Posit~ NA Many White Bloo~ 1
## 15 Other Viral Pneumon~ Gram Positive C~ NA White Blood Cel~ 1
## 16 Other Viral Pneumon~ No Organisms Se~ Few Red Blood C~ Rare White Bloo~ 1
## 17 Other Viral Pneumon~ No Organisms Se~ NA Few White Blood~ 1
## 18 Other Viral Pneumon~ No Organisms Se~ NA No WBC's seen. 1
## 19 Other Viral Pneumon~ No Organisms Se~ Red Blood Cells~ White Blood Cel~ 1
## # A tibble: 10 x 7
## # Groups: pna_type, any_bacterial, any_influenza, any_viral, any_culture [10]
## pna_type any_bacterial any_influenza any_viral any_culture any_viral_non_c~
## <chr> <lgl> <lgl> <lgl> <lgl> <lgl>
## 1 COVID-19 FALSE FALSE FALSE FALSE FALSE
## 2 Other Vir~ FALSE FALSE FALSE FALSE FALSE
## 3 Other Pne~ FALSE FALSE FALSE FALSE FALSE
## 4 Other Pne~ FALSE FALSE FALSE TRUE FALSE
## 5 COVID-19 FALSE FALSE FALSE TRUE FALSE
## 6 Other Vir~ FALSE FALSE TRUE FALSE TRUE
## 7 COVID-19 TRUE FALSE FALSE FALSE FALSE
## 8 Other Pne~ TRUE FALSE FALSE FALSE FALSE
## 9 Other Vir~ FALSE TRUE TRUE FALSE TRUE
## 10 Other Vir~ FALSE TRUE TRUE TRUE TRUE
## # ... with 1 more variable: Freq <int>
## # A tibble: 6 x 3
## # Groups: pna_type [3]
## pna_type gender Freq
## <chr> <chr> <int>
## 1 COVID-19 Male 11
## 2 Other Viral Pneumonia Male 5
## 3 Other Pneumonia Male 4
## 4 COVID-19 Female 3
## 5 Other Pneumonia Female 3
## 6 Other Viral Pneumonia Female 3
## # A tibble: 14 x 4
## # Groups: pna_type, ethnicity [6]
## pna_type ethnicity races Freq
## <chr> <chr> <chr> <int>
## 1 Other Pneumonia Not Hispanic or Latino White 5
## 2 COVID-19 Hispanic or Latino White 4
## 3 COVID-19 Not Hispanic or Latino White 4
## 4 Other Viral Pneumonia Not Hispanic or Latino White 3
## 5 COVID-19 Hispanic or Latino Unknown or Not Reported 2
## 6 COVID-19 Not Hispanic or Latino Black/African American 2
## 7 Other Viral Pneumonia Hispanic or Latino White 2
## 8 COVID-19 Unknown or Not Reported Unknown or Not Reported 1
## 9 COVID-19 Unknown or Not Reported White 1
## 10 Other Pneumonia Not Hispanic or Latino Asian 1
## 11 Other Pneumonia Not Hispanic or Latino Black/African American 1
## 12 Other Viral Pneumonia Hispanic or Latino Unknown or Not Reported 1
## 13 Other Viral Pneumonia Not Hispanic or Latino Black/African American 1
## 14 Other Viral Pneumonia Not Hispanic or Latino Unknown or Not Reported 1
## # A tibble: 9 x 3
## # Groups: pna_type [3]
## pna_type binned_outcome Freq
## <chr> <chr> <int>
## 1 COVID-19 Home 7
## 2 Other Pneumonia Deceased 4
## 3 Other Viral Pneumonia Deceased 4
## 4 COVID-19 LTAC 3
## 5 Other Pneumonia LTAC 3
## 6 Other Viral Pneumonia Inpatient Facility 3
## 7 COVID-19 Deceased 2
## 8 COVID-19 Inpatient Facility 2
## 9 Other Viral Pneumonia Home 1
## # A tibble: 8 x 3
## # Groups: pna_type [3]
## pna_type smoking_status Freq
## <chr> <chr> <int>
## 1 Other Viral Pneumonia Never Smoker 6
## 2 COVID-19 NA 5
## 3 COVID-19 Never Smoker 5
## 4 COVID-19 Past Smoker 4
## 5 Other Pneumonia Never Smoker 4
## 6 Other Pneumonia NA 2
## 7 Other Viral Pneumonia Past Smoker 2
## 8 Other Pneumonia Past Smoker 1
## # A tibble: 5 x 3
## # Groups: pna_type [3]
## pna_type Superinfection Freq
## <chr> <chr> <int>
## 1 COVID-19 Primary Only 11
## 2 Other Pneumonia NA 7
## 3 Other Viral Pneumonia Primary Only 7
## 4 COVID-19 Superinfection 3
## 5 Other Viral Pneumonia Superinfection 1
## # A tibble: 6 x 3
## # Groups: pna_type [3]
## pna_type ECMO_yn Freq
## <chr> <chr> <int>
## 1 COVID-19 NA 11
## 2 Other Viral Pneumonia NA 7
## 3 Other Pneumonia NA 6
## 4 COVID-19 1 3
## 5 Other Pneumonia 1 1
## 6 Other Viral Pneumonia 1 1
## # A tibble: 19 x 5
## # Groups: pna_type, GRAM_STAIN_REPORT_Organisms, GRAM_STAIN_REPORT_RBC [13]
## pna_type GRAM_STAIN_REPO~ GRAM_STAIN_REPO~ GRAM_STAIN_REPO~ Freq
## <chr> <chr> <chr> <chr> <int>
## 1 COVID-19 No Organisms Se~ NA White Blood Cel~ 7
## 2 Other Viral Pneumon~ No Organisms Se~ NA White Blood Cel~ 3
## 3 COVID-19 No Organisms Se~ Many Red Blood ~ Many White Bloo~ 2
## 4 COVID-19 No Organisms Se~ Red Blood Cells~ White Blood Cel~ 2
## 5 COVID-19 Gram Positive R~ Red Blood Cells~ White Blood Cel~ 1
## 6 COVID-19 No Organisms Se~ Many Red Blood ~ Few White Blood~ 1
## 7 COVID-19 No Organisms Se~ NA Moderate White ~ 1
## 8 Other Pneumonia Few Gram Positi~ NA Many White Bloo~ 1
## 9 Other Pneumonia Gram Positive C~ NA White Blood Cel~ 1
## 10 Other Pneumonia Gram Positive R~ NA White Blood Cel~ 1
## 11 Other Pneumonia No Organisms Se~ NA Few White Blood~ 1
## 12 Other Pneumonia No Organisms Se~ NA Rare White Bloo~ 1
## 13 Other Pneumonia No Organisms Se~ NA White Blood Cel~ 1
## 14 Other Pneumonia Rare Gram Posit~ NA Many White Bloo~ 1
## 15 Other Viral Pneumon~ Gram Positive C~ NA White Blood Cel~ 1
## 16 Other Viral Pneumon~ No Organisms Se~ Few Red Blood C~ Rare White Bloo~ 1
## 17 Other Viral Pneumon~ No Organisms Se~ NA Few White Blood~ 1
## 18 Other Viral Pneumon~ No Organisms Se~ NA No WBC's seen. 1
## 19 Other Viral Pneumon~ No Organisms Se~ Red Blood Cells~ White Blood Cel~ 1
