Histopathology Data

A simulated dataset for histopathological research, containing patient demographics, clinical findings, and hypothetical molecular data. This dataset is intended for demonstration and testing of analysis functions.

Usage

data(histopathology)

Format

A data frame with 250 rows and 38 variables:

ID

Numeric. Unique patient identifier.

Name

Character. Patient's name (simulated).

Sex

Character. Patient's sex (e.g., "Male", "Female").

Age

Numeric. Patient's age in years.

Race

Character. Patient's race (e.g., "White", "Black").

PreinvasiveComponent

Character. Presence of preinvasive component (e.g., "Present", "Absent").

LVI

Character. Lymphovascular invasion status (e.g., "Present", "Absent").

PNI

Character. Perineural invasion status (e.g., "Present", "Absent").

LastFollowUpDate

POSIXct. Date and time of the last follow-up.

Death

Character. Death status (e.g., "YANLIŞ" for False/No, "DOĞRU" for True/Yes). Indicates if the patient died.

Group

Character. Treatment or control group (e.g., "Control", "Treatment").

Grade

Numeric. Tumor grade (e.g., 1, 2, 3).

TStage

Numeric. Tumor stage (e.g., 1, 2, 3, 4).

Anti-X-intensity

Numeric. Intensity of Anti-X marker staining.

Anti-Y-intensity

Numeric. Intensity of Anti-Y marker staining.

LymphNodeMetastasis

Character. Lymph node metastasis status (e.g., "Present", "Absent").

Valid

Character. Validity status (e.g., "YANLIŞ", "DOĞRU"). Meaning needs context.

Smoker

Character. Smoking status (e.g., "YANLIŞ", "DOĞRU").

Grade_Level

Character. Tumor grade categorized (e.g., "low", "high", "moderate").

SurgeryDate

POSIXct. Date and time of surgery.

DeathTime

Character. Time to death category (e.g., "Within1Year").

int

Character. Interval string, likely representing the duration between two dates.

OverallTime

Numeric. Overall time, likely survival time in some unit (e.g., months).

Outcome

Numeric. Outcome variable, likely coded (e.g., 0 for alive, 1 for deceased).

Mortality5yr

Character. 5-year mortality status (e.g., "Alive", "Dead").

Rater 1

Numeric. Rating from Rater 1.

Rater 2

Numeric. Rating from Rater 2.

Rater 3

Numeric. Rating from Rater 3.

Rater A

Numeric. Rating from Rater A.

Rater B

Numeric. Rating from Rater B.

New Test

Numeric. Result of a new diagnostic test.

Golden Standart

Numeric. Result of a gold standard diagnostic test.

MeasurementA

Numeric. A continuous measurement.

MeasurementB

Numeric. Another continuous measurement.

Disease Status

Character. Disease status (e.g., "Ill", "Healthy").

Measurement1

Numeric. Measurement from a test or observation.

Measurement2

Numeric. Another measurement from a test or observation.

Outcome2

Character. A secondary outcome measure with levels like "DOD" (Dead of Disease), "DOOC" (Dead of Other Cause), "AWD" (Alive with Disease), "AWOD" (Alive Without Disease).

Examples

data(histopathology)
str(histopathology)
#> spc_tbl_ [250 × 38] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
#>  $ ID                  : num [1:250] 1 2 3 4 5 6 7 8 9 10 ...
#>  $ Name                : chr [1:250] "Tonisia" "Daniyah" "Naviana" "Daerion" ...
#>  $ Sex                 : chr [1:250] "Male" "Female" "Male" "Male" ...
#>  $ Age                 : num [1:250] 27 36 65 51 58 53 33 26 25 68 ...
#>  $ Race                : chr [1:250] "White" "White" "White" "White" ...
#>  $ PreinvasiveComponent: chr [1:250] "Present" "Absent" "Absent" "Absent" ...
#>  $ LVI                 : chr [1:250] "Present" "Absent" "Absent" "Present" ...
#>  $ PNI                 : chr [1:250] "Absent" "Absent" "Absent" "Absent" ...
#>  $ LastFollowUpDate    : chr [1:250] "2019.10.22 00:00:00" "2019.06.22 00:00:00" "2019.08.22 00:00:00" "2019.03.22 00:00:00" ...
#>  $ Death               : chr [1:250] "YANLIŞ" "DOĞRU" "DOĞRU" "YANLIŞ" ...
#>  $ Group               : chr [1:250] "Control" "Treatment" "Control" "Treatment" ...
#>  $ Grade               : num [1:250] 2 2 1 3 2 2 1 2 3 3 ...
#>  $ TStage              : num [1:250] 4 4 4 4 1 4 2 3 4 4 ...
#>  $ Anti-X-intensity    : num [1:250] 3 2 2 3 3 3 2 2 1 2 ...
#>  $ Anti-Y-intensity    : num [1:250] 1 1 2 3 3 2 2 2 1 3 ...
#>  $ LymphNodeMetastasis : chr [1:250] "Present" "Absent" "Absent" "Absent" ...
#>  $ Valid               : chr [1:250] "YANLIŞ" "DOĞRU" "YANLIŞ" "DOĞRU" ...
#>  $ Smoker              : chr [1:250] "YANLIŞ" "YANLIŞ" "DOĞRU" "YANLIŞ" ...
#>  $ Grade_Level         : chr [1:250] "high" "low" "low" "high" ...
#>  $ SurgeryDate         : chr [1:250] "2019.07.08 00:00:00" "2019.03.18 00:00:00" "2019.05.18 00:00:00" "2018.10.24 00:00:00" ...
#>  $ DeathTime           : chr [1:250] "Within1Year" "Within1Year" "Within1Year" "Within1Year" ...
#>  $ int                 : chr [1:250] "2019-07-08 UTC--2019-10-22 UTC" "2019-03-18 UTC--2019-06-22 UTC" "2019-05-18 UTC--2019-08-22 UTC" "2018-10-24 UTC--2019-03-22 UTC" ...
#>  $ OverallTime         : num [1:250] 3.5 3.1 3.1 4.9 3.3 9.3 6.3 9 5.8 9.9 ...
#>  $ Outcome             : num [1:250] 0 1 1 0 0 0 1 1 1 0 ...
#>  $ Mortality5yr        : chr [1:250] "Alive" "Dead" "Dead" "Alive" ...
#>  $ Rater 1             : num [1:250] 0 1 1 0 0 0 1 1 1 0 ...
#>  $ Rater 2             : num [1:250] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ Rater 3             : num [1:250] 1 1 1 0 1 1 1 1 1 1 ...
#>  $ Rater A             : num [1:250] 3 2 3 3 2 3 1 1 2 1 ...
#>  $ Rater B             : num [1:250] 3 2 3 3 2 3 1 1 2 1 ...
#>  $ New Test            : num [1:250] 0 0 0 0 0 0 1 0 0 0 ...
#>  $ Golden Standart     : num [1:250] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ MeasurementA        : num [1:250] -1.63432 0.37071 0.01585 -1.23584 -0.00141 ...
#>  $ MeasurementB        : num [1:250] 0.611 0.554 0.742 0.622 0.527 ...
#>  $ Disease Status      : chr [1:250] "Ill" "Ill" "Healthy" "Ill" ...
#>  $ Measurement1        : num [1:250] 0.387 0.829 0.159 2.447 0.847 ...
#>  $ Measurement2        : num [1:250] 1.8654 0.5425 0.0701 2.4071 0.5564 ...
#>  $ Outcome2            : chr [1:250] "DOD" "DOOC" "AWD" "AWOD" ...
#>  - attr(*, "spec")=List of 3
#>   ..$ cols   :List of 38
#>   .. ..$ ID                  : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Name                : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Sex                 : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Age                 : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Race                : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ PreinvasiveComponent: list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ LVI                 : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ PNI                 : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ LastFollowUpDate    : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Death               : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Group               : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Grade               : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ TStage              : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Anti-X-intensity    : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Anti-Y-intensity    : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ LymphNodeMetastasis : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Valid               : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Smoker              : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Grade_Level         : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ SurgeryDate         : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ DeathTime           : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ int                 : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ OverallTime         : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Outcome             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Mortality5yr        : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Rater 1             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Rater 2             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Rater 3             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Rater A             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Rater B             : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ New Test            : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Golden Standart     : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ MeasurementA        : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ MeasurementB        : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Disease Status      : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ Measurement1        : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Measurement2        : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ Outcome2            : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   ..$ default: list()
#>   .. ..- attr(*, "class")= chr [1:2] "collector_guess" "collector"
#>   ..$ skip   : num 1
#>   ..- attr(*, "class")= chr "col_spec"
head(histopathology)
#> # A tibble: 6 × 38
#>      ID Name    Sex      Age Race  PreinvasiveComponent LVI     PNI    
#>   <dbl> <chr>   <chr>  <dbl> <chr> <chr>                <chr>   <chr>  
#> 1     1 Tonisia Male      27 White Present              Present Absent 
#> 2     2 Daniyah Female    36 White Absent               Absent  Absent 
#> 3     3 Naviana Male      65 White Absent               Absent  Absent 
#> 4     4 Daerion Male      51 White Absent               Present Absent 
#> 5     5 Tamyiah Female    58 Black Absent               Absent  Absent 
#> 6     6 Donnajo Female    53 White Absent               Present Present
#> # ℹ 30 more variables: LastFollowUpDate <chr>, Death <chr>, Group <chr>,
#> #   Grade <dbl>, TStage <dbl>, `Anti-X-intensity` <dbl>,
#> #   `Anti-Y-intensity` <dbl>, LymphNodeMetastasis <chr>, Valid <chr>,
#> #   Smoker <chr>, Grade_Level <chr>, SurgeryDate <chr>, DeathTime <chr>,
#> #   int <chr>, OverallTime <dbl>, Outcome <dbl>, Mortality5yr <chr>,
#> #   `Rater 1` <dbl>, `Rater 2` <dbl>, `Rater 3` <dbl>, `Rater A` <dbl>,
#> #   `Rater B` <dbl>, `New Test` <dbl>, `Golden Standart` <dbl>, …
summary(histopathology$Age)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
#>   25.00   38.00   49.00   49.44   62.00   73.00       1 
hist(histopathology$TStage)