In sbalci/histopathology-template: Template of R Codes Used in Histopathology Research.
library("ggplot2")
library("pander")
ggAggHist <- getFromNamespace("ggAggHist", "dataMaid")
ggAggBarplot <- getFromNamespace("ggAggBarplot", "dataMaid")
Data report overview
The dataset examined has the following dimensions:
Feature Result
Number of observations 250
Number of variables 21
Checks performed
The following variable checks were performed, depending on the data type of each variable:
character factor labelled haven labelled numeric integer logical Date
Identify miscoded missing values $\times$ $\times$ $\times$ $\times$ $\times$ $\times$ $\times$
Identify prefixed and suffixed whitespace $\times$ $\times$ $\times$ $\times$
Identify levels with < 6 obs. $\times$ $\times$ $\times$ $\times$
Identify case issues $\times$ $\times$ $\times$ $\times$
Identify misclassified numeric or integer variables $\times$ $\times$ $\times$ $\times$
Identify outliers $\times$ $\times$ $\times$
Please note that all numerical values in the following have been rounded to 2 decimals.
Summary table
Variable class # unique values Missing observations Any problems?
[ID] character 250 0.00 % $\times$
[Name] character 250 0.40 % $\times$
[Sex] character 3 0.40 %
[Age] numeric 50 0.40 %
[Race] character 7 0.40 % $\times$
[PreinvasiveComponent] character 3 0.40 %
[LVI] character 3 0.40 %
[PNI] character 3 0.40 %
[LastFollowUpDate] POSIXct 13 0.40 % $\times$
[Death] logical 3 0.40 %
[Group] character 3 0.40 %
[Grade] character 4 0.40 %
[TStage] character 5 0.40 %
[AntiX_intensity] numeric 4 0.40 %
[AntiY_intensity] numeric 4 0.40 %
[LymphNodeMetastasis] character 3 0.40 %
[Valid] logical 3 0.40 %
[Smoker] logical 3 0.40 %
[Grade_Level] character 4 0.40 %
[SurgeryDate] POSIXct 218 0.40 % $\times$
[DeathTime] character 2 0.00 %
Variable list
ID
- The variable is a key (distinct values for each observation).
\fullline
Name
- The variable is a key (distinct values for each observation).
\fullline
Sex
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Male"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Female",
"Male"), class = "factor"), y = c(111L, 138L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "Sex")
\emini
\fullline
Age
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 49
Median 51
1st and 3rd quartiles 37; 63
Min. and max. 25; 73
\emini
\bminitwo
ggAggHist(data = structure(list(xmin = c(25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L), xmax = c(30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L), ymin = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0), ymax = c(26L, 26L, 26L, 24L, 21L, 28L, 24L, 28L, 31L, 15L
)), class = "data.frame", row.names = c(NA, -10L)), vnam = "Age")
\emini
\fullline
Race
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 6
Mode "White"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:6, .Label = c("Asian",
"Bi-Racial", "Black", "Hispanic", "Native", "White"), class = "factor"),
y = c(10L, 5L, 31L, 37L, 1L, 165L)), class = "data.frame", row.names = c(NA,
-6L)), vnam = "Race")
\emini
- Note that the following levels have at most five observations: \"Bi-Racial\", \"Native\".
\fullline
PreinvasiveComponent
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent",
"Present"), class = "factor"), y = c(208L, 41L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "PreinvasiveComponent")
\emini
\fullline
LVI
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent",
"Present"), class = "factor"), y = c(146L, 103L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "LVI")
\emini
\fullline
PNI
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent",
"Present"), class = "factor"), y = c(181L, 68L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "PNI")
\emini
\fullline
LastFollowUpDate
- The variable has class POSIXct which is not supported by dataMaid.
\fullline
Death
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE",
"TRUE"), class = "factor"), y = c(72L, 177L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "Death")
\emini
\fullline
Group
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Control"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Control",
"Treatment"), class = "factor"), y = c(129L, 120L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "Group")
\emini
\fullline
Grade
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "3"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1",
"2", "3"), class = "factor"), y = c(60L, 84L, 105L)), class = "data.frame", row.names = c(NA,
-3L)), vnam = "Grade")
\emini
\fullline
TStage
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 4
Mode "4"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:4, .Label = c("1",
"2", "3", "4"), class = "factor"), y = c(23L, 46L, 69L, 111L)), class = "data.frame", row.names = c(NA,
-4L)), vnam = "TStage")
\emini
\fullline
AntiX_intensity
- Note that this variable is treated as a factor variable below, as it only takes a few unique values.
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "3"
Reference category 1
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1",
"2", "3"), class = "factor"), y = c(30L, 98L, 121L)), class = "data.frame", row.names = c(NA,
-3L)), vnam = "AntiX_intensity")
\emini
\fullline
AntiY_intensity
- Note that this variable is treated as a factor variable below, as it only takes a few unique values.
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "2"
Reference category 1
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1",
"2", "3"), class = "factor"), y = c(82L, 95L, 72L)), class = "data.frame", row.names = c(NA,
-3L)), vnam = "AntiY_intensity")
\emini
\fullline
LymphNodeMetastasis
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent",
"Present"), class = "factor"), y = c(154L, 95L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "LymphNodeMetastasis")
\emini
\fullline
Valid
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE",
"TRUE"), class = "factor"), y = c(109L, 140L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "Valid")
\emini
\fullline
Smoker
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE",
"TRUE"), class = "factor"), y = c(120L, 129L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "Smoker")
\emini
\fullline
Grade_Level
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "high"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("high",
"low", "moderate"), class = "factor"), y = c(102L, 75L, 72L)), class = "data.frame", row.names = c(NA,
-3L)), vnam = "Grade_Level")
\emini
\fullline
SurgeryDate
- The variable has class POSIXct which is not supported by dataMaid.
\fullline
DeathTime
\bminione
Feature Result
Variable type character
Number of missing obs. 0 (0 %)
Number of unique values 2
Mode "Within1Year"
\emini
\bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("MoreThan1Year",
"Within1Year"), class = "factor"), y = c(101L, 149L)), class = "data.frame", row.names = c(NA,
-2L)), vnam = "DeathTime")
\emini
\fullline
Report generation information:
-
Created by: Serdar BALCI old (username: serdarbalciold).
-
Report creation time: Wed May 13 2020 15:25:41
-
Report was run from directory: /Users/serdarbalciold/histopathRprojects/histopathology-template
-
dataMaid v1.4.0 [Pkg: 2019-12-10 from CRAN (R 3.6.0)]
-
R version 3.6.3 (2020-02-29).
-
Platform: x86_64-apple-darwin15.6.0 (64-bit)(macOS Catalina 10.15.4).
-
Function call: dataMaid::makeDataReport(data = mydata, render = FALSE, file = here::here("out",
"dataMaid_mydata.Rmd"), replace = TRUE, quiet = TRUE, openResult = FALSE)
sbalci/histopathology-template documentation built on June 29, 2023, 5:52 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library("ggplot2") library("pander")
ggAggHist <- getFromNamespace("ggAggHist", "dataMaid") ggAggBarplot <- getFromNamespace("ggAggBarplot", "dataMaid")
Data report overview
The dataset examined has the following dimensions:
Feature Result
Number of observations 250
Number of variables 21
Checks performed
The following variable checks were performed, depending on the data type of each variable:
character factor labelled haven labelled numeric integer logical Date
Identify miscoded missing values $\times$ $\times$ $\times$ $\times$ $\times$ $\times$ $\times$
Identify prefixed and suffixed whitespace $\times$ $\times$ $\times$ $\times$
Identify levels with < 6 obs. $\times$ $\times$ $\times$ $\times$
Identify case issues $\times$ $\times$ $\times$ $\times$
Identify misclassified numeric or integer variables $\times$ $\times$ $\times$ $\times$
Identify outliers $\times$ $\times$ $\times$
Please note that all numerical values in the following have been rounded to 2 decimals.
Summary table
Variable class # unique values Missing observations Any problems?
[ID] character 250 0.00 % $\times$
[Name] character 250 0.40 % $\times$
[Sex] character 3 0.40 %
[Age] numeric 50 0.40 %
[Race] character 7 0.40 % $\times$
[PreinvasiveComponent] character 3 0.40 %
[LVI] character 3 0.40 %
[PNI] character 3 0.40 %
[LastFollowUpDate] POSIXct 13 0.40 % $\times$
[Death] logical 3 0.40 %
[Group] character 3 0.40 %
[Grade] character 4 0.40 %
[TStage] character 5 0.40 %
[AntiX_intensity] numeric 4 0.40 %
[AntiY_intensity] numeric 4 0.40 %
[LymphNodeMetastasis] character 3 0.40 %
[Valid] logical 3 0.40 %
[Smoker] logical 3 0.40 %
[Grade_Level] character 4 0.40 %
[SurgeryDate] POSIXct 218 0.40 % $\times$
[DeathTime] character 2 0.00 %
Variable list
ID
- The variable is a key (distinct values for each observation).
\fullline
Name
- The variable is a key (distinct values for each observation).
\fullline
Sex
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Male"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Female", "Male"), class = "factor"), y = c(111L, 138L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "Sex")
\emini
\fullline
Age
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 49
Median 51
1st and 3rd quartiles 37; 63
Min. and max. 25; 73
\emini \bminitwo
ggAggHist(data = structure(list(xmin = c(25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L), xmax = c(30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L), ymin = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), ymax = c(26L, 26L, 26L, 24L, 21L, 28L, 24L, 28L, 31L, 15L )), class = "data.frame", row.names = c(NA, -10L)), vnam = "Age")
\emini
\fullline
Race
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 6
Mode "White"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:6, .Label = c("Asian", "Bi-Racial", "Black", "Hispanic", "Native", "White"), class = "factor"), y = c(10L, 5L, 31L, 37L, 1L, 165L)), class = "data.frame", row.names = c(NA, -6L)), vnam = "Race")
\emini
- Note that the following levels have at most five observations: \"Bi-Racial\", \"Native\".
\fullline
PreinvasiveComponent
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", "Present"), class = "factor"), y = c(208L, 41L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "PreinvasiveComponent")
\emini
\fullline
LVI
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", "Present"), class = "factor"), y = c(146L, 103L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "LVI")
\emini
\fullline
PNI
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", "Present"), class = "factor"), y = c(181L, 68L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "PNI")
\emini
\fullline
LastFollowUpDate
- The variable has class POSIXct which is not supported by dataMaid.
\fullline
Death
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", "TRUE"), class = "factor"), y = c(72L, 177L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "Death")
\emini
\fullline
Group
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Control"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Control", "Treatment"), class = "factor"), y = c(129L, 120L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "Group")
\emini
\fullline
Grade
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "3"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", "2", "3"), class = "factor"), y = c(60L, 84L, 105L)), class = "data.frame", row.names = c(NA, -3L)), vnam = "Grade")
\emini
\fullline
TStage
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 4
Mode "4"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:4, .Label = c("1", "2", "3", "4"), class = "factor"), y = c(23L, 46L, 69L, 111L)), class = "data.frame", row.names = c(NA, -4L)), vnam = "TStage")
\emini
\fullline
AntiX_intensity
- Note that this variable is treated as a factor variable below, as it only takes a few unique values.
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "3"
Reference category 1
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", "2", "3"), class = "factor"), y = c(30L, 98L, 121L)), class = "data.frame", row.names = c(NA, -3L)), vnam = "AntiX_intensity")
\emini
\fullline
AntiY_intensity
- Note that this variable is treated as a factor variable below, as it only takes a few unique values.
\bminione
Feature Result
Variable type numeric
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "2"
Reference category 1
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", "2", "3"), class = "factor"), y = c(82L, 95L, 72L)), class = "data.frame", row.names = c(NA, -3L)), vnam = "AntiY_intensity")
\emini
\fullline
LymphNodeMetastasis
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "Absent"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", "Present"), class = "factor"), y = c(154L, 95L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "LymphNodeMetastasis")
\emini
\fullline
Valid
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", "TRUE"), class = "factor"), y = c(109L, 140L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "Valid")
\emini
\fullline
Smoker
\bminione
Feature Result
Variable type logical
Number of missing obs. 1 (0.4 %)
Number of unique values 2
Mode "TRUE"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", "TRUE"), class = "factor"), y = c(120L, 129L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "Smoker")
\emini
\fullline
Grade_Level
\bminione
Feature Result
Variable type character
Number of missing obs. 1 (0.4 %)
Number of unique values 3
Mode "high"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("high", "low", "moderate"), class = "factor"), y = c(102L, 75L, 72L)), class = "data.frame", row.names = c(NA, -3L)), vnam = "Grade_Level")
\emini
\fullline
SurgeryDate
- The variable has class POSIXct which is not supported by dataMaid.
\fullline
DeathTime
\bminione
Feature Result
Variable type character
Number of missing obs. 0 (0 %)
Number of unique values 2
Mode "Within1Year"
\emini \bminitwo
ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("MoreThan1Year", "Within1Year"), class = "factor"), y = c(101L, 149L)), class = "data.frame", row.names = c(NA, -2L)), vnam = "DeathTime")
\emini
\fullline
Report generation information:
-
Created by: Serdar BALCI old (username:
serdarbalciold). -
Report creation time: Wed May 13 2020 15:25:41
-
Report was run from directory:
/Users/serdarbalciold/histopathRprojects/histopathology-template -
dataMaid v1.4.0 [Pkg: 2019-12-10 from CRAN (R 3.6.0)]
-
R version 3.6.3 (2020-02-29).
-
Platform: x86_64-apple-darwin15.6.0 (64-bit)(macOS Catalina 10.15.4).
-
Function call:
dataMaid::makeDataReport(data = mydata, render = FALSE, file = here::here("out", "dataMaid_mydata.Rmd"), replace = TRUE, quiet = TRUE, openResult = FALSE)
R Package Documentation
Browse R Packages
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