| Type: | Package |
| Title: | Classification Using Binary Procrustes Rotation |
| Version: | 0.6.2 |
| Description: | Implements a classification method described by Grice (2011, ISBN:978-0-12-385194-9) using binary procrustes rotation; a simplified version of procrustes rotation. |
| License: | GPL (≥ 3) |
| URL: | https://timbeechey.github.io/clubpro/ |
| BugReports: | https://github.com/timbeechey/clubpro/issues |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.3.1 |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress |
| Imports: | Rcpp, lattice, stats, graphics |
| Suggests: | knitr, rmarkdown, tinytest |
| SystemRequirements: | C++17 |
| Depends: | R (≥ 2.10) |
| VignetteBuilder: | knitr |
| NeedsCompilation: | yes |
| Packaged: | 2024-06-07 13:47:16 UTC; tim |
| Author: | Timothy Beechey 
[aut, cre] |
| Maintainer: | Timothy Beechey <tim.beechey@proton.me> |
| Repository: | CRAN |
| Date/Publication: | 2024-06-07 15:50:02 UTC |
Classification accuracy for each observation.
Description
Classification accuracy for each observation.
Usage
accuracy(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns a character vector containing a string corresponding to each observation indicating whether classification of that observation was "correct", "incorrect", or "ambigous".
Value
a table
Examples
mod <- club(rate ~ dose, data = caffeine)
accuracy(mod)
Convert the output of csi() to a data.frame.
Description
Convert the output of csi() to a data.frame.
Usage
## S3 method for class 'clubprocsi'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)
Arguments
x |
an object of class "clubprocsi" |
row.names |
ignored |
optional |
ignored |
... |
ignored |
Details
This function is useful to format pcc replicates data for plotting.
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- csi(mod)
as.data.frame(z)
Convert the output of pcc_replicates() to a data.frame.
Description
Convert the output of pcc_replicates() to a data.frame.
Usage
## S3 method for class 'clubprorand'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)
Arguments
x |
an object of class "clubprorand" |
row.names |
ignored |
optional |
ignored |
... |
ignored |
Details
This function is useful to format pcc replicates data for plotting.
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- pcc_replicates(mod)
as.data.frame(z)
Caffeine data
Description
Effect of three different doses of caffeine on finger tapping rate.
Usage
caffeine
Format
A data frame with 30 rows and 2 columns:
- dose
dose of caffeine in mg
- rate
finger taps per minute
Source
Hand D.J., Daly F., Lunn A.D., McConway K.J., Ostrowski E. (1994) A Handbook of Small Data Sets. London: Chapman & Hall. Data set 50.
Classify observations.
Description
club() is used to classify obervations using binary procrustes
rotation.
Usage
club(
f,
data,
imprecision,
nreps,
normalise_cols,
reorder_obs,
display_progress
)
Arguments
f |
a formula. |
data |
a data.frame. |
imprecision |
a number indicting the margin of imprecision allowed in classification. |
nreps |
the number of replicates to use in the randomisation test. |
normalise_cols |
a boolean indicating whether to normalise matrix columns. |
reorder_obs |
a string indicating the method for reordering observations to calculate c-values. |
display_progress |
a boolean indictaing whether a progress bar should be displayed. |
Value
an object of class "clubprofit" is a list containing the folllowing components:
- prediction
a character vector of predicted classifications.
- accuracy
a character vector indicating whether each classification is "correct", "incorrect", or "ambiguous".
- pcc
the percentage of correct classifications.
- cval
the chance of randomly reordered data producing a PCC >= the observed PCC.
- pcc_replicates
a vector of PCCs generated from randomly reordered data used to calculate
cval.- call
the matched call.
Examples
mod <- club(rate ~ dose, data = caffeine)
Compare models.
Description
Compare models.
Usage
compare(m1, m2)
Arguments
m1 |
an object of class "clubprofit" produced by |
m2 |
an object of class "clubprofit" produced by |
Details
Compare the PCC of two clubprofit models and compute the chance-value of the difference.
Value
an object of type "clubprocomparison"
Examples
m1 <- club(width ~ location, jellyfish)
m2 <- club(length ~ location, jellyfish)
compare(m1, m2)
Classification strength indices.
Description
Classification strength indices.
Usage
csi(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns a vector containing the classification strength index for each observation.
Value
a numeric vector.
Examples
mod <- club(rate ~ dose, data = caffeine)
csi(mod)
Chance value.
Description
Chance value.
Usage
cval(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Compute the chance that randomly reordered data results in a percentage of correctly classified observations at least as high as the observed data.
Value
a numeric value.
Examples
mod <- club(rate ~ dose, data = caffeine)
cval(mod)
Individual level classification results.
Description
Individual level classification results.
Usage
individual_results(m, digits)
Arguments
m |
an object of class "clubprofit" produced by |
digits |
an integer |
Details
Returns a data.frame containing predicted classifications and classification accuracy for each individual observation.
Value
a data.frame containing a columns of predictions and prediction accuracy
Examples
mod <- club(rate ~ dose, data = caffeine)
individual_results(mod)
Jellyfish dimension data
Description
Sizes of jellyfish from two locations in the Hawkesbury River, New South Wales, Australia.
Usage
jellyfish
Format
A data frame with 46 rows and 3 columns:
- location
location where jellyfish was caught
- width
jellyfish width in mm
- length
jellyfish length in mm
Source
Hand D.J., Daly F., Lunn A.D., McConway K.J., Ostrowski E. (1994) A Handbook of Small Data Sets. London: Chapman & Hall. Data set 225.
Median classification strength index.
Description
Median classification strength index.
Usage
median_csi(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns the median classification strength index.
Value
a numeric vector.
Examples
mod <- club(rate ~ dose, data = caffeine)
median_csi(mod)
Number of ambiguous classifications.
Description
Number of ambiguous classifications.
Usage
n_ambiguous(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns the number of observations which were classified ambiguously by the model.
Value
an integer.
Examples
mod <- club(rate ~ dose, data = caffeine)
n_ambiguous(mod)
Number of correct classifications.
Description
Number of correct classifications.
Usage
n_correct(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns the number of observations which were classified correctly by the model.
Value
an integer.
Examples
mod <- club(rate ~ dose, data = caffeine)
n_correct(mod)
Number of incorrect classifications.
Description
Number of incorrect classifications.
Usage
n_incorrect(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns the number of observations which were classified incorrectly by the model.
Value
an integer.
Examples
mod <- club(rate ~ dose, data = caffeine)
n_incorrect(mod)
Percentage of correct classifications.
Description
Percentage of correct classifications.
Usage
pcc(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns the percentage of correctly classified observations.
Value
a numeric value.
Examples
mod <- club(rate ~ dose, data = caffeine)
pcc(mod)
PCC replicates.
Description
PCC replicates.
Usage
pcc_replicates(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns an object containing a vector of PCC replicates used to calculate the chance-value.
Value
an object of class clubprorand.
Examples
mod <- club(rate ~ dose, data = caffeine)
head(pcc_replicates(mod))
Plot accuracy.
Description
Plot accuracy.
Usage
## S3 method for class 'clubproaccuracy'
plot(x, ...)
Arguments
x |
an object of class "clubproaccuracy" |
... |
ignored |
Details
Produces a mosaic plot of predictio naccuracy by category
Value
called for side-effects only
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- accuracy(mod)
plot(z)
Plot model comparison.
Description
Plot model comparison.
Usage
## S3 method for class 'clubprocomparison'
plot(x, ...)
Arguments
x |
an object of class "clubprocomparison". |
... |
ignored |
Details
Plot a distribution of PCCs computed from randomly reordered data used to calculate the chance-value for a model comparison.
Value
no return value, called for side effects only.
Examples
m1 <- club(width ~ location, jellyfish)
m2 <- club(length ~ location, jellyfish)
z <- compare(m1, m2)
plot(z)
Plot classification strength indices.
Description
Plot classification strength indices.
Usage
## S3 method for class 'clubprocsi'
plot(x, ...)
Arguments
x |
an object of class "clubprocsi" |
... |
ignored |
Details
Produces dotplot showing classification strength for each individual.
Value
called for side-effects only
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- csi(mod)
plot(z)
Plot classification accuracy.
Description
Plot classification accuracy.
Usage
## S3 method for class 'clubprofit'
plot(x, ...)
Arguments
x |
an object of class "clubprofit" produced by |
... |
ignored |
Details
Produces bar plot showing counts of individuals against observed values within each target grouping. Fill colours indicate whether each individual was classified correctly, incorrectly or ambiguously.
Value
called for side-effects only
Examples
mod <- club(rate ~ dose, data = caffeine)
plot(mod)
Plot predictions.
Description
Plot predictions.
Usage
## S3 method for class 'clubpropredictions'
plot(x, ...)
Arguments
x |
an object of class "clubpropredictions" |
... |
ignored |
Details
Produces a mosaic plot of observed versus predicted categories
Value
called for side-effects only
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- predict(mod)
plot(z)
Plot PCC replicates.
Description
Plot PCC replicates.
Usage
## S3 method for class 'clubprorand'
plot(x, ...)
Arguments
x |
an object of class "clubprofit" produced by |
... |
ignored |
Details
Plot the distribution of PCCs computed from randomly reordered data used to calculate the chance-value.
Value
no return value, called for side effects only.
Examples
mod <- club(rate ~ dose, data = caffeine)
plot(pcc_replicates(mod))
Plot PCC as a function of binary category boundary location.
Description
Plot PCC as a function of binary category boundary location.
Usage
## S3 method for class 'clubprothreshold'
plot(x, ...)
Arguments
x |
an object of class "clubprothreshold" |
... |
ignored |
Details
Produces an xyplot showing the PCC returned for each possible category boundary.
Value
called for side-effects only
Examples
mod <- club(rate ~ dose, data = caffeine)
z <- threshold(mod)
plot(z)
Predicted category for each observation.
Description
Predicted category for each observation.
Usage
## S3 method for class 'clubprofit'
predict(object, ...)
Arguments
object |
an object of class "clubprofit" produced by |
... |
ignored |
Details
Returns a character vector containing the name of the predicted category for each observed value.
Value
a table
Examples
mod <- club(rate ~ dose, data = caffeine)
predict(mod)
Generate a summary of a comparison of clubprofit models.
Description
Generate a summary of a comparison of clubprofit models.
Usage
## S3 method for class 'clubprocomparison'
summary(object, ...)
Arguments
object |
an object of class "clubprocomparison". |
... |
ignored |
Value
No return value, called for side effects.
Examples
m1 <- club(width ~ location, jellyfish)
m2 <- club(length ~ location, jellyfish)
z <- compare(m1, m2)
summary(z)
Generate a summary of results from a fitted clubpro model.
Description
Generate a summary of results from a fitted clubpro model.
Usage
## S3 method for class 'clubprofit'
summary(object, ...)
Arguments
object |
an object of class "clubprofit". |
... |
ignored |
Value
No return value, called for side effects.
Examples
mod <- club(rate ~ dose, data = caffeine)
summary(mod)
Classification strength indices.
Description
Classification strength indices.
Usage
threshold(m)
Arguments
m |
an object of class "clubprofit" produced by |
Details
Returns a vector containing the classification strength index for each observation.
Value
an object of class clubprothreshold
Examples
mod <- club(width ~ location, data = jellyfish)
threshold(mod)