...
 
Commits (10)
......@@ -21,6 +21,7 @@ tmp_.*
^make\.R$
^\.log\.Rout$
^log$
^revdep$
^\.log\.log$
^doc$
^Meta$
......@@ -10,3 +10,7 @@ package_tools/
HandTill2001.Rcheck
doc
Meta
revdep/checks/
revdep/data.sqlite
revdep/library/
......@@ -11,23 +11,23 @@ Description: An S4 implementation of Eq. (3) and Eq. (7) by
David J. Hand and Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
License: BSD_2_clause + file LICENSE
URL: https://gitlab.com/fvafrCU/HandTill2001
Depends:
Depends:
R (>= 2.14)
Imports:
Imports:
methods,
utils
Suggests:
Suggests:
devtools,
knitr,
MASS,
rpart,
mda,
nnet,
knitr,
rmarkdown,
pkgload,
testthat,
rmarkdown,
rpart,
rprojroot,
RUnit,
devtools,
rprojroot
testthat
VignetteBuilder:
knitr
utils
RoxygenNote: 7.0.2
#' Class \code{"cap"} in Package \pkg{HandTill2001}
#' Class and Prediction Objects
#'
#' A virtual class for \code{"bincap"} and \code{"multcap"}.
#' A virtual class for \code{bincap} and \code{multcap}.
#'
#'
#' @name cap-class
#' @docType class
#' @section Objects from the Class: A virtual Class: No objects may be created
#' from it.
#' @author Andreas Dominik Cullmann
#' @seealso \code{"\link[=bincap-class]{class?bincap}"},
#' \code{"\link[=multcap-class]{class?multcap}"}
#' @seealso \code{\link[=bincap-class]{class?HandTill2001::bincap}},
#' \code{\link[=multcap-class]{class?HandTill2001::multcap}}
#' @export
#' @keywords internal
#' @keywords classes
setClass(Class = "cap"
, representation = representation(
......@@ -22,9 +22,9 @@ setClass(Class = "cap"
}
)
#' Class \code{"bincap"} in Package \pkg{HandTill2001}
#' Binary Class and Prediction Objects
#'
#' S4 class for a two class response and corresponding (predicted)
#' S4 class for a binary class response and corresponding (predicted)
#' probabilities.
#'
#'
......@@ -34,16 +34,16 @@ setClass(Class = "cap"
#' \code{true}, there is no trying to guess it from the \code{levels} of
#' \code{response}.
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("bincap", ...)}. They are used to store a two class response (one
#' \code{new("bincap", ...)}. They are used to store a binary class response
#' (one
#' of the two \code{levels} of which is supposed to be \code{true}), the
#' information which of the two \code{levels} of the two class response is
#' information which of the two \code{levels} of the binary class response is
#' thought of as 'true'/'positive'/'present' (the other one would then be
#' thought of as 'false'/'negative'/'absence') and the predicted probabilities
#' that \code{response} is \code{true}.
#' @author Andreas Dominik Cullmann
#' @seealso \code{"\link[=cap-class]{class?cap}"} ,
#' \code{"\link[=multcap-class]{class?multcap}"} ,
#' \code{"\link[=bincap]{?bincap}"}
#' @seealso \code{\link[=cap-class]{class?HandTill2001::cap}} ,
#' \code{\link[=multcap-class]{class?HandTill2001::multcap}} ,
#' \code{\link[=bincap]{?HandTill2001::bincap}}
#' @keywords classes
#' @export
#' @examples
......@@ -65,12 +65,12 @@ setClass(Class = "bincap"
if(length(object@true) > 1)
return("give a single character for the 'true'/'presence' class.")
if(length(levels(object@response)) > 2)
return("response has to be a two class factor.")
return("response has to be a binary class factor.")
}
)
#' Class \code{"multcap"} in Package \pkg{HandTill2001}
#' Multiple Class and Prediction Objects
#'
#' S4 class for a multiple class response and corresponding (predicted)
#' probabilities.
......@@ -81,10 +81,9 @@ setClass(Class = "bincap"
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("multcap", ...)}. They are used to store a multiple class response
#' and the predicted probabilities for each of the \code{levels(response)}.
#' @author Andreas Dominik Cullmann
#' @seealso \code{"\link[=cap-class]{class?cap}"} ,
#' \code{"\link[=bincap-class]{class?bincap}"} ,
#' \code{"\link[=multcap]{?multcap}"}
#' @seealso \code{\link[=cap-class]{class?HandTill2001::cap}} ,
#' \code{\link[=bincap-class]{class?HandTill2001::bincap}} ,
#' \code{\link[=multcap]{?HandTill2001::multcap}}
#' @keywords classes
#' @export
#' @examples
......
#' a ui-constructor for Class \code{"bincap"} in Package \pkg{HandTill2001}
#' A Constructor for Objects of Class \code{bincap}
#'
#' \code{bincap(\dots{})} is an alias to \code{new("bincap", \dots{})}.
#' \code{bincap(\dots)} is an alias to \code{new("bincap", \dots)}.
#'
#' There is no casting or conversion of data. \code{bincap(\dots{})} is just an
#' alias to \code{new("bincap",\dots{})}.
#' There is no casting or conversion of data. \code{bincap(\dots)} is just an
#' alias to \code{new("bincap", \dots)}.
#'
#' @param response Object of class \code{"factor"}.
#' @param predicted Object of class \code{"numeric"}.
#' @param true Object of class \code{"character"}.
#' @return An object of class \code{"bincap"}
#' @author Andreas Dominik Cullmann
#' @seealso \code{"\link[=bincap-class]{class?bincap}"}
#' @param response Object of class \code{factor}.
#' @param predicted Object of class \code{numeric}.
#' @param true Object of class \code{character}.
#' @return An object of class \code{bincap}.
#' @seealso \code{\link[=bincap-class]{class?HandTill2001::bincap}}
#' @keywords ui-constructor
#' @examples
#'
......@@ -25,7 +24,7 @@
#' )
#'
#'
#' @export bincap
#' @export
bincap <- function (response, predicted, true = "1") {
new <- methods::new(Class = "bincap", response = response,
predicted = predicted, true = true)
......@@ -35,18 +34,17 @@ bincap <- function (response, predicted, true = "1") {
#' a ui-constructor for Class \code{"multcap"} in Package \pkg{HandTill2001}
#' A Constructor for Objects of Class \code{multcap}
#'
#' \code{multcap(\dots{})} is an alias to \code{new("multcap", \dots{})}.
#' \code{multcap(\dots)} is an alias to \code{new("multcap", \dots)}.
#'
#' There is no casting or conversion of data. \code{multcap(\dots{})} is just
#' an alias to \code{new("multcap", \dots{})}.
#' There is no casting or conversion of data. \code{multcap(\dots)} is just
#' an alias to \code{new("multcap", \dots)}.
#'
#' @param response Object of class \code{"factor"}.
#' @param predicted Object of class \code{"matrix"}.
#' @return An object of class \code{"bincap"}
#' @author Andreas Dominik Cullmann
#' @seealso \code{"\link[=multcap-class]{class?multcap}"}
#' @param response Object of class \code{factor}.
#' @param predicted Object of class \code{matrix}.
#' @return An object of class \code{multcap}.
#' @seealso \code{\link[=multcap-class]{class?HandTill2001::multcap}}
#' @keywords ui-constructor
#' @examples
#'
......@@ -60,7 +58,7 @@ bincap <- function (response, predicted, true = "1") {
#' )
#'
#'
#' @export multcap
#' @export
multcap <- function (response, predicted) {
new <- methods::new(Class = "multcap", response = response,
predicted = predicted)
......
setGeneric(name = "auc"
, def = function(object){standardGeneric("auc")}
)
setGeneric(name = "auc",
def = function(object){standardGeneric("auc")})
......@@ -10,15 +10,15 @@
#' @aliases HandTill2001-package HandTill2001
#' @docType package
#' @seealso \code{help(package="HandTill2001")}, especially
#' \code{"\link[=auc-methods]{methods?auc}"}; various packages that calculate
#' two class AUC (\code{"\link[ROCR:performance]{ROCR}"}) or multiple class AUC
#' (pROC, \code{"\link[caTools:caTools-package]{caTools}"}).
#' \code{\link[=auc-methods]{?HandTill2001::auc}}; various packages that calculate
#' binary class AUC (\code{\link[ROCR:performance]{ROCR}}) or multiple class AUC
#' (pROC, \code{\link[caTools:caTools-package]{caTools}}).
#' @references \cite{David J. Hand and Robert J. Till (2001). A Simple
#' Generalisation of the Area Under the ROC Curve for Multiple Class
#' Classification Problems. \emph{Machine Learning} \bold{45}(2), p. 171--186.
#' DOI:
#' \href{http://dx.doi.org/10.1023/A:1010920819831}{10.1023/A:1010920819831}}.
#' @keywords AUC, ROC
#' @keywords AUC ROC
#' @examples
#'
#' library(HandTill2001)
......
#' What it Does (One Line, Title Case)
#'
#' A description is a paragraph consisting of one or more sentences.
#'
#' You will find the details in\cr
#' \code{vignette("An_Introduction_to_HandTill2001", package =
#' "HandTill2001")}.
#'
#' @name HandTill2001-package
#' @aliases HandTill2001-package
#' @docType package
#' @keywords package
NULL
#' Methods for Function \code{auc} in Package \pkg{HandTill2001}
#'
#' Calculate area under curve of the receiver operating characteristic for two
#' or more prediction classes.
#' Calculate area under curve of the receiver operating characteristic for
#' two or more prediction classes.
#'
#' Depending on whether \code{object} is of class \code{"bincap"} or of class
#' \code{"multcap"}, a two class or multiple class AUC is calculated.
#' Depending on whether \code{object} is of class \code{bincap} or of class
#' \code{multcap}, a binary class or multiple class AUC is calculated.
#'
#' @param object An object of \code{class} \emph{bincap} or \emph{multcap}.
#' @name auc-methods
......@@ -13,14 +13,14 @@
#' @return An object of class \code{"numeric"}.
#' @section Methods: \describe{
#'
#' \item{list("signature(object = \"bincap\")")}{ calculates the AUC statistic
#' for a two class response following \cite{Hand and Till (2001)}, Eq. (3). }
#' \item{signature(object = "bincap")}{ calculates the AUC statistic
#' for a binary class response following \cite{Hand and Till (2001)}, Eq. (3). }
#'
#' \item{list("signature(object = \"multcap\")")}{ calculates the AUC statistic
#' \item{signature(object = "multcap")}{ calculates the AUC statistic
#' for a multiple class response following \cite{Hand and Till (2001)}, Eq.
#' (7). } }
#' @seealso \code{"\link[=bincap-class]{class?bincap}"},
#' \code{"\link[=multcap-class]{class?multcap}"}
#' @seealso \code{\link[=bincap-class]{class?bincap}},
#' \code{\link[=multcap-class]{class?multcap}}
#' @references \cite{David J. Hand and Robert J. Till (2001). A Simple
#' Generalisation of the Area Under the ROC Curve for Multiple Class
#' Classification Problems. \emph{Machine Learning} \bold{45}(2), p. 171--186.
......@@ -29,31 +29,18 @@
#' @keywords methods auc
#' @export
#' @examples
#'
#' library(HandTill2001)
#' data(ht01.twoclass)
#' data(ht01.multipleclass)
#' message(" == AUC for a two class response")
#' data(ht01.twoclass, package = "HandTill2001")
#' message(" == AUC for a binary class response")
#' message(" == == HandTill2001 result:")
#' HandTill2001::auc(HandTill2001::bincap(response = as.factor(ht01.twoclass[["observed"]]),
#' predicted = ht01.twoclass[["predicted"]],
#' true = "1"))
#' \dontrun{
#' message(" == == ROCR result:")
#' library(ROCR)
#' performance(prediction(labels=ht01.twoclass$observed
#' , predictions=ht01.twoclass$predicted
#' )
#' , measure = "auc")
#' message(" == == ROCR result:")
#' ROCR::performance(ROCR::prediction(labels = ht01.twoclass[["observed"]] ,
#' predictions = ht01.twoclass[["predicted"]]),
#' measure = "auc")@y.values
#' }
#' message(" == == HandTill2001 result:")
#' auc(bincap(
#' response = as.factor(ht01.twoclass$observed)
#' , predicted = ht01.twoclass$predicted
#' , true = "1"
#' ))
#' message(" == AUC for a multiple class response")
#' auc(multcap(
#' response = ht01.multipleclass$observed
#' , predicted = as.matrix(ht01.multipleclass[, levels(ht01.multipleclass$observed)])
#' ))
#'
setMethod(f = "auc"
, signature(object = "bincap")
, function(object){
......@@ -72,6 +59,15 @@ setMethod(f = "auc"
)
}
)
#' @rdname auc-methods
#' @export
#' @examples
#' data(ht01.multipleclass, package = "HandTill2001")
#' message(" == AUC for a multiple class response")
#' predicted <- as.matrix(ht01.multipleclass[, levels(ht01.multipleclass[["observed"]])])
#' HandTill2001::auc(HandTill2001::multcap(response = ht01.multipleclass[["observed"]],
#' predicted = predicted))
setMethod(f = "auc"
, signature(object = "multcap")
, function(object){
......@@ -81,7 +77,7 @@ setMethod(f = "auc"
, response
, predicted){
df <- as.data.frame(predicted) ## factor and matrix -> need data.frame
df$obs <- response
df[["obs"]] <- response
dfs <- subset(df, get("obs") %in% levels)
t <- levels[1]
aij <- auc(methods::new("bincap"
......
#' ht01.multipleclass data in Package \pkg{HandTill2001}
#' Example Data for Multiple Classes
#'
#' multiple class data and probability predictions thereof.
#' Multiple class data and probability predictions thereof.
#'
#' multiple class data ('observed': \code{MASS::fgl$type}) and probability
#' Multiple class data ('observed': \code{MASS::fgl$type}) and probability
#' predictions (\code{predict(fgl.rp4)}, cf. Venables and Ripley (2002), p. 264
#' and \sQuote{Source}) from \code{rpart::rpart}.
#'
......@@ -37,13 +37,12 @@
#'
NULL
#' ht01.twoclass data in Package \pkg{HandTill2001}
#' Example Data for Binary Classes
#'
#' two class data and probability predictions thereof.
#' Binary class data and probability predictions thereof.
#'
#' two class data ('observed': \code{MASS::birthwt$low}) and probability
#' Binary class data ('observed': \code{MASS::birthwt$low}) and probability
#' predictions
#'
#' (\code{predict(birthwt.step2, type = "response")}, cf. Venables and Ripley
#' (2002), pp. 195f and \sQuote{Source}) from \code{stats::glm}.
#'
......@@ -54,8 +53,8 @@ NULL
#' \item{predicted}{a numeric vector} }
#' @references Venables, W. N and Ripley, B. D. (2002), \emph{Modern Applied
#' Statistics with S} (4th edition). Springer, ISBN 0-387-95457-0
#' @source \preformatted{ ## From: A two class data example Venables and Ripley
#' pp. 194--199 library(MASS); data("birthwt"); attach(birthwt) race <-
#' @source \preformatted{ ## From: A binary class data example Venables and
#' Ripley pp. 194--199 library(MASS); data("birthwt"); attach(birthwt) race <-
#' (factor(race, labels = c("white", "black", "other"))) ptd <- factor(ptl > 0)
#' ftv <- factor(ftv) levels(ftv)[-(1:2)] <- "2+" bwt <- data.frame(low =
#' factor(low), age, lwt, race, smoke = (smoke > 0) , ptd, ht = (ht > 0), ui =
......
......@@ -45,9 +45,9 @@ help("HandTill2001-package", package = "HandTill2001")
#>
#> See Also:
#>
#> 'help(package="HandTill2001")', especially '"methods?auc"';
#> various packages that calculate two class AUC ('"ROCR"') or
#> multiple class AUC (pROC, '"caTools"').
#> 'help(package="HandTill2001")', especially '?HandTill2001::auc';
#> various packages that calculate binary class AUC ('ROCR') or
#> multiple class AUC (pROC, 'caTools').
#>
#> Examples:
#>
......
......@@ -9,8 +9,8 @@ Best, Andreas Dominik
# Package HandTill2001 0.2-12.9000
## Test environments
- R Under development (unstable) (2019-10-17 r77308)
- R Under development (unstable) (2019-12-18 r77593)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Devuan GNU/Linux ascii
0 errors | 2 warnings | 1 note
0 errors | 1 warning | 1 note
- win-builder (devel)
csplitpref=/tmp/.csplit
csplit ./HandTill2001/R/HandTill2001-package.R "/NULL/" {*} -f ${csplitpref}
for file in $(ls -1 ${csplitpref}*)
do
Rd=$(grep '@name' $file | cut -f2 -d' ').Rd
if test $(echo ${Rd}| wc -c) -gt 4; then
sed -n -e"/\\preformatted/,/}/p" < ${file} | sed -e 's/@source//' -e"s/^#'//" -e'/^$/d' | head --lines=-1 | tail --lines=+2 > /tmp/${Rd}
sed -ne "/\\preformatted.*/ {p; r /tmp/${Rd}" -e ":a; n; /.*}/{p; b}; ba}; p" ./HandTill2001/man/${Rd} > /tmp/foo.${Rd}
mv /tmp/foo.${Rd} ./HandTill2001/man/${Rd}
fi
done
rm ${csplitpref}*
## KLUDGE \preformatted gets messed up by roxygen2
## using inst/preformatted.sh to work around.
## This requires each instance of \preformatted
## in the R/*.R files to start and end with a line
## containing only:
#'
......@@ -3,9 +3,6 @@
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
......
* using log directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck’
* using R Under development (unstable) (2019-10-17 r77308)
* using R Under development (unstable) (2019-12-18 r77593)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--run-donttest --as-cran’
......@@ -15,16 +15,6 @@ New maintainer:
Andreas Dominik Cullmann <[email protected]>
Old maintainer(s):
Andreas Dominik Cullmann <[email protected]>
Found the following (possibly) invalid URLs:
URL: DOI:10.1023/A:1010920819831
From: inst/doc/An_Introduction_to_HandTill2001.html
Message: Invalid URI scheme
Found the following \keyword or \concept entries
which likely give several index terms:
File ‘HandTill2001-package.Rd’:
\keyword{AUC,}
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
......@@ -64,8 +54,7 @@ See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
......@@ -91,4 +80,4 @@ Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
Status: 1 WARNING, 1 NOTE
Loading HandTill2001
<error in cleanr::check_package(".", check_return = FALSE): . /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 62 counts 81 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 63 counts 90 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 129 counts 81 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 132 counts 81 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 20 counts 86 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 56 counts 94 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 59 counts 89 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 54 counts 91 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 83 counts 102 characters.
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. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/HandTill2001-package.R: line 29 counts 89 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 128 counts 81 characters.
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. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 19 counts 86 characters.
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/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 57 counts 89 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 35 counts 93 characters.
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. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/HandTill2001-package.R: line 13 counts 82 characters.
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. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/throw.R: line 15 counts 87 characters.>
Warning messages:
1: In getPackageName(where) :
Created a package name, ‘2019-12-12 20:33:53’, when none found
Created a package name, ‘2019-12-18 15:05:25’, when none found
2: In getPackageName(where) :
Created a package name, ‘2019-12-12 20:33:53’, when none found
Created a package name, ‘2019-12-18 15:05:25’, when none found
......@@ -13,16 +13,3 @@ New maintainer:
Andreas Dominik Cullmann <[email protected]>
Old maintainer(s):
Andreas Dominik Cullmann <[email protected]>
Found the following (possibly) invalid URLs:
URL: DOI:10.1023/A:1010920819831
From: inst/doc/An_Introduction_to_HandTill2001.html
Message: Invalid URI scheme
Found the following \keyword or \concept entries
which likely give several index terms:
File ‘HandTill2001-package.Rd’:
\keyword{AUC,}
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
checking for file ‘/tmp/RtmponEqfQ/remotes67c25376efd1/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/tmp/RtmponEqfQ/remotes67c25376efd1/HandTill2001/DESCRIPTION’
checking for file ‘/tmp/Rtmp9aAsun/remotes6d4928a2e08b/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/tmp/Rtmp9aAsun/remotes6d4928a2e08b/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
checking vignette meta-information ... ✔ checking vignette meta-information
✔ checking vignette meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
......
checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
Running /home/qwer/svn/R/r-devel/build/bin/R CMD INSTALL \
/tmp/RtmpVGtZ8S/HandTill2001_0.2-12.9000.tar.gz --install-tests
/tmp/RtmpEJaDgo/HandTill2001_0.2-12.9000.tar.gz --install-tests
* installing to library ‘/home/qwer/svn/R/r-devel/build/library’
* installing *source* package ‘HandTill2001’ ...
** using staged installation
......@@ -30,17 +27,14 @@
* DONE (HandTill2001)
checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
✔ checking DESCRIPTION meta-information
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
Running /usr/lib/R/bin/R CMD INSTALL \
/tmp/RtmpZ448nq/HandTill2001_0.2-12.9000.tar.gz --install-tests
/tmp/RtmpvOPHT5/HandTill2001_0.2-12.9000.tar.gz --install-tests
* installing to library ‘/home/qwer/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘HandTill2001’ ...
** R
......
This diff is collapsed.
R Under development (unstable) (2019-10-17 r77308) -- "Unsuffered Consequences"
R Under development (unstable) (2019-12-18 r77593) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
......@@ -21,6 +21,9 @@ Type 'q()' to quit R.
Writing NAMESPACE
Loading HandTill2001
Writing NAMESPACE
Writing cap-class.Rd
Writing bincap-class.Rd
Writing multcap-class.Rd
Warning message:
roxygen2 requires Encoding: UTF-8
>
......
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/transitional.dtd">
<html><head><title>RUNIT TEST PROTOCOL--Thu Dec 12 20:42:24 2019</title>
<html><head><title>RUNIT TEST PROTOCOL--Wed Dec 18 15:08:28 2019</title>
</head>
<body><h1 TRUE>RUNIT TEST PROTOCOL--Thu Dec 12 20:42:24 2019</h1>
<body><h1 TRUE>RUNIT TEST PROTOCOL--Wed Dec 18 15:08:28 2019</h1>
<p>Number of test functions: 1</p>
<p>Number of errors: 0</p>
<p>Number of failures: 0</p>
......@@ -53,19 +53,19 @@
<td>2019</td>
</tr>
<tr><td>month</td>
<td>10</td>
<td>12</td>
</tr>
<tr><td>day</td>
<td>17</td>
<td>18</td>
</tr>
<tr><td>svn rev</td>
<td>77308</td>
<td>77593</td>
</tr>
<tr><td>language</td>
<td>R</td>
</tr>
<tr><td>version.string</td>
<td>R Under development (unstable) (2019-10-17 r77308)</td>
<td>R Under development (unstable) (2019-12-18 r77593)</td>
</tr>
<tr><td>nickname</td>
<td>Unsuffered Consequences</td>
......
RUNIT TEST PROTOCOL -- Thu Dec 12 20:42:24 2019
RUNIT TEST PROTOCOL -- Wed Dec 18 15:08:28 2019
***********************************************
Number of test functions: 1
Number of errors: 0
......
DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'.
WORD FOUND IN
Andreas bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
bincap auc-methods.Rd:14
consenus consensus_auc.Rnw:75
DOI auc-methods.Rd:69
bincap auc-methods.Rd:16
DOI auc-methods.Rd:63
HandTill2001-package.Rd:32
description:2
An_Introduction_to_HandTill2001.Rmd:14
Dominik bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
Eq auc-methods.Rd:31,34
Eq auc-methods.Rd:33,36
HandTill2001-package.Rd:10
description:1
An_Introduction_to_HandTill2001.Rmd:13
eval consensus_auc.Rnw:24
fgl consensus_auc.Rnw:18,24,33
Generalisation auc-methods.Rd:67
eval consensus_auc.Rnw:23
fgl consensus_auc.Rnw:17,23,32
Generalisation auc-methods.Rd:61
HandTill2001-package.Rd:30
gitlab README.md:71
README.Rmd:43
gitlab README.md:67
README.Rmd:39
HandTill throw.Rd:19,22
NEWS.md:1
README.md:15,71
README.Rmd:21,43
An_Introduction_to_HandTill2001.Rmd:2
modelling consensus_auc.Rnw:19
multcap auc-methods.Rd:14
multinom consensus_auc.Rnw:47
multipleclass ht01.multipleclass.Rd:6
nnet consensus_auc.Rnw:19,47
README.md:15,67
README.Rmd:21,39
modelling consensus_auc.Rnw:18
multcap auc-methods.Rd:16
multinom consensus_auc.Rnw:46
nnet consensus_auc.Rnw:18,46
pre consensus_auc.Rnw:76,99
pROC HandTill2001-package.Rd:39
rpart consensus_auc.Rnw:19,33
rpart consensus_auc.Rnw:18,32
RStudio README.md:8,9
README.Rmd:8,9
Springer ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
ht01.twoclass.Rd:40
th ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
twoclass ht01.twoclass.Rd:6
ui bincap.Rd:5
multcap.Rd:5
ht01.twoclass.Rd:40
Venables ht01.multipleclass.Rd:32,43
ht01.twoclass.Rd:29,40
ht01.twoclass.Rd:28,39
Warning message:
spell check failed
Building HandTill2001 vignettes
--- re-building ‘An_Introduction_to_HandTill2001.Rmd’ using rmarkdown
--- finished re-building ‘An_Introduction_to_HandTill2001.Rmd’
--- re-building ‘consensus_auc.Rnw’ using Sweave
Loading required package: class
Loaded mda 0.4-10
--- finished re-building ‘consensus_auc.Rnw’
Moving An_Introduction_to_HandTill2001.html, consensus_auc.pdf, An_Introduction_to_HandTill2001.R, consensus_auc.R to doc/
Copying An_Introduction_to_HandTill2001.Rmd, consensus_auc.Rnw to doc/
Moving consensus_auc.pdf, consensus_auc.R to doc/
Copying consensus_auc.Rnw to doc/
Building vignette index
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/An_Introduction_to_HandTill2001.Rmd
| | | 0% | |....................... | 33% | |............................................... | 67% | |......................................................................| 100%
output file: ./inst/doc/An_Introduction_to_HandTill2001.R
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw
| | | 0% | |... | 4% | |..... | 7% | |........ | 11% | |.......... | 15% | |............. | 19% | |................ | 22% | |.................. | 26% | |..................... | 30% | |....................... | 33% | |.......................... | 37% | |............................. | 41% | |............................... | 44% | |.................................. | 48% | |.................................... | 52% | |....................................... | 56% | |......................................... | 59% | |............................................ | 63% | |............................................... | 67% | |................................................. | 70% | |.................................................... | 74% | |...................................................... | 78% | |......................................................... | 81% | |............................................................ | 85% | |.............................................................. | 89% | |................................................................. | 93% | |................................................................... | 96% | |......................................................................| 100%
output file: ./inst/doc/consensus_auc.Rnw
[[1]]
[1] "./inst/doc/An_Introduction_to_HandTill2001.R"
[[2]]
[1] "./inst/doc/consensus_auc.Rnw"
Warning message:
In remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 8, 9, 10, 21, 25, 34, 48, 54, 64, 78, 86, 100, 114, 122, 128, 133; you may need Sweave2knitr("/home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw") to convert it to knitr
It seems you are using the Sweave-specific syntax in line(s) 8, 9, 10, 20, 24, 33, 47, 53, 63, 78, 86, 100, 114, 122, 128, 133; you may need Sweave2knitr("/home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw") to convert it to knitr
......
......@@ -34,9 +34,9 @@ DOI:
}
\seealso{
\code{help(package="HandTill2001")}, especially
\code{"\link[=auc-methods]{methods?auc}"}; various packages that calculate
two class AUC (\code{"\link[ROCR:performance]{ROCR}"}) or multiple class AUC
(pROC, \code{"\link[caTools:caTools-package]{caTools}"}).
\code{\link[=auc-methods]{?HandTill2001::auc}}; various packages that calculate
binary class AUC (\code{\link[ROCR:performance]{ROCR}}) or multiple class AUC
(pROC, \code{\link[caTools:caTools-package]{caTools}}).
}
\keyword{AUC,}
\keyword{AUC}
\keyword{ROC}
......@@ -9,6 +9,8 @@
\title{Methods for Function \code{auc} in Package \pkg{HandTill2001}}
\usage{
\S4method{auc}{bincap}(object)
\S4method{auc}{multcap}(object)
}
\arguments{
\item{object}{An object of \code{class} \emph{bincap} or \emph{multcap}.}
......@@ -17,50 +19,42 @@
An object of class \code{"numeric"}.
}
\description{
Calculate area under curve of the receiver operating characteristic for two
or more prediction classes.
Calculate area under curve of the receiver operating characteristic for
two or more prediction classes.
}
\details{
Depending on whether \code{object} is of class \code{"bincap"} or of class
\code{"multcap"}, a two class or multiple class AUC is calculated.
Depending on whether \code{object} is of class \code{bincap} or of class
\code{multcap}, a binary class or multiple class AUC is calculated.
}
\section{Methods}{
\describe{
\item{list("signature(object = \"bincap\")")}{ calculates the AUC statistic
for a two class response following \cite{Hand and Till (2001)}, Eq. (3). }
\item{signature(object = "bincap")}{ calculates the AUC statistic
for a binary class response following \cite{Hand and Till (2001)}, Eq. (3). }
\item{list("signature(object = \"multcap\")")}{ calculates the AUC statistic
\item{signature(object = "multcap")}{ calculates the AUC statistic
for a multiple class response following \cite{Hand and Till (2001)}, Eq.
(7). } }
}
\examples{
library(HandTill2001)
data(ht01.twoclass)
data(ht01.multipleclass)
message(" == AUC for a two class response")
data(ht01.twoclass, package = "HandTill2001")
message(" == AUC for a binary class response")
message(" == == HandTill2001 result:")
HandTill2001::auc(HandTill2001::bincap(response = as.factor(ht01.twoclass[["observed"]]),
predicted = ht01.twoclass[["predicted"]],
true = "1"))
\dontrun{
message(" == == ROCR result:")
library(ROCR)
performance(prediction(labels=ht01.twoclass$observed
, predictions=ht01.twoclass$predicted
)
, measure = "auc")
message(" == == ROCR result:")
ROCR::performance(ROCR::prediction(labels = ht01.twoclass[["observed"]] ,
predictions = ht01.twoclass[["predicted"]]),
measure = "auc")@y.values
}
message(" == == HandTill2001 result:")
auc(bincap(
response = as.factor(ht01.twoclass$observed)
, predicted = ht01.twoclass$predicted
, true = "1"
))
data(ht01.multipleclass, package = "HandTill2001")
message(" == AUC for a multiple class response")
auc(multcap(
response = ht01.multipleclass$observed
, predicted = as.matrix(ht01.multipleclass[, levels(ht01.multipleclass$observed)])
))
predicted <- as.matrix(ht01.multipleclass[, levels(ht01.multipleclass[["observed"]])])
HandTill2001::auc(HandTill2001::multcap(response = ht01.multipleclass[["observed"]],
predicted = predicted))
}
\references{
\cite{David J. Hand and Robert J. Till (2001). A Simple
......@@ -70,8 +64,8 @@ DOI:
\href{http://dx.doi.org/10.1023/A:1010920819831}{10.1023/A:1010920819831}}.
}
\seealso{
\code{"\link[=bincap-class]{class?bincap}"},
\code{"\link[=multcap-class]{class?multcap}"}
\code{\link[=bincap-class]{class?bincap}},
\code{\link[=multcap-class]{class?multcap}}
}
\keyword{auc}
\keyword{methods}
......@@ -3,9 +3,9 @@
\docType{class}
\name{bincap-class}
\alias{bincap-class}
\title{Class \code{"bincap"} in Package \pkg{HandTill2001}}
\title{Binary Class and Prediction Objects}
\description{
S4 class for a two class response and corresponding (predicted)
S4 class for a binary class response and corresponding (predicted)
probabilities.
}
\note{
......@@ -15,9 +15,10 @@ No defaults are set. Especially, you have to explicitly initialize
}
\section{Objects from the Class}{
Objects can be created by calls of the form
\code{new("bincap", ...)}. They are used to store a two class response (one
\code{new("bincap", ...)}. They are used to store a binary class response
(one
of the two \code{levels} of which is supposed to be \code{true}), the
information which of the two \code{levels} of the two class response is
information which of the two \code{levels} of the binary class response is
thought of as 'true'/'positive'/'present' (the other one would then be
thought of as 'false'/'negative'/'absence') and the predicted probabilities
that \code{response} is \code{true}.
......@@ -29,11 +30,8 @@ showClass("bincap")
}
\seealso{
\code{"\link[=cap-class]{class?cap}"} ,
\code{"\link[=multcap-class]{class?multcap}"} ,
\code{"\link[=bincap]{?bincap}"}
}
\author{
Andreas Dominik Cullmann
\code{\link[=cap-class]{class?HandTill2001::cap}} ,
\code{\link[=multcap-class]{class?HandTill2001::multcap}} ,
\code{\link[=bincap]{?HandTill2001::bincap}}
}
\keyword{classes}
......@@ -2,26 +2,26 @@
% Please edit documentation in R/AllConstructors.R
\name{bincap}
\alias{bincap}
\title{a ui-constructor for Class \code{"bincap"} in Package \pkg{HandTill2001}}
\title{A Constructor for Objects of Class \code{bincap}}
\usage{
bincap(response, predicted, true = "1")
}
\arguments{
\item{response}{Object of class \code{"factor"}.}
\item{response}{Object of class \code{factor}.}
\item{predicted}{Object of class \code{"numeric"}.}
\item{predicted}{Object of class \code{numeric}.}
\item{true}{Object of class \code{"character"}.}
\item{true}{Object of class \code{character}.}
}
\value{
An object of class \code{"bincap"}
An object of class \code{bincap}.
}
\description{
\code{bincap(\dots{})} is an alias to \code{new("bincap", \dots{})}.
\code{bincap(\dots)} is an alias to \code{new("bincap", \dots)}.
}
\details{
There is no casting or conversion of data. \code{bincap(\dots{})} is just an
alias to \code{new("bincap",\dots{})}.
There is no casting or conversion of data. \code{bincap(\dots)} is just an
alias to \code{new("bincap", \dots)}.
}
\examples{
......@@ -38,9 +38,6 @@ bincap(
}
\seealso{
\code{"\link[=bincap-class]{class?bincap}"}
}
\author{
Andreas Dominik Cullmann
\code{\link[=bincap-class]{class?HandTill2001::bincap}}
}
\keyword{ui-constructor}
......@@ -3,9 +3,9 @@
\docType{class}
\name{cap-class}
\alias{cap-class}
\title{Class \code{"cap"} in Package \pkg{HandTill2001}}
\title{Class and Prediction Objects}
\description{
A virtual class for \code{"bincap"} and \code{"multcap"}.
A virtual class for \code{bincap} and \code{multcap}.
}
\section{Objects from the Class}{
A virtual Class: No objects may be created
......@@ -13,10 +13,8 @@ from it.
}
\seealso{
\code{"\link[=bincap-class]{class?bincap}"},
\code{"\link[=multcap-class]{class?multcap}"}
}
\author{
Andreas Dominik Cullmann
\code{\link[=bincap-class]{class?HandTill2001::bincap}},
\code{\link[=multcap-class]{class?HandTill2001::multcap}}
}
\keyword{classes}
\keyword{internal}
......@@ -3,7 +3,7 @@
\docType{data}
\name{ht01.multipleclass}
\alias{ht01.multipleclass}
\title{ht01.multipleclass data in Package \pkg{HandTill2001}}
\title{Example Data for Multiple Classes}
\format{A data frame with 214 observations on the following 7 variables.
\describe{
\item{observed}{a factor with levels
......@@ -25,10 +25,10 @@ predict(fgl.rp4)) write.table(ht01.multipleclass, file =
"ht01.multipleclass.txt") }
}
\description{
multiple class data and probability predictions thereof.
Multiple class data and probability predictions thereof.
}
\details{
multiple class data ('observed': \code{MASS::fgl$type}) and probability
Multiple class data ('observed': \code{MASS::fgl$type}) and probability
predictions (\code{predict(fgl.rp4)}, cf. Venables and Ripley (2002), p. 264
and \sQuote{Source}) from \code{rpart::rpart}.
}
......
......@@ -3,13 +3,13 @@
\docType{data}
\name{ht01.twoclass}
\alias{ht01.twoclass}
\title{ht01.twoclass data in Package \pkg{HandTill2001}}
\title{Example Data for Binary Classes}
\format{A data frame with 189 observations on the following 2 variables.
\describe{ \item{observed}{a numeric vector}
\item{predicted}{a numeric vector} }}
\source{
\preformatted{ ## From: A two class data example Venables and Ripley
pp. 194--199 library(MASS); data("birthwt"); attach(birthwt) race <-
\preformatted{ ## From: A binary class data example Venables and
Ripley pp. 194--199 library(MASS); data("birthwt"); attach(birthwt) race <-
(factor(race, labels = c("white", "black", "other"))) ptd <- factor(ptl > 0)
ftv <- factor(ftv) levels(ftv)[-(1:2)] <- "2+" bwt <- data.frame(low =
factor(low), age, lwt, race, smoke = (smoke > 0) , ptd, ht = (ht > 0), ui =
......@@ -20,12 +20,11 @@ data.frame(observed = bwt$low , predicted = predict(birthwt.step2 , type =
"response")) write.table(ht01.twoclass, file = "ht01.twoclass.txt") }
}
\description{
two class data and probability predictions thereof.
Binary class data and probability predictions thereof.
}
\details{
two class data ('observed': \code{MASS::birthwt$low}) and probability
Binary class data ('observed': \code{MASS::birthwt$low}) and probability
predictions
(\code{predict(birthwt.step2, type = "response")}, cf. Venables and Ripley
(2002), pp. 195f and \sQuote{Source}) from \code{stats::glm}.
}
......
......@@ -3,7 +3,7 @@
\docType{class}
\name{multcap-class}
\alias{multcap-class}
\title{Class \code{"multcap"} in Package \pkg{HandTill2001}}
\title{Multiple Class and Prediction Objects}
\description{
S4 class for a multiple class response and corresponding (predicted)
probabilities.
......@@ -20,11 +20,8 @@ showClass("multcap")
}
\seealso{
\code{"\link[=cap-class]{class?cap}"} ,
\code{"\link[=bincap-class]{class?bincap}"} ,
\code{"\link[=multcap]{?multcap}"}
}
\author{
Andreas Dominik Cullmann
\code{\link[=cap-class]{class?HandTill2001::cap}} ,
\code{\link[=bincap-class]{class?HandTill2001::bincap}} ,
\code{\link[=multcap]{?HandTill2001::multcap}}
}
\keyword{classes}
......@@ -2,24 +2,24 @@
% Please edit documentation in R/AllConstructors.R
\name{multcap}
\alias{multcap}
\title{a ui-constructor for Class \code{"multcap"} in Package \pkg{HandTill2001}}
\title{A Constructor for Objects of Class \code{multcap}}
\usage{
multcap(response, predicted)
}
\arguments{
\item{response}{Object of class \code{"factor"}.}
\item{response}{Object of class \code{factor}.}
\item{predicted}{Object of class \code{"matrix"}.}
\item{predicted}{Object of class \code{matrix}.}
}
\value{
An object of class \code{"bincap"}
An object of class \code{multcap}.
}
\description{
\code{multcap(\dots{})} is an alias to \code{new("multcap", \dots{})}.
\code{multcap(\dots)} is an alias to \code{new("multcap", \dots)}.
}
\details{
There is no casting or conversion of data. \code{multcap(\dots{})} is just
an alias to \code{new("multcap", \dots{})}.
There is no casting or conversion of data. \code{multcap(\dots)} is just
an alias to \code{new("multcap", \dots)}.
}
\examples{
......@@ -35,9 +35,6 @@ multcap(
}
\seealso{
\code{"\link[=multcap-class]{class?multcap}"}
}
\author{
Andreas Dominik Cullmann
\code{\link[=multcap-class]{class?HandTill2001::multcap}}
}
\keyword{ui-constructor}
# Platform
|field |value |
|:--------|:--------------------------------------------------|
|version |R Under development (unstable) (2019-12-18 r77593) |
|os |Devuan GNU/Linux ascii |
|system |x86_64, linux-gnu |
|ui |X11 |
|language |en_US:en |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Berlin |
|date |2019-12-18 |
# Dependencies
|package |old |new |Δ |
|:------------|:------|:-----------|:--|
|HandTill2001 |0.2-12 |0.2-12.9000 |* |
# Revdeps
## Failed to check (1)
|package |version |error |warning |note |
|:--------|:-------|:-----|:-------|:----|
|ModelMap |? | | | |
# ModelMap
<details>
* Version:
* Source code: ???
* URL: https://gitlab.com/fvafrCU/HandTill2001
* Number of recursive dependencies: 0
Run `revdep_details(,"")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
*Wow, no problems at all. :)*
\ No newline at end of file
%\VignetteIndexEntry{Consenus models weighted by multiclass AUC}
\documentclass[a4paper]{article}
\bibliographystyle{apalike}
\usepackage[utf8]{inputenc}
%\VignetteIndexEntry{Consensus models}
\title{Consensus models weighted by AUC for multiple class responses}
\author{Andreas Dominik Cullmann}
\SweaveOpts{echo=FALSE}
\SweaveOpts{print=FALSE}
\SweaveOpts{width=60}
%\VignetteIndexEntry{Consenus models}
\begin{document}
\maketitle
\providecommand{\rpack}[1]{package \texttt{#1}}
......@@ -72,7 +71,8 @@ auc(multcap(response = fgl[ind.eval, "type"],
newdata = fgl[ind.eval, TRUE],
type = "probs")))
@
To enhance predictive performance, we decide to use both models to build a consenus model.
To enhance predictive performance, we decide to use both models to build a
consensus model.
Furthermore, we want to use the 'weighted average' consensus method given by \cite[Eqn 1]{marmion2009}, which uses the pre-evaluated AUC of the models as weights.
So we split the training set into two complementary subsets: 'inner training' and 'inner evaluation'.
<<echo=true>>=
......