reShape: Reshape Matrices and Serial Data
In harrelfe/Hmisc: Harrell Miscellaneous
reShape R Documentation
Reshape Matrices and Serial Data
Description
If the first argument is a matrix, reShape strings out its values
and creates row and column vectors specifying the row and column each
element came from. This is useful for sending matrices to Trellis
functions, for analyzing or plotting results of table or
crosstabs, or for reformatting serial data stored in a matrix (with
rows representing multiple time points) into vectors. The number of
observations in the new variables will be the product of the number of
rows and number of columns in the input matrix. If the first
argument is a vector, the id and colvar variables are used to
restructure it into a matrix, with NAs for elements that corresponded
to combinations of id and colvar values that did not exist in the
data. When more than one vector is given, multiple matrices are
created. This is useful for restructuring irregular serial data into
regular matrices. It is also useful for converting data produced by
expand.grid into a matrix (see the last example). The number of
rows of the new matrices equals the number of unique values of id,
and the number of columns equals the number of unique values of
colvar.
When the first argument is a vector and the id is a data frame
(even with only one variable),
reShape will produce a data frame, and the unique groups are
identified by combinations of the values of all variables in id.
If a data frame constant is specified, the variables in this data
frame are assumed to be constant within combinations of id
variables (if not, an arbitrary observation in constant will be
selected for each group). A row of constant corresponding to the
target id combination is then carried along when creating the
data frame result.
A different behavior of reShape is achieved when base and reps
are specified. In that case x must be a list or data frame, and
those data are assumed to contain one or more non-repeating
measurements (e.g., baseline measurements) and one or more repeated
measurements represented by variables named by pasting together the
character strings in the vector base with the integers 1, 2, ...,
reps. The input data are rearranged by repeating each value of the
baseline variables reps times and by transposing each observation's
values of one of the set of repeated measurements as reps
observations under the variable whose name does not have an integer
pasted to the end. if x has a row.names attribute, those
observation identifiers are each repeated reps times in the output
object. See the last example.
Usage
reShape(x, ..., id, colvar, base, reps, times=1:reps,
timevar='seqno', constant=NULL)
Arguments
x
a matrix or vector, or, when base is specified, a list or data frame
...
other optional vectors, if x is a vector
id
A numeric, character, category, or factor variable containing subject
identifiers, or a data frame of such variables that in combination form
groups of interest. Required if x is a vector, ignored otherwise.
colvar
A numeric, character, category, or factor variable containing column
identifiers. colvar is using a "time of data collection" variable.
Required if x is a vector, ignored otherwise.
base
vector of character strings containing base names of repeated
measurements
reps
number of times variables named in base are repeated. This must be
a constant.
times
when base is given, times is the vector of times to create
if you do not want to use consecutive integers beginning with 1.
timevar
specifies the name of the time variable to create if times is
given, if you do not want to use seqno
constant
a data frame with the same number of rows in id and x,
containing auxiliary information to be merged into the resulting data
frame. Logically, the rows of constant within each group
should have the same value of all of its variables.
Details
In converting dimnames to vectors, the resulting variables are
numeric if all elements of the matrix dimnames can be converted to
numeric, otherwise the corresponding row or column variable remains
character. When the dimnames if x have a names attribute, those
two names become the new variable names. If x is a vector and
another vector is also given (in ...), the matrices in the resulting
list are named the same as the input vector calling arguments. You
can specify customized names for these on-the-fly by using
e.g. reShape(X=x, Y=y, id= , colvar= ). The new names will then be
X and Y instead of x and y. A new variable named seqnno is
also added to the resulting object. seqno indicates the sequential
repeated measurement number. When base and times are
specified, this new variable is named the character value of timevar and the values
are given by a table lookup into the vector times.
Value
If x is a matrix, returns a list containing the row variable, the
column variable, and the as.vector(x) vector, named the same as the
calling argument was called for x. If x is a vector and no other
vectors were specified as ..., the result is a matrix. If at least
one vector was given to ..., the result is a list containing k
matrices, where k one plus the number of vectors in .... If x
is a list or data frame, the same type of object is returned. If
x is a vector and id is a data frame, a data frame will be
the result.
Author(s)
Frank Harrell
Department of Biostatistics
Vanderbilt University School of Medicine
fh@fharrell.com
See Also
reshape, as.vector,
matrix, dimnames,
outer, table
Examples
set.seed(1)
Solder <- factor(sample(c('Thin','Thick'),200,TRUE),c('Thin','Thick'))
Opening <- factor(sample(c('S','M','L'), 200,TRUE),c('S','M','L'))
tab <- table(Opening, Solder)
tab
reShape(tab)
# attach(tab) # do further processing
# An example where a matrix is created from irregular vectors
follow <- data.frame(id=c('a','a','b','b','b','d'),
month=c(1, 2, 1, 2, 3, 2),
cholesterol=c(225,226, 320,319,318, 270))
follow
attach(follow)
reShape(cholesterol, id=id, colvar=month)
detach('follow')
# Could have done :
# reShape(cholesterol, triglyceride=trig, id=id, colvar=month)
# Create a data frame, reshaping a long dataset in which groups are
# formed not just by subject id but by combinations of subject id and
# visit number. Also carry forward a variable that is supposed to be
# constant within subject-visit number combinations. In this example,
# it is not constant, so an arbitrary visit number will be selected.
w <- data.frame(id=c('a','a','a','a','b','b','b','d','d','d'),
visit=c( 1, 1, 2, 2, 1, 1, 2, 2, 2, 2),
k=c('A','A','B','B','C','C','D','E','F','G'),
var=c('x','y','x','y','x','y','y','x','y','z'),
val=1:10)
with(w,
reShape(val, id=data.frame(id,visit),
constant=data.frame(k), colvar=var))
# Get predictions from a regression model for 2 systematically
# varying predictors. Convert the predictions into a matrix, with
# rows corresponding to the predictor having the most values, and
# columns corresponding to the other predictor
# d <- expand.grid(x2=0:1, x1=1:100)
# pred <- predict(fit, d)
# reShape(pred, id=d$x1, colvar=d$x2) # makes 100 x 2 matrix
# Reshape a wide data frame containing multiple variables representing
# repeated measurements (3 repeats on 2 variables; 4 subjects)
set.seed(33)
n <- 4
w <- data.frame(age=rnorm(n, 40, 10),
sex=sample(c('female','male'), n,TRUE),
sbp1=rnorm(n, 120, 15),
sbp2=rnorm(n, 120, 15),
sbp3=rnorm(n, 120, 15),
dbp1=rnorm(n, 80, 15),
dbp2=rnorm(n, 80, 15),
dbp3=rnorm(n, 80, 15), row.names=letters[1:n])
options(digits=3)
w
u <- reShape(w, base=c('sbp','dbp'), reps=3)
u
reShape(w, base=c('sbp','dbp'), reps=3, timevar='week', times=c(0,3,12))
harrelfe/Hmisc documentation built on Nov. 21, 2024, 3:47 p.m.
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| reShape | R Documentation |
Reshape Matrices and Serial Data
Description
If the first argument is a matrix, reShape strings out its values
and creates row and column vectors specifying the row and column each
element came from. This is useful for sending matrices to Trellis
functions, for analyzing or plotting results of table or
crosstabs, or for reformatting serial data stored in a matrix (with
rows representing multiple time points) into vectors. The number of
observations in the new variables will be the product of the number of
rows and number of columns in the input matrix. If the first
argument is a vector, the id and colvar variables are used to
restructure it into a matrix, with NAs for elements that corresponded
to combinations of id and colvar values that did not exist in the
data. When more than one vector is given, multiple matrices are
created. This is useful for restructuring irregular serial data into
regular matrices. It is also useful for converting data produced by
expand.grid into a matrix (see the last example). The number of
rows of the new matrices equals the number of unique values of id,
and the number of columns equals the number of unique values of
colvar.
When the first argument is a vector and the id is a data frame
(even with only one variable),
reShape will produce a data frame, and the unique groups are
identified by combinations of the values of all variables in id.
If a data frame constant is specified, the variables in this data
frame are assumed to be constant within combinations of id
variables (if not, an arbitrary observation in constant will be
selected for each group). A row of constant corresponding to the
target id combination is then carried along when creating the
data frame result.
A different behavior of reShape is achieved when base and reps
are specified. In that case x must be a list or data frame, and
those data are assumed to contain one or more non-repeating
measurements (e.g., baseline measurements) and one or more repeated
measurements represented by variables named by pasting together the
character strings in the vector base with the integers 1, 2, ...,
reps. The input data are rearranged by repeating each value of the
baseline variables reps times and by transposing each observation's
values of one of the set of repeated measurements as reps
observations under the variable whose name does not have an integer
pasted to the end. if x has a row.names attribute, those
observation identifiers are each repeated reps times in the output
object. See the last example.
Usage
reShape(x, ..., id, colvar, base, reps, times=1:reps,
timevar='seqno', constant=NULL)
Arguments
x |
a matrix or vector, or, when |
... |
other optional vectors, if |
id |
A numeric, character, category, or factor variable containing subject
identifiers, or a data frame of such variables that in combination form
groups of interest. Required if |
colvar |
A numeric, character, category, or factor variable containing column
identifiers. |
base |
vector of character strings containing base names of repeated measurements |
reps |
number of times variables named in |
times |
when |
timevar |
specifies the name of the time variable to create if |
constant |
a data frame with the same number of rows in |
Details
In converting dimnames to vectors, the resulting variables are
numeric if all elements of the matrix dimnames can be converted to
numeric, otherwise the corresponding row or column variable remains
character. When the dimnames if x have a names attribute, those
two names become the new variable names. If x is a vector and
another vector is also given (in ...), the matrices in the resulting
list are named the same as the input vector calling arguments. You
can specify customized names for these on-the-fly by using
e.g. reShape(X=x, Y=y, id= , colvar= ). The new names will then be
X and Y instead of x and y. A new variable named seqnno is
also added to the resulting object. seqno indicates the sequential
repeated measurement number. When base and times are
specified, this new variable is named the character value of timevar and the values
are given by a table lookup into the vector times.
Value
If x is a matrix, returns a list containing the row variable, the
column variable, and the as.vector(x) vector, named the same as the
calling argument was called for x. If x is a vector and no other
vectors were specified as ..., the result is a matrix. If at least
one vector was given to ..., the result is a list containing k
matrices, where k one plus the number of vectors in .... If x
is a list or data frame, the same type of object is returned. If
x is a vector and id is a data frame, a data frame will be
the result.
Author(s)
Frank Harrell
Department of Biostatistics
Vanderbilt University School of Medicine
fh@fharrell.com
See Also
reshape, as.vector,
matrix, dimnames,
outer, table
Examples
set.seed(1)
Solder <- factor(sample(c('Thin','Thick'),200,TRUE),c('Thin','Thick'))
Opening <- factor(sample(c('S','M','L'), 200,TRUE),c('S','M','L'))
tab <- table(Opening, Solder)
tab
reShape(tab)
# attach(tab) # do further processing
# An example where a matrix is created from irregular vectors
follow <- data.frame(id=c('a','a','b','b','b','d'),
month=c(1, 2, 1, 2, 3, 2),
cholesterol=c(225,226, 320,319,318, 270))
follow
attach(follow)
reShape(cholesterol, id=id, colvar=month)
detach('follow')
# Could have done :
# reShape(cholesterol, triglyceride=trig, id=id, colvar=month)
# Create a data frame, reshaping a long dataset in which groups are
# formed not just by subject id but by combinations of subject id and
# visit number. Also carry forward a variable that is supposed to be
# constant within subject-visit number combinations. In this example,
# it is not constant, so an arbitrary visit number will be selected.
w <- data.frame(id=c('a','a','a','a','b','b','b','d','d','d'),
visit=c( 1, 1, 2, 2, 1, 1, 2, 2, 2, 2),
k=c('A','A','B','B','C','C','D','E','F','G'),
var=c('x','y','x','y','x','y','y','x','y','z'),
val=1:10)
with(w,
reShape(val, id=data.frame(id,visit),
constant=data.frame(k), colvar=var))
# Get predictions from a regression model for 2 systematically
# varying predictors. Convert the predictions into a matrix, with
# rows corresponding to the predictor having the most values, and
# columns corresponding to the other predictor
# d <- expand.grid(x2=0:1, x1=1:100)
# pred <- predict(fit, d)
# reShape(pred, id=d$x1, colvar=d$x2) # makes 100 x 2 matrix
# Reshape a wide data frame containing multiple variables representing
# repeated measurements (3 repeats on 2 variables; 4 subjects)
set.seed(33)
n <- 4
w <- data.frame(age=rnorm(n, 40, 10),
sex=sample(c('female','male'), n,TRUE),
sbp1=rnorm(n, 120, 15),
sbp2=rnorm(n, 120, 15),
sbp3=rnorm(n, 120, 15),
dbp1=rnorm(n, 80, 15),
dbp2=rnorm(n, 80, 15),
dbp3=rnorm(n, 80, 15), row.names=letters[1:n])
options(digits=3)
w
u <- reShape(w, base=c('sbp','dbp'), reps=3)
u
reShape(w, base=c('sbp','dbp'), reps=3, timevar='week', times=c(0,3,12))
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