R: Common R Scripts and Utilities Used by the Statnet Project Software

# Common R Scripts and Utilities Used by the Statnet Project Software

## Documentation for package ‘statnet.common’ version 4.4.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E F I L M N O P R S T U V W misc

## -- A --

all_identical | Test if all items in a vector or a list are identical.
append.rhs.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
append_rhs.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
as.linwmatrix | A data matrix with row weights
as.linwmatrix.linwmatrix | A data matrix with row weights
as.linwmatrix.logwmatrix | A data matrix with row weights
as.linwmatrix.matrix | A data matrix with row weights
as.logwmatrix | A data matrix with row weights
as.logwmatrix.linwmatrix | A data matrix with row weights
as.logwmatrix.logwmatrix | A data matrix with row weights
as.logwmatrix.matrix | A data matrix with row weights
as.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
as.rle.default | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
as.rle.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.

## -- C --

c.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
check.control.class | Check if the class of the control list is one of those that can be used by the calling function
colMeans.mcmc.list | Utility operations for 'mcmc.list' objects
compact.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
compress | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
compress.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
compress_rows | A generic function to compress a row-weighted table
compress_rows.data.frame | "Compress" a data frame.
compress_rows.linwmatrix | A data matrix with row weights
compress_rows.logwmatrix | A data matrix with row weights
control.list.accessor | Named element accessor for ergm control lists
control.remap | Overwrite control parameters of one configuration with another.

## -- D --

decompress_rows | A generic function to compress a row-weighted table
decompress_rows.compressed_rows_df | "Compress" a data frame.
decompress_rows.wmatrix | A data matrix with row weights
deInf | Truncate values of high magnitude in a vector.
deprecation-utilities | Utilities to help with deprecating functions.
despace | A one-line function to strip whitespace from its argument.
diff.control.list | Identify and the differences between two control lists.

## -- E --

ERRVL | Return the first argument passed (out of any number) that is not a 'try-error' (result of 'try' encountering an error.
eval_lhs.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
EVL | Convenience functions for handling 'NULL' objects.
EVL2 | Convenience functions for handling 'NULL' objects.
EVL3 | Convenience functions for handling 'NULL' objects.
EVL<- | Convenience functions for handling 'NULL' objects.

## -- F --

filter_rhs.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
forkTimeout | Evaluate an R expression with a hard time limit by forking a process
formula.utilities | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.

## -- I --

is.linwmatrix | A data matrix with row weights
is.logwmatrix | A data matrix with row weights
is.na.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
is.wmatrix | A data matrix with row weights

## -- L --

lapply.mcmc.list | Utility operations for 'mcmc.list' objects
length.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
linwmatrix | A data matrix with row weights
list_rhs.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
list_summands.call | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
logspace.utils | Utilities for performing calculations on logarithmic scale.
logwmatrix | A data matrix with row weights
log_mean_exp | Utilities for performing calculations on logarithmic scale.
log_sum_exp | Utilities for performing calculations on logarithmic scale.
lrowweights | Set or extract weighted matrix row weights
lrowweights.linwmatrix | Set or extract weighted matrix row weights
lrowweights.logwmatrix | Set or extract weighted matrix row weights
lrowweights<- | Set or extract weighted matrix row weights
lrowweights<-.linwmatrix | Set or extract weighted matrix row weights
lrowweights<-.logwmatrix | Set or extract weighted matrix row weights
lrowweights<-.matrix | Set or extract weighted matrix row weights
lweighted.mean | Utilities for performing calculations on logarithmic scale.
lweighted.var | Utilities for performing calculations on logarithmic scale.

## -- M --

Math.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
mcmc-utilities | Utility operations for 'mcmc.list' objects
mean.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
message_print | 'print' objects to the 'message' output.

## -- N --

nonsimp.update.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
nonsimp_update.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
NVL | Convenience functions for handling 'NULL' objects.
NVL2 | Convenience functions for handling 'NULL' objects.
NVL3 | Convenience functions for handling 'NULL' objects.
NVL<- | Convenience functions for handling 'NULL' objects.

## -- O --

once | Evaluate a function once for a given input.
Ops.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
opttest | Optionally test code depending on environment variable.
order | Implement the 'sort' and 'order' methods for 'data.frame' and 'matrix', sorting it in lexicographic order.
order.data.frame | Implement the 'sort' and 'order' methods for 'data.frame' and 'matrix', sorting it in lexicographic order.
order.default | Implement the 'sort' and 'order' methods for 'data.frame' and 'matrix', sorting it in lexicographic order.
order.matrix | Implement the 'sort' and 'order' methods for 'data.frame' and 'matrix', sorting it in lexicographic order.

## -- P --

paste.and | Concatenates the elements of a vector (optionaly enclosing them in quotation marks or parentheses) adding appropriate punctuation and conjunctions.
persistEval | Evaluate an expression, restarting on error
persistEvalQ | Evaluate an expression, restarting on error
print.control.list | Pretty print the control list
print.diff.control.list | Identify and the differences between two control lists.
print.linwmatrix | A data matrix with row weights
print.logwmatrix | A data matrix with row weights
print.wmatrix | A data matrix with row weights

## -- R --

rep.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
rle-reexport | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
rowweights | Set or extract weighted matrix row weights
rowweights.linwmatrix | Set or extract weighted matrix row weights
rowweights.logwmatrix | Set or extract weighted matrix row weights
rowweights<- | Set or extract weighted matrix row weights
rowweights<-.linwmatrix | Set or extract weighted matrix row weights
rowweights<-.logwmatrix | Set or extract weighted matrix row weights
rowweights<-.matrix | Set or extract weighted matrix row weights

## -- S --

set.control.class | Set the class of the control list
sort.data.frame | Implement the 'sort' and 'order' methods for 'data.frame' and 'matrix', sorting it in lexicographic order.
split.array | A 'split()' method for 'array' and 'matrix' types on a margin.
split.matrix | A 'split()' method for 'array' and 'matrix' types on a margin.
statnet.cite | 'CITATION' file utilities for Statnet packages (DEPRECATED)
statnet.cite.foot | 'CITATION' file utilities for Statnet packages (DEPRECATED)
statnet.cite.head | 'CITATION' file utilities for Statnet packages (DEPRECATED)
statnet.cite.pkg | 'CITATION' file utilities for Statnet packages (DEPRECATED)
statnetStartupMessage | Construct a "standard" startup message to be printed when the package is loaded.
str.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
Summary.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
sweep.mcmc.list | Utility operations for 'mcmc.list' objects
sweep_cols.matrix | Suptract a elements of a vector from respective columns of a matrix

## -- T --

term.list.formula | Functions for Querying, Validating and Extracting from Formulas A suite of utilities for handling model formulas of the style used in Statnet packages.
trim_env | Make a copy of an environment with just the selected objects.
trim_env.default | Make a copy of an environment with just the selected objects.
trim_env.environment | Make a copy of an environment with just the selected objects.

## -- U --

ult | Extract or replace the _ult_imate (last) element of a vector or a list, or an element counting from the end.
ult<- | Extract or replace the _ult_imate (last) element of a vector or a list, or an element counting from the end.
unwhich | Construct a logical vector with 'TRUE' in specified positions.

## -- V --

vector.namesmatch | reorder vector v into order determined by matching the names of its elements to a vector of names

## -- W --

wmatrix | A data matrix with row weights
wmatrix_weights | Set or extract weighted matrix row weights

## -- misc --

!.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
!=.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
$.control.list | Named element accessor for ergm control lists
&.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
.Deprecate_method | Utilities to help with deprecating functions.
.Deprecate_once | Utilities to help with deprecating functions.
<.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
<=.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
==.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
>.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
>=.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.
[.wmatrix | A data matrix with row weights
[<-.wmatrix | A data matrix with row weights
|.rle | Functions reexported from 'rle' They will no longer be reexported after the next release. Some Ops group methods are exported as well, since as of version 4.0.2, R's 'NextMethod()' does not appear to be able to dispatch from a group member method to a group method.