*** netmeta, version 0.9-5, 2017-05-31 ***
** Major changes **
* New function netleague() to print league table with network
meta-analysis results
* pairwise():
- zero events for binary outcomes or incidence rates are handled
correctly in multi-arm studies by adding an increment to all
treatment arms (in older versions of netmeta inconsistent
treatment effects for multi-arm studies were possible as
increments were considered in individual comparisons instead of
all comparisons for a multi-arm study)
- print warning and information on treatment comparisons with
missing treatment estimate or standard error
* forest.netmeta():
- reference group can be omitted from forest plot
- treatments can be sorted by treatment estimate (TE), standard
error (seTE), number of studies in direct comparison (k), and
proportion of direct information (prop.direct)
* netmeta():
- additional checks for correct number of comparisons in multi-arm
studies and more informative error message for uncorrect number
of comparisons in multi-arm studies due to missing treatment
effects or standard errors in single comparisons
- separator used in comparison names to concatenate treatment
labels can be specified by user (default: ":")
* In decomp.design(), by default, only print designs contributing to
design-specific decomposition of within-designs Q statistic
* Input to netdistance() can be either a netmeta object or a matrix
** User-visible changes **
* forest.netmeta():
- new argument 'drop.reference.group'
- argument 'sortvar' can be used in the following ways:
sortvar = TE, sortvar = -TE, sortvar = seTE, sortvar = -seTE,
sortvar = k, sortvar = -k, sortvar = prop.direct, sortvar = -prop.direct
* print.decomp.design() and netheat():
- new argument 'showall' which defaults to FALSE
* print.summary.netmeta():
- print number of designs
- print preset between-study variance and corresponding
information if argument 'tau.preset' is not NULL in netmeta()
* pairwise():
- in multi-arm studies exclude comparisons with missing sample
size or standard error from calculation of pooled variance for
standardized mean difference (sm = "SMD")
* plot.netposet():
- new default for argument 'arrows', i.e., by default, do not show
arrows in scatter plot
* print.netsplit():
- number of studies providing direct evidence printed
* netdistance():
- argument name changed from 'A' to 'x' in order to reflect that
input of R function can be either a netmeta object or an
adjacency matrix
* Help pages:
- R command 'help(netmeta)' can be used to show brief overview of
R package netmeta
- examples corrected for dataset dietaryfat
- do not run all examples in forest.netmeta() as CRAN only allows
a run time below 10 seconds for examples provided on a help page
- R code to produce forest plot added to examples in dataset
Wood2010
** Internal changes **
* netmeta():
- new list element 'd' with number of designs
- new list element 'B.matrix' with the edge-vertex incidence
matrix
* summary.netmeta():
- new list element 'd' with number of designs
- new list element 'tau.preset'
* netsplit():
- new list element 'k' with number of studies providing direct
evidence
* netconnection():
- argument checks added
- better code documentation
* Internal function decomp.tau():
- detach all designs (including protuding edges)
* New internal function createB() to calculate edge-vertex incidence
matrix
* netmeta(), netconnection(), multiarm(), and chkmultiarm():
- use internal function createB() instead of dedicated R code
* print.summary.netmeta(), nma.ruecker(), and decomp.tau():
- use command pchisq(..., lower.tail = FALSE) instead of
1 - pchisq(...)
*** netmeta, version 0.9-4, 2017-04-07 ***
** Bug fix release **
* netsplit() used wrong comparison labels if argument
'reference.group' was used in netmeta()
* netmeasures() ignores value of argument 'reference.group' in
netmeta object
*** netmeta, version 0.9-3, 2017-03-12 ***
** Major changes **
* Calculate indirect treatment estimates based on direct evidence
proportion
* Ranking of treatments based on fixed effect model added to
netrank()
* New function netsplit() to split direct and indirect evidence
* New functions netposet(), print.netposet(), and plot.netposet() to
calculate, print and plot partial ordering of rankings
* New function hasse() to draw Hasse diagram of partially ordered
treatment rankings
* netmeta():
- can be used with R objects created with pairwise()
- checks for consistency of treatment effects and variances in
multi-arm studies
* Import ginv() from R package MASS (for consistency checks)
* Suggested packages added (for Hasse diagram):
- hasseDiagram
- grid
* Bug fixes:
- netmeta() calculates correct direct evidence estimates under
random effects model (list components 'TE.direct.random',
'seTE.direct.random', ..., 'pval.direct.random'); so far results
from fixed effect model have been used
- netmeta() excludes a treatment from list component 'seq' if all
comparisons containing the respecitve treatment are excluded due to
missing values in treatment effect or standard error
- netmeasures() does not result in an error if no or only one
study with two treatments is available
** User-visible changes **
* New arguments random and tau.preset in netmeasures()
* New functions netsplit() and print.netsplit()
* Consider ordering of treatments in netrank() which is defined by
argument seq in netmeta()
* For multi-arm studoes, calculate pooled standard deviation in
pairwise() if means and standard deviations are provided and
summary measure is equal to "SMD"
** Internal changes **
* netmeta():
- new list element 'k.direct' with number of studies in
meta-analyses with direct evidence
* nma.ruecker():
- bug fix such that estimates from random effects model are used
for direct treatment estimates if argument 'tau.direct' is
larger than zero
* nma.krahn():
- bug fix such that use of function does not result in an error if
either no or only one study with two treatments is available
* pairwise():
- data.frame commands use argument stringsAsFactors = FALSE
* chkmultiarm():
new internal function to check consistency of treatment effects
and variances in multi-arm studies; calls ginv() from MASS library
* lowertri():
new internal function to extract elements from the lower triangle
of a matrix
*** netmeta, version 0.9-2, 2016-11-19 ***
** Major changes **
* R package rgl moved from imported to suggested packages as
- 3-D network plots are not essential for network meta-analysis
- installation of netmeta package breaks under Mac OS if XQuartz
is not available
** User-visible changes **
* Help page of netgraph() updated (information on rgl package)
** Internal changes **
* Use chkclass() from meta package to check for class membership
*** netmeta, version 0.9-1, 2016-10-13 ***
** Major changes **
* Number of studies can be added to network graph
* Distance matrix can be provided directly to generate network graph
* shadowtext() from TeachingDemos package by Greg Snow added to
netmeta package
* P-scores can be printed in forest plot
** User-visible changes **
* help page with brief overview of netmeta package added
* netgraph():
- new arguments to add number of studies to network graph
(number.of.studies, cex.number.of.studies,
col.number.of.studies, bg.number.of.studies)
- plastic look retained for highlighted comparisons
- new argument D.matrix to provide treatment distances directly
* netmeta():
- function can be used with a single pairwise comparison without
resulting in an error
* forest.netmeta():
- argument sortvar can be equal to Pscore, "Pscore", -Pscore, or
"-Pscore" to sort treatments according to ranking generated by
netrank()
- argument leftcols or rightcols can include "Pscore" to add a
column with P-Scores to the forest plot
- new arguments small.values and digits.Pscore for P-Scores
* print.netmeta():
- use correct layout for network meta-analysis with a single
pairwise comparison
* decomp.design(), netheat(), netmeasures():
- print a warning and return NULL for network meta-analysis with a
single design
* netconnection():
- print sensible error message if argument treat2 is missing or of
different length than argument treat 1
* netdistance():
- print sensible error message if argument A is not a matrix
* Help pages updated:
decomp.design(), print.decomp.design(),
netgraph(), netheat(), netmeasures()
** Internal changes **
* New function:
- shadowtext() to print number of studies
* nma.ruecker():
- keep dimension of matrices W and B.matrix for network
meta-analysis with a single pairwise comparison
* nma.krahn():
- print a warning and return NULL for network meta-analysis with a
single design
* decomp.tau(), tau.within():
- return NULL for network meta-analysis with a single design
2016-04-26, version 0.9-0
New functions:
- netdistance (calculate distance matrix; replacement for internal
function nodedist)
- netconnection (Get connectivity information for network)
- print.netconnection (corresponding print function)
Internal function nodedist removed (replaced by netdistance function)
Import functions from R package rgl (for 3-D plots)
New dataset Woods2010 (use long format in pairwise function)
Function netmeta:
- check connectivity of network and stop with informative error
message if network is not fully connected
- new list components:
'Cov.fixed' (variance-covariance matrix for fixed effect model)
'Cov.random' (variance-covariance matrix for random effects model)
Function pairwise:
- extension to long data format (see example on help page)
Function netmeta:
- new arguments 'dim', 'eig3', and 'zpos' to generate 3-D network
plots
Function stress (used internally):
- extension to generate 3-D network plots
- use netdistance function instead of nodedist
Function nma.ruecker (used internally):
- use of netmeta function does not result in an error for networks
without heterogeneity / inconsistency, i.e. networks with zero
degrees of freedom (e.g. a star-shaped network with only a single
study for each comparison; simple example: single comparisons A-B,
A-C, A-D)
- calculate variance-covariance matrix
Function print.netrank:
- print title of meta-analysis (if available)
Function print.summary.netmeta:
- print "--" instead of "< 0.0001" in networks without heterogeneity
/ inconsistency
- print "0" instead of "< 0.0001" if tau-squared is zero
- print 'p-value' instead of 'p.value'
Function print.decomp.design:
- print 'p-value' instead of 'p.value'
Help page of netmeta function:
- more details on contrast- and arm-based data format
- reference to book "Meta-Analysis with R" and Rücker & Schwarzer (2014) added
- add information that hazard ratio is a possible summary measure
- change error in description of adjustment in random effects model
Help page of netgraph function:
- example for 3-D network plot added
Help page of netrank function:
- reference to Rücker & Schwarzer (2015) updated
Help page of pairwise function:
- description on use of long data format added
- more information on additional arguments for meta-analysis functions
New help pages:
- netconnection, print.netconnection
- netdistance
- Wooks2010 dataset
2015-06-26, version 0.8-0
New functions netrank and print.netrank:
- frequentist method to rank treatments in network
Function netmeta:
- print less irritating warning if treatment comparisons are resorted
(as this is more a note than a warning)
Function print.netmeta:
- minor change in printout (old: "Data utilised in network
meta-analysis ..."; new: "Results ...")
Help pages:
- new help page for netrank function
- reference Rücker & Schwarzer (2015) added in help page of netgraph
function
- link to pairwise function added in help page of netmeta function
2015-02-04, version 0.7-0
Version of R package meta must be larger or equal 4.0-0
Title of R package changed.
New function pairwise:
- transforms data that are given in an arm-based format (e.g. input
for WinBUGS is of this format) to contrast-based format that can be
read by function netmeta
New datasets:
- dietaryfat (dataset with incidence rates as outcomes)
- parkinson (continuous outcomes)
- smokingcessation (binary outcomes)
Function netmeta:
- implement a general check for correct number of comparisons for
multi-arm studies
- use setseq function to check and set value of argument 'seq'
- use setref function to check and set value of argument
'reference.group'
- use chklevel function from R package meta to check levels of
confidence intervals
- consider attribute 'sm' from R objects generated with R function
pairwise
- function can be used for a pairwise meta-analysis (bug fix in
nma.ruecker function used internally)
Function netgraph:
- check that matrix 'thickness' (if provided) has same row and column
names as argument 'labels'
- use setseq function to check and set value of argument 'seq'
- stop with an error message if argument 'seq' or 'labels' is NULL
Function netheat:
- no net heat plot produced if (i) the number of designs is equal or
smaller than 2 or (ii) no between-design heterogeneity exists
- unintentional warnings omitted
Function forest.netmeta:
- print a warning that the first treatment is used as reference if the
reference group is unspecified instead of producing an error
- use setseq function to check and set value of argument 'seq'
- use setref function to check and set value of argument
'reference.group'
Function print.summary.netmeta:
- print "." instead of "0" or "1" for diagonal elements of treatment
effect and confidence interval matrices
- print "." instead of "0" or "1" for reference group (if provided)
- use setref function to check and set value of argument
'reference.group'
- use is.relative.effect function from R package meta to check if a
relative effect measure is used (argument 'sm')
Function print.netmeta:
- use setref function to check and set value of argument
'reference.group'
- use is.relative.effect function from R package meta to check if a
relative effect measure is used (argument 'sm')
Function summary.netmeta:
- use setref function to check and set value of argument
'reference.group'
Function decomp.tau and tau.within (used internally):
- bug fix such that no error is produced in decomp.design and netheat
function for networks without heterogeneity and inconsistency
Function print.decomp.design:
- omit printing of information on between-designs Q statistic after
detaching of single designs if no between-design heterogeneity
exists
- use format.tau function from R package meta to print "0" instead of
"< 0.0001" if tau-squared is zero
New functions (used internally):
- setseq - check and set argument 'seq' (and argument 'sortvar' in
forest.meta function)
- setref - check and set argument 'reference.group'
- chklist - check for a list
New help pages for function pairwise and datasets dietaryfat,
parkinson, and smokingcessation.
2014-07-29, version 0.6-0
Function netgraph:
- complete rewrite of this function (without changing previous default
settings substantially)
- list of major new features:
- additional layouts beside circular presentation (see argument
'start.layout')
- implementation of stress majorization algorithm to optimize layout
(argument 'iterate')
- additional methods to determine width of lines connecting
treatments (argument 'thickness')
- highlight multi-arm studies (arguments 'multiarm' and
'col.multiarm')
- possibility to provide a neighborhood matrix to specify
neighborhood differently than using the adjacency matrix, for
example content-based (argument 'N.matrix')
- possibility to provide x- and y-coordinates for network plot
(arguments 'xpos' and 'ypos')
Function netmeta:
- calculate treatment estimates from all direct pairwise treatment
comparisons (both fixed effect and random effects model)
- new list components:
'tau.preset', 'TE.direct.fixed', 'seTE.direct.fixed',
'lower.direct.fixed', 'upper.direct.fixed', 'zval.direct.fixed',
'pval.direct.fixed', 'TE.direct.random', 'seTE.direct.random',
'lower.direct.random', 'upper.direct.random', 'zval.direct.random',
'pval.direct.random'
Function nma.ruecker (used internally)
- changed accordingly to reflect changes in netmeta function
Function forest.netmeta:
- new argument sortvar (default: sort treatment effect estimates
according to list component 'seq' of netmeta object)
New functions stress and nodedist (used internally)
- auxiliary functions for netgraph function
Help pages updated accordingly
2014-06-24, version 0.5-0
Functions nma.krahn, netmeasures, netheat, decomp.design, and
print.decomp.design:
- random effects network meta-analysis added
Function netheat:
- new argument 'random'
Functions nma.krahn, decomp.design, and netheat:
- new argument 'tau.preset'
Function decomp.design:
- correct design-specific decomposition of Q statistic in network
meta-analysis with multi-arm studies
- list component 'Q.design' renamed to 'Q.het.design'
- list component 'Q.detach' renamed to 'Q.inc.detach'
- list component 'residuals' renamed to 'residuals.inc.detach'
- new list components:
'Q.inc.random', 'Q.inc.random.preset',
'Q.inc.design.random.preset', 'residuals.inc.detach.random.preset',
'tau.preset'
New functions tau.within and decomp.tau (used internally)
Help pages updated accordingly
2014-05-27, version 0.4-4
Functions netmeta and nma.ruecker:
- modified such that the estimated tau-squared in random effects model
considers multi-arm studies
Function print.netmeta:
- information on percentage weight not printed as interpretation is
difficult
Dataset Senn2013:
- use of unpooled standard error for each treatment comparison
2014-04-14, version 0.4-3
Function netmeta:
- numeric values for arguments 'treat1' and 'treat2' not converted to
character values (only factors converted to characters)
- check whether treatments are different (arguments 'treat1' and
'treat2')
Function print.summary.netmeta:
- print random effects estimates according to argument 'seq'
Function forest.netmeta:
- sort treatment effect estimates according to argument 'seq'
Function nma.ruecker (used internally):
- changed such that all treatment effects are calculated irregardless
of treatment order (some treatment effects remained NA depending on
order of treatments)
2014-03-31, version 0.4-2
Function netmeasures:
- bug fix using correct formula to calculate direct evidence
proportion (variance instead of standard error)
2014-03-21, version 0.4-1
Function netmeta:
- Argument 'seq' added (see also R function netgraph)
Function netgraph:
- new default for argument 'seq'
Help pages updated accordingly
Some internal code cleaning to improve readability of R functions
2014-03-07, version 0.4-0
New functions added:
- netgraph (network graph)
- netheat (net heat graph)
- netmeasures (measures for network meta-analysis)
- decomp.design (design-based decomposition of Cochran's Q)
- print.decomp.design (corresponding print function)
- p.ci, format.TE, nma.krahn, nma.ruecker (used internally)
Function netmeta:
- Check added whether all pairwise comparisons are provided for
multi-arm studies
Help pages added for new functions
Help page of function netmeta updated
2013-08-01, version 0.3-1
Functions netmeta and summary.netmeta:
- new list component n (number of treatments)
Function print.summary.netmeta:
- modified such that number of treatments is printed
- modified such that argument 'reference.group' works as expected for
random effects model
2013-07-24, version 0.3-0
First version released on CRAN