*** netmeta, version 0.9-7, 2017-12-06 ***
** Major changes **
* Version of R package meta must be larger or equal 4.9-0
* New function to produce forest plots with network, direct, and
indirect evidence
* New function to estimate additive network meta-analysis for
combinations of treatments
* New default in function netsplit(): treatment comparisons are
selected from upper treatment estimates matrix, i.e., comparisons
are "A vs B", "A vs C", and "B vs C" for treatments "A", "B", and
"C" instead of "B vs A", etc.
* Zero treatment arm variance in multi-arm studies results in a
warning instead of an error message
* League tables can be exported as CSV or Excel file
* New argument 'backtransf' indicating whether estimates should be
back-transformed in printouts and plots, e.g., to show results as
odds ratios instead of log odds ratios
* P-values can be printed in scientific notation
* P-values equal to 0 are actually printed as "0" instead of
"< 0.0001"
* Thousands separator can be used in printouts and forest plots for
large numbers
** User-visible changes **
* new functions:
- forest.netsplit() to produce forest plots with direct and
indirect evidence
- print.netleague() to print league table
- treats() to create uniquely abbreviated treatment names
- netcomb() and netcomb.netmeta() to estimate additive network
meta-analysis models for combinations of treatments
- summary.netcomb(), print.netcomb(), and print.summary.netcomb()
to print (summaries of) netcomb objects
* print.decomp.design(), print.netmeta(), print.netsplit(), and
print.summary.netmeta():
- new argument 'big.mark' to specify character printed as
thousands separator, e.g., big.mark = "," will result in
printing of 1,000 for the number 1000
- new argument 'scientific.pval' to print p-values in scientific
notation, e.g., 1.2345e-01 instead of 0.12345
* netmeta():
- new argument 'backtransf' (see above)
- new argument 'nchar.trts' to abbreviate treatment names in
printouts
* netleague():
- function does not print league table, but only generates it
(necessary for export of league table)
- new arguments 'bracket' and 'separator' to define layout of
confidence intervals (see R function cilayout() from R package
meta)
* netsplit():
- new argument 'upper' to specify whether lower or upper triangle
of treatment estimate matrix should be used to build comparisons
- column with comparisons added to data frames with network, direct,
and indirect estimates
- additional new arguments (see help file):
'reference.group', 'baseline.reference', 'sep.trts', 'quote'
* netmeasures():
- do not round results to four digits
* print.netmeta(), print.summary.netmeta():
- new arguments 'backtransf' and 'nchar.trts' (see above)
- argument 'logscale' removed (replaced by argument 'backtransf')
* Dataset Senn2013:
- new columns 'treat1.long' and 'treat2.long' with full treatment
names added
* Help pages:
- new help pages for forest.netsplit(), print.netleague(), and
treats()
- updated help pages for netposet() and netsplit()
** Bug fixes **
* netsplit():
- order of treatments in printouts corresponds to treatment
comparison, e.g., "A:B" means that treatment "A" was compared
with treatment "B" (and not the other way around).
Side note, not sure whether this is a bug or a feature as "A:B"
noted the design "comparison A and B" so far.
* netposet():
- function works with a ranking matrix that contains missing
elements, i.e., rankings that do not include all treatments
* netgraph():
- areas for multi-arm studies are printed at the correct locations
if argument 'start.layout' is not equal to "circle" and argument
'seq' defines a specific treatment order (this bug was
introduced in netmeta, version 0.7-0)
** Internal changes **
* chkmultiarm():
- warning for zero treatment arm variance instead of an error
* new internal function uppertri() to extract elements from the
upper triangle of a matrix
* new internal function treats() to abbreviate treatment names
* new internal function nma.additive() for estimation of additive
network meta-analysis models
* new internal function createC() to create C matrix used as input
to nma.additive()
* new internal functions prcombs() and prcomps() for printing of
netcomb objects
* Internal function p.ci() replaced with formatCI() from R package
meta
* Internal function format.TE() replaced with formatN() from R
package meta
*** netmeta, version 0.9-6, 2017-08-09 ***
** Major changes **
* Prediction intervals can be calculated for treatment estimates
from a network meta-analysis
* In netmeta(), Q statistics for heterogeneity and design
inconsistency are calculated according to Krahn et al. (2013);
see help page of decomp.design()
* In printouts and forest plots, the reference treatment can be
considered as treatment of interest or comparator (default),
i.e., either comparisons of reference vs other treatments or
other treatments vs reference are reported
* Tests for heterogeneity and design inconsistency are shown in
printouts
* A biplot can be generated to show partial ordering of treatment
rankings for more than two outcomes
* Additional checks implemented for multi-arm studies:
- negative or zero treatment arm variances
- duplicate treatment comparisons or incomplete sets of
treatment comparisons within a study
** User-visible changes **
* netmeta():
- new arguments 'prediction' and 'level.predict' to calculate
prediction intervals
- list elements 'Q.heterogeneity' and 'Q.inconsistency' based on
Krahn et al. (2013)
- new list elements 'prediction', 'lower.predict',
'upper.predict', 'df.Q.heterogeneity',
'pval.Q.heterogeneity','df.Q.inconsistency', and
'pval.Q.inconsistency'
- list element 'df' renamed to 'df.Q'
- stop with an informative error message if (i) any treatment arm
variance derived from the treatment comparison variances is
negative or zero, or (ii) in case of duplicate comparisons or an
incomplete set of treatment comparisons within a study
- argument 'details.tol.multiarm' renamed to 'details.chkmultiarm'
* netmeta(), forest.netmeta(), print.netmeta(),
print.summary.netmeta(), and summary.netmeta():
- new argument 'baseline.reference' to print results for
comparisons between reference and other treatments, or vice versa
* print.netmeta(), print.summary.netmeta(), and summary.netmeta():
- new argument 'prediction' to print prediction intervals
* print.summary.netmeta():
- print information on tests for overall heterogeneity and
inconsistency
* summary.netmeta():
- arguments 'level' and 'level.comb' removed from R function
(i.e., one has to re-run the netmeta() command for confidence
intervals with other coverage levels)
* plot.netposet():
- new argument 'plottype' to choose between scatter plot or biplot
- new arguments to modify layout ('cex.text', 'col.text', pch,
cex.points, col.points)
* decomp.design() and netmeasures():
- new argument 'warn' to suppress printing of warnings
** Internal changes **
* New internal function upgradenetmeta() to add missing list
elements to older netmeta objects
* R function ci() from R package meta added to namespace
* chkmultiarm():
- additional checks for (i) negative and zero variances as well as
(ii) duplicate treatment comparisons or incomplete sets of
treatment comparisons within a study
*** 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:
- 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
* new internal function lowertri() 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