-
Krzysztof Ciomek added as a contributor to the R package netmeta
-
Modified version of R functions from the R package hasseDiagram added to construct Hasse diagrams
-
Hasse diagrams and calculation of network contributions available without installation of additional packages
-
R packages Rgraphviz, graph, and methods added to Imports
-
R package igraph moved from Suggests to Imports
-
R package hasseDiagram removed from Suggests
- netmetabin():
- fix error if all comparisons containing the specified reference treatment had a zero event in one group
- hasse():
- new argument 'shape' to change the shape of node borders
- new arguments 'col.lines' and 'col.nodes' to change the colour of lines and treatment node borders
- new argument 'lwd' to change the width of lines and node borders
-
Network meta-analysis of studies with correlated treatment arms implemented
-
Theodoros Evrenoglou added as a contributor to the R package netmeta
-
Logistic regression with penalised likelihood implemented for network meta-analysis of rare events (Evrenoglou et al., 2022)
-
Subgroup network meta-analysis implemented
-
Component network meta-analysis:
- numbers of events and sample sizes can be provided for disconnected networks
- node size and line width can be changed in network graphs of disconnected networks
- league tables can be constructed for connected or disconnect networks
- auxiliary functions createC() and combinations() to fit interaction CNMA models more easily
- warn / inform about unidentifiable components only appearing together which could be merged to make the combination identifiable
-
Rankograms can be constructed from samples
-
R functions pairwise() and subset.pairwise() moved from R package netmeta to meta
-
R function pairwise() can be used with dose-response data
-
New R function settings.netmeta() to define and print default settings for network meta-analyses in R package netmeta
-
New R function crossnma2netmeta() to create a netmeta object from a crossnma object
-
By default, no reference group line is displayed in forest plots (argument 'drop.reference.group = TRUE' instead of 'drop.reference.group = FALSE')
-
In R function netsplit(), only show results for pairwise comparisons providing both direct and indirect evidence by default (argument 'show = "both"' instead of 'show = "all"')
-
R function netmeta() does not automatically return the R object created with rma.mv() from metafor to calculate the between-study variance for the REML or ML estimator of the between-study variance (argument 'keeprma = FALSE')
-
Use the GitHub version of R package hasseDiagram which has been archived on CRAN on 2025-01-15
-
R packages mvtnorm, grid, and colorspace moved from Suggests to Imports
-
New R functions subgroup.netmeta() and forest.subgroup.netmeta() to conduct subgroup meta-analysis
-
New generic function rankogram() to calculate rankograms
-
New functions rankogram.netmeta(), replacing the older rankogram(), and rankogram.default()
-
New generic function netpairwise() to conduct pairwise meta-analyses for all comparisons with direct evidence
-
New functions netpairwise.netmeta(), replacing the older netpairwise(), and netpairwise.netmetabin()
-
print.rankogram():
- by default, sort treatments by SUCRAs
- new logical argument 'sort' to sort treatments by SUCRA values
-
netmeta():
- new argument 'correlated' to conduct network meta-analysis of correlated treatment arms
- new argument 'keeprma' to return the R object created with rma.mv() from metafor to calculate the between-study variance for the REML or ML method
- only list element 'rma.tau' with the rma.mv() object is returned if argument 'keeprma = TRUE' (instead of elements '.metafor', '.dat.tau', '.V', '.formula.trts', 'version.metafor'); 'rma.tau' replaces '.metafor', all other information is part of the R object created with rma.mv()
-
netmetabin():
- new argument 'method.incr' indicating continuity correction method (replaces deprecated arguments 'addincr' and 'allincr')
- argument 'method = "LRP"' can be used for penalized logistic regression
- argument 'reference.group' uses setting from pairwise object
-
discomb():
- new arguments 'n1', 'n2', 'event1', 'event2', 'incr', 'na.unident', and 'keepdata'
-
netmeta(), netmetabin(), discomb(), netcomb(), summary.netmeta(), summary.netcomb(), print.netmeta(), print.netcomb(), print.summary.netmeta(), print.summary.netcomb(), forest.netmeta(), forest.netcomb():
- new argument 'overall.hetstat' to specify whether to print heterogeneity information
-
netleague():
- new argument 'details' to control printing of details on comparisons in lower and upper triangle
-
forest.netmeta():
- new argument 'col.subgroup' replaces argument 'col.by'
- new arguments 'print.tau2' and 'print.tau'
- print text 'Common Effects Model' for Mantel-Haenszel and non-central hypergeometrical model as details can be printed in forest plots using argument 'details.methods = TRUE'
-
print.rankogram():
- new argument 'sort' to return rankings sorted by SUCRA values
-
print.netmeta(), print.summary.netmeta():
- new arguments 'zero.pval', 'JAMA.pval', 'print.tau2', 'print,tau', 'print.Q', 'print.I2', 'print.I2.ci', 'details.methods'
-
print.netcomb(), print.summary.netcomb():
- new arguments 'print.tau2', 'print,tau', 'print.Q', 'print.I2', 'print.I2.ci', 'details.methods'
-
netimpact():
- new arguments 'nchar.trts' and 'nchar.studlab'
-
print.netimpact():
- new arguments 'nchar.trts', 'nchar.studlab', 'details.methods', 'legend.studlab'
-
netconnection.pairwise():
- new argument 'drop.NA' to consider comparisons with missing estimates or standard errors (e.g., to generate network graph for comparisons with missing estimates or standard errors)
-
netdistance.netmeta(), netdistance.netcomb():
- new argument 'sort' to sort (sub)networks by treatment names
-
New function summary.netconnection() to print list of studies in subnetworks
-
New function print.netdistance() to print distance matrix
-
New generic function hasse() for Hasse diagrams
-
New functions hasse.netposet() replacing the older hasse()
-
In help pages, use requireNamespace() for R commands using R packages listed under Suggests
-
Do not print the start-up message concerning older version of R package netmeta for readers of 'Meta-Analysis with R (Use R!)'
-
netmeta(), netmetabin(), discomb():
- consider value for argument 'reference.group' from pairwise() object
-
netmeta():
- set between-study variance to NA for single study if argument 'method.tau = "REML"' or 'method.tau = "ML"'
-
netcomb():
- input for arguments 'common' and 'random' was ignored
-
netcomplex():
- print correct component names for command netcomplex(net1, 2) etc.
-
netcomparison():
- NA was calculated for comparisons containing inestimable components which canceled out, e.g., A + Z vs B + Z with inestimable Z
-
discomb():
- set study labels if argument 'studlab' is missing
-
print.netcomparison():
- do not print information on abbreviated component label for inactive component if it isn't part of the comparison
-
print.netcomb():
- printout resulted in an error if the reference intervention contained an inestimable component
-
New generic function netdistance() to calculate distance matrix
-
New functions netdistance.netmeta(), netdistance.netcomb(), netdistance.netconnection(), netdistance.pairwise(), and netdistance.default()
-
New functions netconnection.netmeta(), netconnection.netcomb(), netconnection.pairwise(), and netconnection.default()
-
New functions netconnection.netmeta(), netconnection.netcomb(), netconnection.pairwise(), and netconnection.default()
-
R function netleague() can be used with netcomb() or discomb() objects
-
By default, R function netleague() uses the setting from argument 'x' as the default for argument 'backtransf'
-
Use backtransf() from R package meta to back-transform results
-
New internal function nma_ruecker() allowing for correlated treatment arms (R function nma.ruecker() still available)
-
R functions nma.additive() and nma.krahn() renamed to nma_additive() and nma_krahn()
-
Do not calculate Q.diff within nma_additive() but netcomb() and discomb()
- Two new methods to calculate network contributions implemented in netcontrib()
-
netcontrib():
- new pseudo-inverse method based on L2 solution implemented (argument 'method = "pseudoinverse"')
- another L1 solution based on R package cccp implemented (argument 'method = "cccp"')
-
netgraph.netmeta(), netgraph.netimpact():
- use original order of multi-arm studies for colouring (argument 'col.multiarm')
- wider lines if argument 'thickness = "equal"'
-
netconnection.pairwise():
- add arguments 'treat1', 'treat2' and 'studlab' for backward compatibility (see bug fix)
- argument 'subset' can be used with a pairwise() object
-
pairwise():
- new argument 'append' to append variables from data set provided in argument 'data' (default: TRUE)
- can be used if only study labels and intervention names are provided (and optionally sample sizes)
-
nettable():
- new argument 'nchar.trts' to abbreviate treatment names
- new argument 'legend' to suppress the printout of the legend describing treatment abbreviations
-
print.nettable():
- new argument 'legend' to suppress printing of legend with abbreviated treatment names
-
print.netsplit(), forest.netsplit():
- new argument 'subset' to define subset of comparisons to print
-
netconnection.pairwise():
- the command 'netconnection(treat1, treat2, studlab, data = pw1)' resulted in an obscure error if argument 'data' was a data set created with pairwise()
-
netgraph.netmeta():
- error if argument 'thickness' was a matrix and argument 'lwd.max' was missing
-
print.netcomplex():
- wrong label for summary measure for risk and odds ratio, e.g., log(OR) for odds ratio and OR for log odds ratio
- New internal R function nodesplit() for node-splitting method
-
Vignette with publication on netmeta in Journal of Statistical Software added (command: vignette("netmeta"))
-
R package R.rsp added to Suggests
- netmeta() / discomb():
- remove leading and trailing whitespace in treatment names
- Use of netsplit() resulted in an obscure error in networks with treatment names containing leading and trailing whitespace
- New citation for R package netmeta: Balduzzi et al. (2023)
- New branch 'release' on GitHub starting with netmeta, version 2.8-1
-
R functions funnel(), metabias(), radial(), trimfill(), metainf(), metacum(), baujat() and metareg() can be applied to netpairwise objects created with argument 'separate = TRUE', i.e., separate meta-analysis for all pairwise comparisons in a network
-
Heat plot implemented showing network estimates with confidence intervals
-
netmeta():
- calculate correct number of studies per treatment for multi-arm studies (list element 'n.trts')
-
netcontrib():
- standard call resulted in an error due to a change in R package igraph, version 1.4-0
-
netpairwise():
- new argument 'order' to specify order of treatments in pairwise meta-analyses
- new argument 'k.min' to specify minimal number of studies in pairwise comparison to show funnel plot, radial plot or conduct test for funnel plot asymmetry
-
print.decomp.design():
- by default, results are sorted by p-values (argument 'sort')
-
print.netmeta():
- only print prediction intervals with common effects network meta-analysis if not printed with random effects results
-
netmeta(), netposet(), netrank(), forest.netmeta():
- possible values "desirable" and "undesirable" instead of "good" and "bad" for argument 'small.values'
-
funnel.netmeta():
- value for argument 'order' can be extracted from network meta-analysis object
-
New functions funnel.netpairwise(), metabias.netpairwise(), radial.netpairwise(), trimfill.netpairwise(), metainf.netpairwise() and metacum.netpairwise()
-
New generic function heatplot() to generate heat plot
-
New generic function netconnection() to check connectivity
-
New functions netconnection.pairwise() and netconnection.default()
-
netgraph.netmeta():
- new row names for invisibly returned data sets with information on nodes and edges
-
netmetabin():
- additional checks and assignments if first argument is a data set
-
New internal function setsv() to set value for argument 'small.value'
- In component network meta-analysis,
- by default, do not return estimates but missing values for unidentifiable components and comparisons
- print more precise labels for combinations and components
-
netcomb():
- new argument 'na.unident' to specify whether missing values should be returned for unidentifiable components and comparisons instead of calculated values
-
print.netcomb():
- print layout similar to print.netmeta()
- show results for comparisons with the reference treatment
- only show incremental effects for existing combinations in the network
- print results for common effects and random effects model jointly
- do not show results for inactive component
-
netcomb(), netcomparison(), netcomplex(), summary.netcomb(), summary.netmeta():
- new argument 'backtransf' indicating whether estimates should be back-transformed in printouts and plots
-
summary.netmeta():
- new argument 'nchar.trts' to print abbreviated treatment names
-
summary.netcomb():
- new argument 'nchar.comps' to print abbreviated component names
-
Help page for netgraph.netmeta():
- add information on thickness of lines and point sizes
-
New internal function armlab() to generate labels for combinations and components in component network meta-analysis
-
netcomb():
- new list elements 'na.unident' (new argument) and 'comps.unident' (vector of unidentifiable components)
- New general layout of network graphs:
- same general layout irrespective whether '3-D look' is used or not (argument 'plastic')
- thickness of lines / edges proportional to the number of studies directly comparing treatments
- more similar thickness of lines if proportional to the number of studies directly comparing treatments by using sqrt() to rescale lines
- more similar point sizes if proportional to the number of observations in treatment arms by using sqrt() to rescale point sizes
- rankogram():
- for backward compatibility, export list elements 'fixed', 'ranking.fixed', 'ranking.matrix.fixed', and 'cumrank.matrix.fixed'
-
netgraph.netmeta():
- thickness of lines / edges proportional to the number of studies directly comparing treatments (previous default: proportional to standard error of direct pairwise comparisons in common effects or random effects model if 'plastic = TRUE' and equal thickness if 'plastic = FALSE')
- print black lines if 'plastic = FALSE' (previous default: slateblue lines)
- print slateblue lines if 'iterate = TRUE'
- new argument 'rescale.thickness' to specify function to rescale line thickness
- new argument 'rescale.pointsize' to specify function to rescale point sizes
- new argument 'points.max' to define maximum point size
- new argument 'points.min' to define minimal point size
-
netgraph.netimpact():
- print black lines if 'plastic = FALSE' (previous default: slateblue lines)
-
netgraph.netconnection():
- argument 'iterate' can be used (was hard-coded as FALSE)
-
netgraph.discomb(), netgraph.netimpact():
- new argument 'plastic'
-
plot.rankogram():
- do not print gray background
-
Use term 'common effects model' instead of 'fixed effects model' in the documentation and argument 'common' instead of 'fixed' to (not) show results for common effects model
-
New function nettable() to create tables with network, direct and indirect estimates from one or more network meta-analyses
-
Excel file with league tables can be created directly with netleague()
-
Nodes in circular network graphs can be rotated
-
R package writexl added to Suggests
-
netcomb():
- report correct number of pairwise comparisons in case of not uniquely identifiable components
-
netmeta():
- return correct design for multi-arm studies in list element 'data$.design'
-
New function subset.pairwise() to select subset of a pairwise object
-
netsplit():
- new arguments 'writexl', 'path' and 'overwrite' to save Excel files
-
netgraph():
- new argument 'rotate' to rotate nodes in circular network graphs
-
netgraph.netconnection():
- new argument 'reference.group' to determine coloring of subnetwork containing the reference group
-
print.netconnection():
- show number of pairwise comparisons and interventions for subnetworks
-
netconnection(), print.netconnection():
- new argument 'details.disconnected'
-
hatmatrix():
- new arguments 'nchar.trts' and 'nchar.studlab'
-
print.netimpact():
- new argument 'legend'
-
Use DerSimonian-Laird estimator of between-study variance to calculate 'tau2.direct' and 'tau.direct' in netmetabin() as REML method did not converge in some network meta-analyses
-
New internal function legendabbr() to print legend with abbreviated and full treatment labels
-
New internal function catch() to catch value for an argument
-
New internal functions comptrts(), direct.indirect(), mat2dat.split(), mat2dat.table(), nettable_internal(), sidde() and sortprop() for netsplit() and nettable()
-
New argument 'equal.length' in setseq()
-
By default, reference group is defined by first treatment in network meta-analysis providing treatment estimate(s) and standard error(s)
-
Function to calculate pseudoinverse of Laplacian matrix (Rücker, 2012) can be specified
-
Function invmat() to calculate pseudoinverse made directly accessible (was an internal function)
-
Only comparisons with a single or multiple treatment(s) can be shown in a 'comparison-adjusted' funnel plot
-
Comparators in 'comparison-adjusted' funnel plot can be lumped
-
R package tictoc added to Suggests
-
netmeta():
- use of REML or ML estimator for between-study variance resulted in an error in networks with at least one multi-arm study
-
netmeta(), pairwise():
- first treatment with outcome data is used as reference group if not specified by the user (to prevent an error if all studies using first treatment do not provide outcome data)
-
rankogram():
- use correct variances in resampling of treatment rankings
-
plot.netrank():
- function ggplot2::xlab() instead of netmeta::xlab() must be used to create image plot
-
print.netcomplex():
- argument 'nchar.comps' was ignored
-
netmeta(), netmetabin(), netcomb(), discomb():
- new argument 'func.inverse' to specify function to calculate pseudoinverse
-
funnel.netmeta():
- argument 'order' can be a single or multiple treatment(s) used as comparator(s)
- new argument 'lump.comparator' to specify whether comparators should be lumped
- new argument 'text.comparator' to mark comparators
-
netcontrib(), netsplit():
- new logical argument 'verbose' to control printing of information on estimation progress
-
print.netconnection():
- print number of studies in subnetworks
-
Data set Linde2016:
- variables with first author, year, number of responders and sample size added
-
Internal function contribution.matrix() returns a list instead of a single matrix with contributions
-
New internal function ranksampling() to conduct the resampling of treatment rankings
-
print.netsplit(), forest.netsplit():
- sorting by direct evidence proportion possible (argument 'sortvar')
-
print.netmeta(), print.netcomb():
- print number of pairwise comparisons after number of studies
- pairwise():
- keep original order of treatments
-
Behaviour of print and print.summary functions switched (to be in line with other print and print.summary functions in R)
-
Annabel Davies [email protected] is a new co-author of the R package netmeta
-
Random walk algorithm implemented to estimate network contributions (Davies et al., 2021)
-
Calculation of standardised mean differences and corresponding standard errors in pairwise() is based on Crippa & Orsini (2016), equations (4) and (5), providing consistent treatment estimates and standard errors for multi-arm studies
-
By default, reference group is defined by first treatment in network meta-analysis
-
Renamed arguments:
- 'fixed' (instead of 'comb.fixed')
- 'random' (instead of 'comb.random')
- 'level.ma' (instead of 'level.comb')
-
New R function hatmatrix() to derive hat matrices
-
New R function netpairwise() to conduct pairwise meta-analyses for comparisons with direct evidence
-
New R function netcomplex() to calculate effect of arbitrary complex interventions in component network meta-analysis
-
New R function netcomparison() to calculate comparison effects of two arbitrary complex interventions in component network meta-analysis
-
I2 from pairwise comparisons shown in forest plot with direct evidence
-
In component network meta-analysis, individual component names instead of full treatment names can be abbreviated for complex interventions with more than one component
-
Do not stop calculations if standard errors of multi-arm studies are inconsistent (instead only check for positive variance estimates of single treatment arms)
-
Generic functions are not exported
-
netmeta():
- fix error in calculation of between-study variance using REML or ML method
-
forest.netbind(), forest.netcomb(), forest.netmeta(), forest.netsplit():
- do not print empty row above descriptions if arguments 'label.left' or 'label.right' is used
-
netcomb(), discomb():
- value provided for argument 'inactive' must be a single treatment component not a combination of treatment components (check was missing)
-
funnel.netmeta():
- works now with numeric treatment labels
-
New functions hatmatrix() and print.hatmatrix() to derive hat matrices
-
New functions netpairwise(), forest.netpairwise(), print.netpairwise(), summary.netpairwise() and print.summary.netpairwise() to conduct pairwise meta-analyses for all comparisons with direct evidence
-
netcontrib():
- new argument 'method' to select method to estimate network contributions
- new logical argument 'hatmatrix.F1000' to specify whether hat matrix given in Papakonstantinou et al. (2018) should be used
- argument 'nchar.trts' from netmeta object considered in printouts
-
decomp.design(), print.decomp.design() print.netsplit(), rankogram(), print.rankogram(), plot.rankogram():
- new argument 'nchar.trts' to print abbreviated treatment names
-
rankogram():
- new list elements 'cumrank.matrix.fixed' and 'cumrank.matrix.random' with cumulative ranking probabilites
- new argument 'cumulative.rankprob' to show cumulative ranking probabilites
- new argument 'trts' to specify subset of treatments
-
plot.rankogram():
- new argument 'pooled' to select results from fixed effect or random effects model
- new argument 'trts' to specify subset of treatments
- new argument 'sort' to specify order of treatments
- new argument 'cumulative.rankprob' to show cumulative ranking probabilities
-
print.rankogram():
- new argument 'cumulative.rankprob' to show cumulative ranking probabilites
-
netrank():
- new arguments 'fixed' and 'random'
- new list elements 'fixed' and 'random'
-
netsplit():
- new argument 'order' to specify order in comparisons; see help page of funnel.netmeta()
-
forest.netsplit():
- print I2 from pairwise comparisons if argument direct = TRUE
-
forest.netsplit(), print.netsplit():
- new argument 'only.reference' to only print comparisons with reference group
- new argument 'sortvar' to sort comparisons
-
pairwise():
- keep all variables from original dataset if variable is missing for one group but not the other (so far, only the first variable was kept)
-
netcomb():
- new argument 'nchar.comps' to abbreviate component names
-
discomb(), print.netcomb(), print.summary.netcomb():
- new argument 'nchar.comps' replaces argument 'nchar.trts'
-
New auxiliary function comps() to create unique comparison labels with abbreviated treatment names
-
netmeta():
- new list elements 'seTE.adj.fixed' and 'seTE.adj.random with adjusted standard errors under fixed effect and random effects model (content of 'seTE.adj.fixed' is identical to the previously existing element 'seTE.adj')
- new list elements 'H.matrix.fixed' (replacing list element 'H.matrix') and 'H.matrix.random'
- new list elements 'Q.direct', 'tau2.direct', 'tau.direct' and 'I2.direct' with information on the between-study heterogeneity of direct comparisons
-
netcomb(), discomb():
- new list elements 'L.matrix.fixed', 'Lplus.matrix.fixed', 'H.matrix.fixed', 'L.matrix.random', 'Lplus.matrix.random' and 'H.matrix.random'
-
compsplit():
- remove leading and trailing blanks
-
setref():
- argument 'reference.group' can be a vector instead of a single value
-
nma.additive():
- new list elements 'L.matrix', 'Lplus.matrix' and 'H.matrix'
-
New internal function hatmatrix.aggr() to calculate the aggregated hat matrix
-
Internal function contribution.matrix() moved to contribution.matrix.tpapak()
-
New internal functions contribution.matrix.davies()
-
New internal function compos() to abbreviate component names
-
New internal function createC.full() to create full C matrix for all k-fold combinations of n components
-
New internal function charfac()
-
New wrapper function contribution.matrix()
-
New argument 'aggr' in createB() to calculate aggregated B matrix
-
Theodoros Papakonstantinou [email protected] is a new co-author of the R package netmeta
-
Rankograms added
-
Surface under the cumulative ranking (SUCRA) can be calculated using resampling methods
-
Method by Papakonstantinou et al. (2018) to estimate the contribution of studies to network meta-analysis implemented
- netgraph.netmeta():
- use of arguments seq = "optimal" and srt.labels = "orthogonal" resulted in wrong rotation of treatment labels
-
New functions rankogram(), print.rankogram() and plot.rankogram() for rankograms
-
New functions netcontrib() and print.netcontrib() to calculate network contributions
-
netrank():
- new argument 'method' to choose between P-scores and SUCRAs
- can be used with an R object created with rankogram()
-
forest.netmeta():
- argument 'digits.Pscore' renamed to 'digits.prop' (as this argument is also used for SUCRAs)
- new argument 'nsim' to specify number of simulations for SUCRAs
-
netgraph.netmeta():
- by default, do not mark multi-arm studies (argument multiarm = FALSE)
- by default, use inverse standard error of random effects estimates for argument 'thickness' if random effects network meta-analysis was conducted
-
netsplit(), forest.netsplit():
- new option "reference.only" for argument 'show'
-
discomb(), netcomb():
- new check for unidentifiable components implemented
- new argument 'details.chkident' to print more details on unidentifiable components
-
Restricted maximum likelihood and maximum likelihood estimator for between-study heterogeneity implemented by calling rma.mv() from R package metafor internally
-
R function pairwise() can be used to generate reduced data set with basic comparisons Rücker & Schwarzer (2014)
-
R function discomb() can be used with an R object created with pairwise()
-
netmeta():
- use of ginv() instead of solve() to calculate pseudo inverse of Laplace matrix resulted in wrong results for some extreme network structures (bug was introduced in netmeta, version 1.3-0)
-
netgraph.netmeta():
- highlighting more than one comparison (argument 'highlight') resulted in an error if argument 'col.highlight' was not of same length
-
netmeta():
- new argument 'method.tau' to select estimation method for between-study variance
- new arguments 'sd1', 'sd2', 'time1', and 'time2' used to calculate variance-covariance matrix for REML and ML estimator of between-study heterogeneity
- do not calculate leverages for multi-arm studies
-
netconnection():
- first argument can be of class 'pairwise'
-
pairwise():
- new arguments 'reference.group' and 'keep.all.comparisons'
- first argument can be of class 'pairwise'
-
netgraph.netconnection():
- print subnetworks in different colors
-
forest.netmeta():
- new argument 'equal.size' to determine whether square size should be equal or proportional to precision of estimates
-
forest.netbind(), forest.netsplit():
- new default for argument 'equal.size', i.e., square sizes are equal
-
forest.netbind():
- new argument 'subset.treatments' to select treatments shown in forest plot
-
netmeasures():
- return direct evidence proportion for single design with two treatments
-
netheat():
- all designs are shown in net heat plot by default
-
New internal function invmat() to calculate inverse of matrix
-
New internal function calcV() to calculate variance-covariance matrix used as input to rma.mv()
-
nma.ruecker(), multiarm():
- use solve() instead of ginv() to calculate inverse of matrix L
-
netmeta():
- new list element 'comparisons' with information on direct comparisons
-
netconnection():
- new list elements 'comparisons' and 'subnet.comparisons' with information on direct comparisons
-
netimpact():
- consider values for arguments 'tol.multiarm' and 'tol.multiarm.se' from network meta-analysis object
-
nma.krahn():
- new argument 'reference.group' to specify the reference group
-
Treatment labels can be rotated in network graphs
-
Additional checks whether net heat plot is feasible
-
Calculate direct evidence proportion and indirect treatment estimates for network meta-analyses created with netmetabin()
-
Network graph for objects created with netconnection(), netcomb() or discomb()
-
In summaries, print z- and p-values for network estimates if a reference group is defined
-
netmetabin():
- not overall heterogeneity / inconsistency statistic calculated for Mantel-Haenszel method, but, the overall inconsistency statistic (treatment effects are aggregated within designs)
-
decomp.design(), netheat():
- do not conduct decomposition of designs for objects created with netmetabin(); reported decomposition and net heat plot referred to reanalysis using netmeta()
-
netmeasures():
- works for network meta-analyses created with netmetabin(); reported results referred to reanalysis using netmeta()
-
netsplit():
- SIDDE method works for network meta-analysis created without argument 'data' or empty networks after dropping a design
-
print.summary.netmeta():
- output states "test of heterogeneity" for a single design and "test of inconsistency" for Mantel-Haenszel method
-
netrank():
- can be used with network meta-analysis object created with netcomb()
-
netmeta():
- new argument 'small.values' passed on to netrank(), forest.netmeta() and netposet()
-
netgraph.netmeta():
- new argument 'srt.labels' to rotate treatment labels
-
plot.netrank():
- get rid of warnings 'Undefined global functions or variables'
-
netbind():
- argument '...' can be a single list of network meta-analysis objects
-
print.netmeta():
- new arguments 'truncate' and 'text.truncate' to only show selection of individual study results (useful for very long printouts or to only show individual results of multi-arm studies))
- print z- and p-values for tests of overall effect against a reference group (argument 'reference.group')
-
print.netconnection():
- new argument 'distance' in order to print the distance matrix
- by default, do not print the distance matrix
-
netsplit():
- new arguments 'comb.fixed', 'comb.random' and 'backtransf'
-
Rename list elements starting with 'zval.' to 'statistic.'
-
netcomb():
- export covariance matrices 'Cov.fixed' and 'Cov.random'
-
netmeta(), netcomb():
- export study design for each pairwise comparison (list element 'design')
-
discomb():
- export study designs (list element 'design'), list of designs ('design') and number of designs ('d')
-
Argument 'single' renamed to 'length' in calls of chkchar(), chkcolor(), chklevel() and chknumeric()
-
New internal function is.zero() to determine whether a small number is essentially zero (i.e., whether abs(x) < 10 * .Machine$double.eps)
-
New internal function updateversion() to update older netmeta objects
-
New internal function designs() to determine study designs
-
New internal function netheat-internal() with auxiliary functions for netheat()
-
nma.ruecker(), nma.additive():
- use ginv() to calculate inverse of matrix L
- set small numbers which are essentially zero to zero in matrix Lstar
-
Function netimpact() can be used with network meta-analysis objects created with netmetabin()
-
No warning is printed that treatments within comparisons have been re-sorted in increasing order (which has been rather a note than a warning)
-
netmetabin():
- bug fix for studies with 0 events and 0 participants
-
discomb():
- return standard errors of individual studies in correct order (list element 'seTE')
-
netbind():
- function can be used with network meta-analysis objects created with netmetabin()
-
as.data.frame.netmeta():
- correct printout if number of studies is equal to the number of treatments to the power of 2
-
summary.netmeta() exported
-
netmeta(), discomb():
- do not print a warning / note that treatments within comparisons have been re-sorted in increasing order
- check whether all studies provide missing estimates and standard errors (and stop execution with an informative error message)
-
netmeta(), netcomb(), discomb():
- export the design matrix (new list element 'X.matrix')
-
discomb():
- export the number of subnetworks
-
forest.netsplit():
- print an informative warning (instead of an obscure error message) if no comparison in the network provides the requested combination of direct and indirect evidence
-
Use Markdown for NEWS
- prepare():
- call metagen() with argument 'method.tau.ci = ""' to suppress calculation of confidence interval for tau2
-
In multi-arm studies, negative weights (resulting from slightly inconsistent standard errors) contributing less than 0.1% to the weight of a study are set to 0
-
Separate consistency tolerances can be specified for treatment estimates and standard errors (which are consistent by design in multi-arm studies, however, can be inconsistent due to rounding of treatment estimates and standard errors)
-
New default for consistency tolerance: 0.001 instead of 0.0005
-
Print tau in addition to tau2 in outputs
-
Print confidence interval for I2 in outputs
-
netmeta(), discomb():
- check for numeric values in arguments 'TE' and 'seTE'
- new argument 'tol.multiarm.se' to check standard errors in multi-arm studies
-
netmetabin():
- check for numeric values in arguments 'event1', 'n1', 'event2', and 'n2'
- new argument 'tol.multiarm.se' to check standard errors in multi-arm studies
-
print.summary.netmeta(), print.summary.netcomb():
- new argument 'digits.tau' to specify number of digits for tau
- new arguments 'text.tau2', 'text.tau', and 'text.I2' to change text printed to identify respective heterogeneity measure
-
Revision of help page examples to reduce runtime below 5 seconds (CRAN requirement)
-
multiarm():
- negative weights contributing less than 0.1% to the weight of a study are set to 0
-
chkmultiarm():
- use same order of arguments as in netmeta()
- new argument 'tol.multiarm.se' to check standard errors
-
nma.ruecker(), nma.additive():
- return lower and upper confidence limits for I2
-
New functions netimpact(), netgraph.netimpact(), print.netimpact() to measure the impact of individual studies to network estimates
-
New function plot.netrank() to produce image plot of P-scores
-
Equivalence limits can be added to forest plots
-
Use roxygen2 for development of R package netmeta
-
netmeta():
- no error if argument 'studlab' is missing
- tackle numerical problems with zero treatment arm variances - actually by changes in internal function multiarm()
- calculate the correct number of patients and events for each treatment arm in networks with multi-arm studies
-
netmetabin():
- only drop single treatment arms without any events in multi-arm studies instead of the complete design (which is the correct behaviour only for two-arm studies)
- keep the original design for multi-arm studies if a single treatment arm without any events has been dropped, e.g., the design X:Y:Z is not changed to X:Z if no events were observed in treatment arm Y in any multi-arm study
- no error if argument 'event1' is not an R object created with pairwise() and argument 'data' is not used
- no error in printing of network meta-analysis object if argument 'event1' is not an R object created with pairwise()
- calculate the correct number of patients and events for each treatment arm in networks with multi-arm studies
-
netgraph():
- argument 'seq' equal to "optimal" works for a single design
- multi-arm studies are highlighted if argument 'labels' is used
- comparisons defined by argument 'highlight' are marked in the network graph if argument 'labels' is used
-
pairwise():
- no error if function is used without argument 'data'
-
netgraph() is a generic function and original function netgraph() renamed to netgraph.netmeta()
-
netgraph.netmeta():
- new argument 'bg.points'
- new argument 'scale.highlight' which replaces argument 'lwd.highlight' (which actually was ignored)
- arguments 'col.highlight' and 'scale.highlight' can be vectors with same length as argument 'highlight'
- print highlighted comparisons in the background of the graph
-
forest.netmeta():
- new argument 'labels' to provide treatment names - similar to netgraph()
- labels set automatically for columns "pscore", "k" and "prop.direct" in argument 'leftcols' and 'rightcols'
-
multiarm():
- use ginv() to calculate inverse of matrix Lt
- set very small negative values in matrix W equal to zero
- object k instead of n denotes number of treatment arms (same notation as Rücker & Schwarzer, 2014)
- more liberal cutpoint to set negative variances to zero
-
chkmultiarm():
- more liberal check for negative variances
-
new auxiliary internal functions for forest plots
- Revision of help page examples
- to reflect changes in netmeta, versions 0.9-8 and 1.0-0
- to reduce runtime below 5 seconds (CRAN requirement)
-
Orestis Efthimiou [email protected] is a new co-author of the R package netmeta
-
New function netmetabin() for network meta-analysis of binary data using the Mantel-Haenszel method or the non-central hypergeometric distribution
-
New function funnel.netmeta() for 'comparison-adjusted' funnel plots
-
New function forest.netcomb() for forest plots of additive network meta-analysis
-
New functions netbind(), forest.netbind(), and print.netbind() to combine network meta-analysis objects and to generate a forest plot with results of several network meta-analyses
-
Separate Indirect from Direct Design Evidence (SIDDE) method implemented in netsplit()
-
All network comparisons can be included in a forest plot
-
Circular network graphs with minimal number of crossings available
-
Default setting for levels of confidence intervals can be specified using R function settings.meta(); the default is still 0.95, i.e., 95% confidence intervals are computed
-
New datasets: Gurusamy2011 and Dong2013
-
netmeta():
- new list elements:
- 'k.trts' with number of studies evaluating a treatment
- 'n.trts' with number of observations receiving a treatment
- 'events.trts' with number of events observed for a treatment
- 'n.matrix' with number of observations in direct comparisons
- 'events.matrix' with number of events in direct comparisons
- 'designs' with treatment designs
- correct entry for list element 'designs' for single design
- only print information on studies with missing treatment effect or standard error if argument 'warn' is TRUE
- new list elements:
-
pairwise():
- keep original order of studies
- arguments 'event' and 'n' can be used for generic meta-analysis method based on arguments 'TE' and 'seTE'
- argument 'n' can be used for meta-analysis with count outcomes (based on arguments 'event' and 'time')
- infinite treatment estimates and standard errors set to NA
- by default, do not print warnings if comparisons will not be included in network meta-analysis
-
netsplit():
- new argument 'method' to choose approach to split direct and indirect evidence
-
forest.netmeta():
- argument 'reference.group' can be a vector in order to include several / all network comparisons in a forest plot
- (invisibly) returns a data frame with information used to produce the forest plot
-
forest.netsplit() and print.netsplit():
- argument 'showall' replaced with 'show' (see help pages)
-
forest.netsplit():
- show prediction intervals as colored bars
- forest plot with layout 'subgroups by comparisons': omit treatment estimates in rows with prediction intervals if network estimates are also shown
-
netcomb() and discomb():
- argument 'seq.components' replaced with 'seq.comps'
-
discomb():
- arguments 'reference.group' and 'baseline.reference'
-
netposet():
- allow for ties in rankings
-
netsplit():
- do not reorder a treatment comparison if reference treatment (argument 'reference.group') is part of a combined treatment, e.g., for reference.group = "A" and treatment comparison "A + B" vs "C", the comparison will not be reordered as "C" vs "A + B"
-
forest.netsplit():
- show correct prediction intervals
-
netgraph():
- arguments 'iterate' and 'allfigures' ignored if argument 'seq' is equal to "optimal"
-
netsplit():
- consider argument 'digits' for treatment estimates, i.e., do not always round to two digits
-
netmeta():
- keep original order of studies in list element 'data'
-
netcomb() and discomb():
- check if argument 'sep.components' is a single character
- similar list elements as for R objects created with netmeta(); especially matrices with all network estimates added to output, see, for example, new list elements 'TE.fixed' and 'TE.random'
-
Internal function nma.additive():
- calculate matrices with all network estimates
-
netleague() is a generic function
-
Help pages:
- examples added for forest.netsplit()
-
Main function netmeta():
- by default, results for fixed effects and random effects network meta-analysis are reported (only results for fixed effects model were reported in older versions)
- keep dataset used to conduct network meta-analysis
- number of events and number of observations can be provided (and are considered from R objects created with pairwise() function)
-
Function pairwise():
- all variables from the original dataset are kept in the output dataset
-
League tables
- show the direct treatment estimates from pairwise comparisons in the upper triangle if the table is created for a single network meta-analysis
- report pairwise comparisons of the treatment in the row versus the treatment in the column in the lower triangle and column versus row in the upper triangle (common presentation for network meta-analyses)
-
Network graphs are much more flexible, e.g., color of lines / edges can be specified for each direct pairwise comparison
-
New function discomb() for disconnected networks sharing at least one common treatment component to apply the additive network model for combinations of treatments
-
Treatment separator (argument 'sep.trts') can be special character from regular expressions
-
Between-study variance tau-squared is reported as NA instead of 0 in networks without heterogeneity / inconsistency
-
netmeta():
- settings for printing of results are defined by settings.meta(), i.e., new default is to print results for both fixed effects and random effects model
- new arguments 'event1', 'event2', 'n1', and 'n2' to provide number of events and observations for the two treatment groups
- new argument 'keepdata' to choose whether original dataset should be part of network meta-analysis object
- new list element 'data' to keep dataset used to conduct network meta-analysis (if argument 'keepdata' is TRUE)
-
netgraph():
- argument 'col' can be a matrix, e.g., created with netmatrix(), to specify the color of lines / edges for each direct pairwise comparison
- arguments 'col.points', 'cex.points', and 'pch.points' can be used to specify the color, size, and plotting symbol for each treatment separately
- new argument 'adj' to specify the adjustment of treatment labels
- new argument 'pos.number.of.studies' to specify the position of the number of treatments on the edges
- (invisibly) returns a list with information on nodes and edges (position, color, etc.) used to produce the network graph
-
pairwise():
- print correct labels in error message for studies with duplicate treatments
- all variables from the original dataset are kept in the output dataset
- print.netmeta():
- print uniquely abbreviated treatment names
-
netconnection() and print.netconnection():
- new argument 'sep.trts' to print abbreviated treatment names
-
netleague():
- 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 'text.NA' to label missing values, i.e., for pairwise comparisons without direct evidence
- new argument 'direct' to print direct treatment estimates (if argument 'y' is not missing)
-
print.netsplit():
- new argument 'legend' to suppress printing of the legend
-
print.summary.netcomb():
- new arguments 'digits.tau2' and 'digits.I2'
-
New auxiliary function netmatrix() to create a matrix with additional information for pairwise comparisons (e.g., risk of bias assessment)
-
netmeta():
- list elements 'P.fixed' and 'P.random' contained wrong values for network meta-analyses with a single design which resulted in an error using forest.netmeta()
-
netcomb():
- use correct between-study variance in random effects additive network meta-analysis model
- use correct order of studies to calculate treatment estimates
- can be used with single pairwise comparison
-
print.summary.netcomb():
- use correct (abbreviated) names for treatment components
-
new internal functions compmatch() and compsplit() for argument 'sep.trts' taking special character from regular expression into account, e.g., sep.trts = "."
-
new internal functions bySummary() which is used in netmeta(), netmatrix(), and pairwise()
-
createC() can be used with netconnection() objects (for disconnected networks)
-
netcomb.netmeta() has been renamed to netcomb()
-
netmeta():
- report I2 as value between 0 and 1 (instead of 0 and 100)
- new list element 'trts' (character vector with treatment names)
-
Internal function nma.ruecker():
- use internal function isquared() from package meta to calculate I2
-
Internal function nma.additive():
- calcuate between-study variance tau2 and heterogeneity statistic I2
-
Internal function prcombs():
- new argument 'seq' to order treatments
-
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
-
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()
-
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)
-
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
-
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
-
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
-
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
-
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
-
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
-
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(...)
-
netsplit() used wrong comparison labels if argument 'reference.group' was used in netmeta()
-
netmeasures() ignores value of argument 'reference.group' in netmeta object
-
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)
-
For Hasse diagrams, hasseDiagram and grid added to Suggests
-
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
-
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 studies, calculate pooled standard deviation in pairwise() if means and standard deviations are provided and summary measure is equal to "SMD"
-
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
- R package rgl moved from Imports to Suggests as
- 3-D network plots are not essential for network meta-analysis
- installation of netmeta breaks under macOS if XQuartz is not available
- Help page of netgraph() updated (information on rgl package)
- Use chkclass() from meta package to check for class membership
-
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
-
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()
-
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
-
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)
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R package rgl added to Imports (for 3-D plots)
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New dataset Woods2010 (use long format in pairwise function)
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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)
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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
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Function stress (used internally):
- extension to generate 3-D network plots
- use netdistance function instead of nodedist
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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
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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
-
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
-
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)
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Function netmeta:
- implement a general check for correct number of comparisons for multi-arm studies
- use setseq() to check and set value of argument 'seq'
- use setref() 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.
-
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
-
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
-
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
-
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)
- Function netmeasures:
- bug fix using correct formula to calculate direct evidence proportion (variance instead of standard error)
-
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
-
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
-
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
- First version released on CRAN