Recent Releases of rnmamod
rnmamod - v0.5.0
- Replaced mcmcplots with coda R package.
- Function plotstudydissimilarities:
- Presents the range of Gower's dissimilarity values for each study in the network, as well as their between- and within-comparison dissimilarities (based on the function comp_clustering).
- Function studyperccontrib:
- Calculates the percentage contributions of each study to every possible pairwise comparison in the investigated network and returns a data-frame. Study percentage contributions are based on Donegan et al., (2018) doi:10.1002/jrsm.1292
- Function covarcontributionplot:
- Returns a scatter plot of the study percentage contributions against the values of a continuous study-level covariate for the treatment effects of the basic parameters, functional parameters or both (based on the function studyperccontrib).
- Function forestplot_juxtapose:
- Provides a forest plot juxtaposing several NMA models (via the functions run_model and run_metareg) based on posterior treatment effects (including predictions) of all treatments versus a selected comparator and a forest plot with the corresponding SUCRA values.
- Function _heterdensityplot _:
- Creates the density plot of two prior distributions for the between-study variance (log-normal and location-scale t distributions) or between-study standard deviation (half-normal distribution). This plot aids in deciding how to define the argument heterprior_ in run_model to run random-effects network meta-analysis.
- Function inconsistencyvarianceprior:
- Calculates the hyperparameters of the log-normal distribution and location-scale t-distribution of the inconsistency variance in the log-odds ratio and standardised mean difference scales, respectively, based on selected empirical distributions for the between-study variance proposed by Turner et al. (2015) doi:10.1002/sim.6381 and Rhodes et al. (2015) doi:10.1016/j.jclinepi.2014.08.012. Calculations are based on Law et al., (2016) doi:10.1186/s12874-016-0184-5.
- Function tabletau2prior:
- Returns a table with the hyperparameters of the predictive distributions for the between-study variance developed by Turner et al. (2015) doi:10.1002/sim.6381 and Rhodes et al. (2015) doi:10.1016/j.jclinepi.2014.08.012. This table aids in selecting the hyperparameters for the function heterogeneityparamprior when considering an informative prior distribution for the between-study variance parameter to conduct random-effects network meta-analysis.
- R
Published by LoukiaSpin about 1 year ago
rnmamod - v0.4.0
- Function comp_clustering:
- Performs quantitative evaluation of the transitivity assumption using inter-trial dissimilarities for various trial-level aggregate participant and methodological characteristics that may act as effect modifiers.
- Function dendro_heatmap:
- Returns the dendrogram with integrated heatmap of the clustered comparisons and trials based on hierarchical agglomerative clustering (performed using the function comp_clustering). The R packages heatmaply and dendextend have been used.
- Function distr_characteristics:
- It returns violin plots with integrated box plots and dots for quantitative characteristics, and stacked barplots for qualitative characteristics across the observed treatment comparisons. The function can also be used to illustrate the distribution of the characteristics across the clusters defined from comp_clustering.
- Function miss_characteristics:
- It returns various plots to visualise the missing cases in the characteristics across trials and treatment comparisons.
- Function gower_distance:
- It returns the N-by-N matrix on Gower's dissimilarity coefficient for all pairs of N trials in a network.
- Function mcmc_diagnostics:
- returns a bar plot on the ratio of MCMC error to the posterior standard deviation and a bar plot on the Gelman-Rubin R diagnostic. Green bars indicate ratio less than 0.05 and R less than 1.10; otherwise, the bars are red.
- Functions baseline_model, run_metareg, run_model,
run_nodesplit, run_sensitivity, runseriesmeta, and run_ume:
- The corresponding models are updated until convergence via the autojags function of the R package R2jags.
- The argument inits has been added to allow the user define the initial values for the parameters, following the documentation of the jags function in the R package R2jags.
- Function describe_network:
- It reports only the tables with the evidence base information on one outcome. The network plot is not reported (see and use netplot, instead).
- Function netplot:
- Self-created function using the R package igraph. This function creates the network plot.
- R
Published by LoukiaSpin over 2 years ago
rnmamod -
- Function baseline_model:
- processes the elements in the argument baserisk_ for a fixed, random or predicted baseline model and passes the output to run_model or run_metareg to obtain the absolute risks for all interventions.
- when a predicted baseline model is conducted, it returns a forest plot with the trial-specific and summary probability of an event for the selected reference intervention.
- Function forestplot_metareg:
- upgraded plot that presents two forest plots side-by-side: (i) one on estimation and prediction from network meta-analysis and network meta-regression for a selected comparator intervention (allows comparison of these two analyses), and (ii) one on SUCRA values from both analyses. Both forest plots present results from network meta-regression for a selected value of the investigated covariate.
- Function leaguetableabsolute_user:
- (only for binary outcome) yields the same graph with the leaguetableabsolute function, but the input is not rnmamod object: the user defines the input and it includes the summary effect and corresponding (credible or confidence) interval for comparisons with a reference intervention. These results stem from a network meta-analysis conducted using another R-package or statistical software.
- Function robustnessindexuser:
- calculates the robustness index for a sensitivity analysis performed using the R-package netmeta or metafor. The user defines the input and the function returns the robustness index. This function returns the same output with the robustness_index function.
- Function trans_quality:
- classifies a systematic review with multiple interventions as having low, unclear or high quality regarding the transitivity evaluation based on five quality criteria.
- R
Published by LoukiaSpin over 3 years ago
rnmamod -
- Typos and links (for functions and packages) in the documentation are corrected.
- Function run_model:
- allows the user to define the reference intervention of the network via the argument ref;
- (only for binary outcome) estimates the absolute risks for all non-reference interventions using a selected baseline risk for the reference intervention (argument baserisk_);
- (only for binary outcome) estimates the relative risks and risk difference as functions of the estimated absolute risks.
- Function leaguetableabsolute:
- (only for binary outcome) it presents the absolute risks per 1000 participants in the main diagonal, the odds ratio on the upper off-diagonals, and the risk difference per 1000 participants in the lower off-diagonal;
- allow the user to select the interventions to present via the argument show (ideal for very large networks that make the league table cluttered).
- Functions league_heatmap and leagueheatmappred:
- allow the user to select the interventions to present via the argument show (ideal for very large networks that make the league table cluttered);
- allow the user to illustrate the results of two outcomes for the same model (i.e. via run_model or run_metareg) or the results of two models on the same outcome (applicable for: (i) run_model versus run_metareg, and (ii) run_model versus runseriesmeta).
- Functions seriesmetaplot and nodesplit_plot:
- present the extent of heterogeneity in the forest plot of tau using different colours for low, reasonable, fairly high, and fairly extreme tau (the classification has been suggested by Spiegelhalter et al., 2004; ISBN 0471499757).
- R
Published by LoukiaSpin over 4 years ago