Posterior summaries of model parameters in stan_nma objects may be produced
using the summary() method and plotted with the plot() method. NOTE: To
produce relative effects, absolute predictions, or posterior ranks, see
relative_effects(), predict.stan_nma(), posterior_ranks(),
posterior_rank_probs().
Arguments
- ...
Additional arguments passed on to other methods
- pars, include
See
rstan::extract()- probs
Numeric vector of specifying quantiles of interest, default
c(0.025, 0.25, 0.5, 0.75, 0.975)- x, object
A
stan_nmaobject- stat
Character string specifying the
ggdistplot stat to use, default"pointinterval"- orientation
Whether the
ggdistgeom is drawn horizontally ("horizontal") or vertically ("vertical"), default"horizontal"- ref_line
Numeric vector of positions for reference lines, by default no reference lines are drawn
- summary
Logical, calculate posterior summaries? Default
TRUE.
Value
A nma_summary object
Details
The plot() method is a shortcut for plot(summary(stan_nma)). For
details of plotting options, see plot.nma_summary().
Examples
## Smoking cessation
# \donttest{
# Run smoking RE NMA example if not already available
if (!exists("smk_fit_RE")) example("example_smk_re", run.donttest = TRUE)
# }
# \donttest{
# Summary and plot of all model parameters
summary(smk_fit_RE)
#> mean sd 2.5% 25% 50% 75% 97.5%
#> mu[1] -2.79 0.33 -3.46 -3.00 -2.78 -2.56 -2.16
#> mu[2] -2.58 0.77 -4.19 -3.06 -2.57 -2.08 -1.12
#> mu[3] -2.14 0.12 -2.39 -2.22 -2.14 -2.06 -1.92
#> mu[4] -4.05 0.56 -5.22 -4.41 -4.03 -3.66 -3.03
#> mu[5] -2.15 0.14 -2.43 -2.25 -2.15 -2.06 -1.89
#> mu[6] -3.42 0.73 -5.07 -3.85 -3.36 -2.92 -2.16
#> mu[7] -3.02 0.44 -3.96 -3.29 -2.99 -2.71 -2.25
#> mu[8] -2.72 0.62 -4.06 -3.11 -2.68 -2.29 -1.63
#> mu[9] -1.85 0.43 -2.72 -2.11 -1.84 -1.55 -1.06
#> mu[10] -2.08 0.12 -2.32 -2.16 -2.08 -2.00 -1.85
#> mu[11] -3.62 0.23 -4.10 -3.77 -3.61 -3.46 -3.20
#> mu[12] -2.22 0.13 -2.48 -2.30 -2.22 -2.13 -1.97
#> mu[13] -2.69 0.44 -3.58 -2.98 -2.67 -2.39 -1.87
#> mu[14] -2.41 0.23 -2.88 -2.57 -2.40 -2.26 -1.97
#> mu[15] -2.69 0.73 -4.30 -3.12 -2.63 -2.18 -1.43
#> mu[16] -2.61 0.34 -3.33 -2.84 -2.60 -2.38 -1.99
#> mu[17] -2.38 0.11 -2.60 -2.45 -2.37 -2.30 -2.17
#> mu[18] -2.57 0.28 -3.14 -2.74 -2.56 -2.38 -2.06
#> mu[19] -1.90 0.12 -2.14 -1.99 -1.90 -1.82 -1.68
#> mu[20] -2.80 0.12 -3.05 -2.88 -2.80 -2.72 -2.57
#> mu[21] -1.11 0.80 -2.69 -1.62 -1.10 -0.60 0.47
#> mu[22] -2.41 0.85 -4.09 -2.96 -2.39 -1.86 -0.80
#> mu[23] -2.32 0.80 -3.87 -2.85 -2.31 -1.79 -0.74
#> mu[24] -2.82 0.84 -4.55 -3.36 -2.81 -2.29 -1.14
#> d[Group counselling] 1.11 0.43 0.28 0.83 1.09 1.38 1.96
#> d[Individual counselling] 0.85 0.24 0.38 0.69 0.85 1.00 1.34
#> d[Self-help] 0.50 0.40 -0.30 0.25 0.50 0.76 1.28
#> tau 0.83 0.18 0.54 0.70 0.81 0.93 1.23
#> delta[1: Individual counselling] 1.07 0.39 0.31 0.81 1.07 1.33 1.86
#> delta[1: Group counselling] 0.37 0.43 -0.50 0.09 0.37 0.65 1.23
#> delta[2: Self-help] 0.68 0.79 -0.82 0.17 0.66 1.16 2.27
#> delta[2: Individual counselling] 0.77 0.77 -0.72 0.27 0.76 1.25 2.35
#> delta[2: Group counselling] 1.00 0.78 -0.49 0.49 0.98 1.49 2.60
#> delta[3: Individual counselling] 2.17 0.14 1.89 2.07 2.17 2.26 2.44
#> delta[4: Individual counselling] 0.90 0.58 -0.21 0.52 0.89 1.27 2.06
#> delta[5: Individual counselling] 0.44 0.15 0.15 0.33 0.44 0.54 0.74
#> delta[6: Individual counselling] 1.71 0.72 0.50 1.20 1.65 2.14 3.35
#> delta[7: Individual counselling] 2.13 0.49 1.26 1.80 2.11 2.44 3.17
#> delta[8: Individual counselling] 1.66 0.63 0.51 1.23 1.63 2.06 3.01
#> delta[9: Individual counselling] 0.60 0.47 -0.31 0.27 0.60 0.90 1.53
#> delta[10: Self-help] 0.00 0.17 -0.32 -0.11 0.00 0.11 0.34
#> delta[11: Self-help] 0.41 0.31 -0.22 0.20 0.41 0.61 1.02
#> delta[12: Individual counselling] 0.41 0.17 0.09 0.30 0.41 0.53 0.74
#> delta[13: Individual counselling] 0.40 0.50 -0.55 0.07 0.40 0.72 1.43
#> delta[14: Individual counselling] 0.63 0.29 0.05 0.43 0.63 0.82 1.21
#> delta[15: Group counselling] 2.15 0.75 0.81 1.62 2.10 2.61 3.77
#> delta[16: Self-help] 0.65 0.40 -0.10 0.38 0.65 0.91 1.43
#> delta[17: Individual counselling] 0.55 0.14 0.28 0.45 0.55 0.65 0.84
#> delta[18: Individual counselling] 0.03 0.31 -0.58 -0.17 0.03 0.24 0.68
#> delta[19: Individual counselling] -0.19 0.17 -0.52 -0.31 -0.19 -0.07 0.14
#> delta[20: Individual counselling] 0.08 0.19 -0.30 -0.05 0.08 0.20 0.43
#> delta[21: Self-help] 0.68 0.80 -0.89 0.18 0.66 1.19 2.26
#> delta[21: Individual counselling] 0.63 0.78 -0.95 0.14 0.63 1.14 2.19
#> delta[22: Self-help] 0.32 0.84 -1.33 -0.23 0.32 0.86 2.02
#> delta[22: Group counselling] 1.28 0.85 -0.30 0.74 1.26 1.82 2.99
#> delta[23: Individual counselling] 0.67 0.78 -0.91 0.17 0.67 1.18 2.16
#> delta[23: Group counselling] 1.28 0.79 -0.28 0.75 1.28 1.80 2.84
#> delta[24: Individual counselling] 1.07 0.82 -0.53 0.54 1.05 1.57 2.80
#> delta[24: Group counselling] 0.91 0.84 -0.76 0.36 0.91 1.46 2.59
#> Bulk_ESS Tail_ESS Rhat
#> mu[1] 5721 3121 1
#> mu[2] 2739 2354 1
#> mu[3] 7281 3087 1
#> mu[4] 4649 2750 1
#> mu[5] 6408 2986 1
#> mu[6] 3052 2287 1
#> mu[7] 4486 2888 1
#> mu[8] 4104 2933 1
#> mu[9] 5637 2874 1
#> mu[10] 7633 3017 1
#> mu[11] 6723 2840 1
#> mu[12] 7081 3186 1
#> mu[13] 4599 2805 1
#> mu[14] 4830 2956 1
#> mu[15] 3275 2521 1
#> mu[16] 5542 2995 1
#> mu[17] 7637 2637 1
#> mu[18] 5825 2592 1
#> mu[19] 8801 2983 1
#> mu[20] 7216 3235 1
#> mu[21] 3000 2832 1
#> mu[22] 2838 2694 1
#> mu[23] 3095 2901 1
#> mu[24] 3352 2569 1
#> d[Group counselling] 2243 2523 1
#> d[Individual counselling] 1190 2147 1
#> d[Self-help] 1897 2560 1
#> tau 1286 1830 1
#> delta[1: Individual counselling] 5647 3246 1
#> delta[1: Group counselling] 5616 3405 1
#> delta[2: Self-help] 2819 2736 1
#> delta[2: Individual counselling] 2848 2718 1
#> delta[2: Group counselling] 2821 2614 1
#> delta[3: Individual counselling] 5896 3387 1
#> delta[4: Individual counselling] 4151 3089 1
#> delta[5: Individual counselling] 6226 2954 1
#> delta[6: Individual counselling] 2700 2108 1
#> delta[7: Individual counselling] 3947 2899 1
#> delta[8: Individual counselling] 3738 2840 1
#> delta[9: Individual counselling] 5164 3128 1
#> delta[10: Self-help] 5594 3428 1
#> delta[11: Self-help] 5464 3345 1
#> delta[12: Individual counselling] 5747 3160 1
#> delta[13: Individual counselling] 4835 3334 1
#> delta[14: Individual counselling] 4971 2971 1
#> delta[15: Group counselling] 2563 2175 1
#> delta[16: Self-help] 4916 2763 1
#> delta[17: Individual counselling] 6046 2677 1
#> delta[18: Individual counselling] 5402 3004 1
#> delta[19: Individual counselling] 6111 3427 1
#> delta[20: Individual counselling] 6150 3577 1
#> delta[21: Self-help] 2917 2812 1
#> delta[21: Individual counselling] 2961 2740 1
#> delta[22: Self-help] 2938 2576 1
#> delta[22: Group counselling] 2739 2711 1
#> delta[23: Individual counselling] 3163 2744 1
#> delta[23: Group counselling] 3104 3138 1
#> delta[24: Individual counselling] 3559 2694 1
#> delta[24: Group counselling] 3664 2935 1
plot(smk_fit_RE)
# Summary and plot of heterogeneity tau only
summary(smk_fit_RE, pars = "tau")
#> mean sd 2.5% 25% 50% 75% 97.5% Bulk_ESS Tail_ESS Rhat
#> tau 0.83 0.18 0.54 0.7 0.81 0.93 1.23 1286 1830 1
plot(smk_fit_RE, pars = "tau")
# Customising plot output
plot(smk_fit_RE,
pars = c("d", "tau"),
stat = "halfeye",
ref_line = 0)
# }