Wrapper of the lavaan parameterEstimates() function for RICF and CGGM algorithms
parameterEstimates(fit, ...)A RICF or constrained GGM fitted model object.
Currently ignored.
A data.frame containing the estimated parameters
ricf1 <- SEMrun(sachs$graph, log(sachs$pkc), sachs$group, algo = "ricf")
#> RICF solver ended normally after 4 iterations
#>
#> deviance/df: 61.84434 srmr: 0.0700967
#>
#> Brown's combined P-value of node activation: 8.881784e-16
#>
#> Brown's combined P-value of node inhibition: 0.0004656197
#>
parameterEstimates(ricf1$fit)
#> lhs op rhs est
#> 1 Raf ~ group -0.467
#> 2 Mek ~ group 0.122
#> 3 Plcg ~ group 0.268
#> 4 PIP2 ~ group 0.110
#> 5 PIP3 ~ group -0.301
#> 6 Erk ~ group 0.179
#> 7 Akt ~ group 0.150
#> 8 PKA ~ group 0.290
#> 9 PKC ~ group 0.116
#> 10 P38 ~ group -0.062
#> 11 Jnk ~ group 0.333
#> 30 group ~~ group 1.000
#> 12 Mek ~ Raf 0.736
#> 13 Erk ~ Mek 0.016
#> 14 PIP2 ~ Plcg 0.199
#> 15 PKC ~ Plcg -0.010
#> 16 PKC ~ PIP2 0.029
#> 17 Plcg ~ PIP3 0.288
#> 18 PIP2 ~ PIP3 0.528
#> 19 Akt ~ PIP3 -0.023
#> 20 Raf ~ PKA 0.008
#> 21 Mek ~ PKA -0.017
#> 22 Erk ~ PKA 0.407
#> 23 Akt ~ PKA 0.507
#> 24 P38 ~ PKA 0.000
#> 25 Jnk ~ PKA -0.002
#> 26 Raf ~ PKC 0.007
#> 27 Mek ~ PKC -0.015
#> 28 P38 ~ PKC 0.652
#> 29 Jnk ~ PKC 0.096
#> 31 Raf ~~ Raf 0.785
#> 32 Mek ~~ Mek 0.524
#> 33 Plcg ~~ Plcg 0.892
#> 34 PIP2 ~~ PIP2 0.653
#> 35 PIP3 ~~ PIP3 0.909
#> 36 PKA ~~ PIP3 -0.016
#> 37 Erk ~~ Erk 0.762
#> 38 Akt ~~ Akt 0.672
#> 39 PKA ~~ PKA 0.916
#> 40 PKC ~~ PKC 0.986
#> 41 P38 ~~ P38 0.580
#> 42 Jnk ~~ Jnk 0.873
cggm1 <- SEMrun(sachs$graph, log(sachs$pkc), sachs$group, algo = "cggm")
#> DAG conversion : TRUE
#> GGM (de-biased nodewise L1) solver ended normally after 11 iterations
#>
#> deviance/df: 60.18925 srmr: 0.0703002
#>
#> Brown's combined P-value of node activation: 3.330669e-15
#>
#> Brown's combined P-value of node inhibition: 0.2568374
#>
parameterEstimates(cggm1$fit)
#> lhs op rhs est se z_test pvalue ci.lower ci.uppper
#> 1 PKA ~ group 0.290 0.023 12.720 0.000 0.245 0.334
#> 2 PIP3 ~ group -0.301 0.023 -13.278 0.000 -0.346 -0.257
#> 3 PKC ~ group 0.115 0.024 4.766 0.000 0.068 0.162
#> 6 Mek ~ group 0.120 0.020 5.929 0.000 0.080 0.159
#> 10 Raf ~ group -0.465 0.022 -21.032 0.000 -0.509 -0.422
#> 13 PIP2 ~ group 0.108 0.021 5.188 0.000 0.067 0.149
#> 16 Plcg ~ group 0.266 0.024 11.308 0.000 0.220 0.312
#> 18 Jnk ~ group 0.332 0.023 14.237 0.000 0.286 0.378
#> 21 P38 ~ group -0.061 0.019 -3.223 0.001 -0.099 -0.024
#> 24 Akt ~ group 0.149 0.021 7.040 0.000 0.108 0.191
#> 27 Erk ~ group 0.178 0.022 8.007 0.000 0.134 0.221
#> 4 PKC ~ PIP2 0.028 0.025 1.101 0.271 -0.022 0.077
#> 5 PKC ~ Plcg -0.008 0.025 -0.314 0.753 -0.058 0.042
#> 7 Mek ~ PKA -0.016 0.018 -0.884 0.376 -0.051 0.019
#> 8 Mek ~ PKC -0.014 0.017 -0.823 0.410 -0.048 0.020
#> 9 Mek ~ Raf 0.734 0.019 37.816 0.000 0.696 0.772
#> 11 Raf ~ PKA 0.007 0.022 0.303 0.762 -0.036 0.050
#> 12 Raf ~ PKC 0.006 0.021 0.297 0.767 -0.035 0.048
#> 14 PIP2 ~ PIP3 0.527 0.021 25.119 0.000 0.486 0.568
#> 15 PIP2 ~ Plcg 0.198 0.020 9.751 0.000 0.158 0.238
#> 17 Plcg ~ PIP3 0.286 0.024 12.159 0.000 0.240 0.332
#> 19 Jnk ~ PKA 0.000 0.023 -0.018 0.985 -0.046 0.045
#> 20 Jnk ~ PKC 0.095 0.022 4.245 0.000 0.051 0.139
#> 22 P38 ~ PKA 0.000 0.019 0.000 1.000 -0.037 0.037
#> 23 P38 ~ PKC 0.651 0.018 35.721 0.000 0.616 0.687
#> 25 Akt ~ PKA 0.506 0.020 24.844 0.000 0.466 0.546
#> 26 Akt ~ PIP3 -0.023 0.020 -1.112 0.266 -0.063 0.017
#> 28 Erk ~ PKA 0.406 0.022 18.741 0.000 0.364 0.449
#> 29 Erk ~ Mek 0.015 0.021 0.688 0.491 -0.027 0.056