diff --git a/articles/idopNetwork_vignette.html b/articles/idopNetwork_vignette.html index 9d42643..2244c5d 100644 --- a/articles/idopNetwork_vignette.html +++ b/articles/idopNetwork_vignette.html @@ -449,20 +449,30 @@

3.3 initial parameters#> number of iterations exceeded maximum of 1000 #> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : #> number of iterations exceeded maximum of 1000 +#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : +#> number of iterations exceeded maximum of 1000 +#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : +#> number of iterations exceeded maximum of 1000 +#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : +#> number of iterations exceeded maximum of 1000 +#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : +#> number of iterations exceeded maximum of 1000 +#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : +#> number of iterations exceeded maximum of 1000 #> $initial_cov_params #> [1] 0.50000 1.09618 #> #> $initial_mu_params -#> a b -#> [1,] 6.856174e+02 -3.235497 -#> [2,] 4.378423e+07 -11.252193 -#> [3,] 1.085234e+09 -12.807990 -#> [4,] 7.206028e-41 58.213660 +#> a b +#> [1,] 1.222931e+15 -21.7299294 +#> [2,] 2.241187e-35 50.4618037 +#> [3,] 1.275766e+01 -0.8462029 +#> [4,] 1.930699e+02 -3.6047139 #> #> $initial_probibality #> #> 1 2 3 4 -#> 0.03278689 0.36065574 0.26229508 0.34426230 +#> 0.24590164 0.27868852 0.06557377 0.40983607 #use kmeans to get initial centers tmp = kmeans(log10(df+1),4)$centers @@ -481,77 +491,71 @@

3.4 functional clustering (pow fun_clu(result1$original_data, k = 3, iter.max = 5) #> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : #> number of iterations exceeded maximum of 1000 -#> Error in nls(y ~ a * x^b, start = list(a = a, b = b), control = nls.control(maxiter = 1000, : -#> number of iterations exceeded maximum of 1000 -#> initial value 1225.809009 -#> iter 10 value 1131.213293 -#> final value 1125.868090 +#> initial value 1224.701250 +#> final value 1224.701250 #> converged #> #> iter = 1 -#> Log-Likelihood = 1125.868 -#> initial value 1118.632899 -#> iter 10 value 1115.215803 -#> iter 10 value 1115.215803 -#> iter 10 value 1115.215803 -#> final value 1115.215803 +#> Log-Likelihood = 1229.444 +#> initial value 1228.240624 +#> final value 1228.240624 #> converged #> #> iter = 2 -#> Log-Likelihood = 1115.216 -#> initial value 1113.154279 -#> final value 1112.161474 +#> Log-Likelihood = 1225.461 +#> initial value 1224.705979 +#> final value 1224.705979 #> converged #> #> iter = 3 -#> Log-Likelihood = 1112.161 -#> initial value 1111.441667 -#> final value 1111.183066 +#> Log-Likelihood = 1226.112 +#> initial value 1225.588016 +#> final value 1225.588016 #> converged #> #> iter = 4 -#> Log-Likelihood = 1111.183 -#> initial value 1110.923563 -#> final value 1110.833857 +#> Log-Likelihood = 1224.793 +#> initial value 1224.655751 +#> final value 1224.655751 #> converged #> #> iter = 5 -#> Log-Likelihood = 1110.834 -#> initial value 1110.730885 -#> final value 1110.694607 +#> Log-Likelihood = 1224.97 +#> initial value 1224.822485 +#> final value 1224.822485 #> converged #> #> iter = 6 -#> Log-Likelihood = 1110.695 +#> Log-Likelihood = 1227.894 #> $cluster_number #> [1] 3 #> #> $Log_likelihodd -#> [1] 1110.695 +#> [1] 1227.894 #> #> $AIC -#> [1] 2241.389 +#> [1] 2475.787 #> #> $BIC -#> [1] 2260.101 +#> [1] 2494.499 #> #> $cov_par -#> [1] 0.3550810 0.7415481 +#> [1] 0.500000 1.098059 #> #> $mu_par #> [,1] [,2] -#> [1,] 1.595896e+13 -19.044474 -#> [2,] 4.803194e+01 -1.683865 -#> [3,] 4.142917e-26 36.857815 +#> [1,] 2.161219e-15 21.401464 +#> [2,] 4.804131e+01 -1.686739 +#> [3,] 2.210693e+16 -23.629600 #> #> $probibality -#> [1] 0.46813133 0.08309011 0.44877856 +#> [1] 0.57603917 0.07110126 0.35285957 #> #> $omega #> [,1] [,2] [,3] -#> [1,] 9.998988e-01 3.154768e-10 1.011961e-04 -#> [2,] 9.978411e-01 1.159312e-10 2.158880e-03 -#> [3,] 9.398918e-01 9.560049e-18 6.010819e-02 +#> [1,] 2.536304e-01 3.140715e-04 7.460555e-01 +#> [2,] 4.400950e-01 2.237826e-04 5.596812e-01 +#> [3,] 5.594828e-01 1.463402e-06 4.405157e-01 #> [ reached getOption("max.print") -- omitted 45 rows ] #> #> $cluster @@ -677,7 +681,7 @@

4.1 For Modules#> [1] "M5" #> #> $coefficient -#> [1] 6.01101 +#> [1] 5.964078

4.2 For Microbes diff --git a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-12-1.png b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-12-1.png index 2a3ef39..27208a2 100644 Binary files a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-12-1.png and b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-36-1.png b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-36-1.png index 4330b8d..a5e3d74 100644 Binary files a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-36-1.png and b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-36-1.png differ diff --git a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-37-1.png b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-37-1.png index a424b7f..2e762eb 100644 Binary files a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-37-1.png and b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-37-1.png differ diff --git a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-9-1.png b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-9-1.png index 94925d6..6e5ec1b 100644 Binary files a/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-9-1.png and b/articles/idopNetwork_vignette_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/pkgdown.yml b/pkgdown.yml index db42c87..6779cdc 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: idopNetwork_vignette: idopNetwork_vignette.html -last_built: 2023-06-07T07:35Z +last_built: 2023-06-07T08:06Z diff --git a/reference/normalization.html b/reference/normalization.html index 11dfa73..417b8a9 100644 --- a/reference/normalization.html +++ b/reference/normalization.html @@ -77,21 +77,21 @@

Value

Examples

normalization(runif(100,min = -100, max = 100))
-#>   [1] 0.6356808 0.2746821 1.1645029 0.7364645 1.0435525 1.1047125 1.0572523
-#>   [8] 0.9510173 0.2688871 0.8630330 0.2000000 1.0288534 0.4734507 0.2338975
-#>  [15] 1.1188266 0.7446844 0.8837038 0.3770692 0.7661596 0.3833575 1.0246352
-#>  [22] 1.0377021 0.7052357 1.1973209 0.5435634 0.6548367 1.0682962 0.3450311
-#>  [29] 0.4699458 0.6353543 0.5663773 0.7025899 0.2477763 1.2000000 1.1544633
-#>  [36] 0.4369299 0.3092371 0.2861391 1.1755645 1.1237178 0.5836080 0.5535394
-#>  [43] 0.6151213 0.8907511 0.8462842 0.7642252 0.9021730 0.6796724 0.9695114
-#>  [50] 0.7748442 1.1769726 0.7141303 0.4098960 1.1107290 0.8331241 0.2469039
-#>  [57] 0.2466221 0.8268214 0.6961542 0.8417122 0.7091734 0.7556101 0.4900692
-#>  [64] 0.8490456 0.8037341 0.4097176 0.3091402 0.7901114 0.8747484 0.6208499
-#>  [71] 1.1255611 0.7640073 0.8943431 0.2373456 0.7811730 0.9285995 1.0081371
-#>  [78] 0.8661011 0.2556796 0.8006038 0.3457432 0.6767077 0.7347640 0.8872909
-#>  [85] 0.7387071 0.2140297 0.5914572 0.5528925 0.9242247 0.8660430 0.8655467
-#>  [92] 0.8202865 0.8052809 0.5117076 1.1228117 0.4160374 0.8173515 0.2986884
-#>  [99] 1.1001981 0.3715910
+#>   [1] 1.1510589 0.2476292 0.7367324 0.5586049 0.5255539 1.1084477 0.2000000
+#>   [8] 0.2277490 0.4848044 0.5578120 0.8904043 0.9883270 0.2577476 0.5797915
+#>  [15] 0.5554236 0.2157199 0.2272967 0.5667839 0.3386641 0.4446630 0.5670892
+#>  [22] 0.6899854 0.8348485 0.5307690 1.1444937 0.4245751 0.7563026 1.1236064
+#>  [29] 1.0195918 0.3948366 1.1548522 0.7490662 0.4760451 1.1148149 0.7377722
+#>  [36] 0.7977747 0.5922773 0.9963358 0.4254980 0.6278139 0.2875985 0.6632019
+#>  [43] 0.8846421 1.0937344 1.0485238 0.3068374 1.1691096 0.7800008 0.5551105
+#>  [50] 1.2000000 0.2030559 1.0421576 0.9439466 0.7924078 0.8941292 0.7309837
+#>  [57] 0.7393831 0.7597967 0.4955920 0.9312759 0.2019229 0.4734186 0.6558163
+#>  [64] 0.9452958 0.7859047 0.5716284 1.1721367 0.8878192 1.0006656 1.0743742
+#>  [71] 0.7819281 1.0178895 0.9881970 0.2537964 1.1261894 0.3285456 1.0399635
+#>  [78] 0.9627544 0.9728276 0.3543639 1.0316505 0.2244575 0.5190788 0.4165089
+#>  [85] 0.7275234 0.4739869 0.6313623 0.8321674 0.8934819 0.3215161 0.8740262
+#>  [92] 0.7850888 0.3658523 0.4695465 0.2432662 0.2286203 0.9598520 0.2675089
+#>  [99] 1.1258065 0.7426678