diff --git a/README.Rmd b/README.Rmd index ed2518d4..f4a5e4bc 100644 --- a/README.Rmd +++ b/README.Rmd @@ -58,13 +58,7 @@ You can install the latest official release version via install.packages("posterior") ``` -Alternatively, you can install binaries of the current development version via - -```{r install_mc_stan, eval=FALSE} -install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) -``` - -or directly build the package from GitHub via +or build the developmental version directly from GitHub via ```{r install_github, eval=FALSE} # install.packages("remotes") diff --git a/README.md b/README.md index e9644306..c36943d4 100644 --- a/README.md +++ b/README.md @@ -43,14 +43,7 @@ You can install the latest official release version via install.packages("posterior") ``` -Alternatively, you can install binaries of the current development -version via - -``` r -install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) -``` - -or directly build the package from GitHub via +or build the developmental version directly from GitHub via ``` r # install.packages("remotes") @@ -300,12 +293,12 @@ x4 <- bind_draws(x1, x3, along = "variable") print(x4) #> # A draws_matrix: 5 iterations, 1 chains, and 3 variables #> variable -#> draw alpha beta theta -#> 1 0.240 1 0.59 -#> 2 0.232 1 0.25 -#> 3 -1.234 1 0.70 -#> 4 0.479 1 1.41 -#> 5 0.013 1 1.28 +#> draw alpha beta theta +#> 1 -0.82 1 0.54 +#> 2 0.53 1 0.54 +#> 3 -0.79 1 0.38 +#> 4 0.92 1 0.58 +#> 5 -0.17 1 0.17 ``` Or, we can bind `x1` and `x2` together along the `'draw'` dimension: @@ -315,17 +308,17 @@ x5 <- bind_draws(x1, x2, along = "draw") print(x5) #> # A draws_matrix: 10 iterations, 1 chains, and 2 variables #> variable -#> draw alpha beta -#> 1 0.2400 1 -#> 2 0.2319 1 -#> 3 -1.2345 1 -#> 4 0.4795 1 -#> 5 0.0134 1 -#> 6 -1.0251 2 -#> 7 -1.9515 2 -#> 8 -0.0013 2 -#> 9 1.6684 2 -#> 10 0.2678 2 +#> draw alpha beta +#> 1 -0.820 1 +#> 2 0.527 1 +#> 3 -0.789 1 +#> 4 0.925 1 +#> 5 -0.169 1 +#> 6 -0.193 2 +#> 7 1.535 2 +#> 8 0.502 2 +#> 9 -0.207 2 +#> 10 -0.085 2 ``` As with all **posterior** methods, `bind_draws` can be used with all @@ -344,27 +337,27 @@ x <- as_draws_matrix(x) print(x) #> # A draws_matrix: 10 iterations, 1 chains, and 5 variables #> variable -#> draw V1 V2 V3 V4 V5 -#> 1 -0.382 -0.429 0.1463 0.762 2.33 -#> 2 -0.160 -0.211 0.9480 -0.760 1.11 -#> 3 -0.048 0.085 0.5779 -0.627 -0.88 -#> 4 0.513 1.053 -0.7525 1.033 -1.09 -#> 5 1.455 -0.779 1.4205 -1.766 0.16 -#> 6 0.019 -1.131 0.0088 -0.094 0.54 -#> 7 0.767 -1.511 0.7245 0.843 0.28 -#> 8 -0.953 -0.200 1.9397 0.520 -0.58 -#> 9 1.173 -0.325 -0.4821 0.948 1.14 -#> 10 0.873 0.486 1.4913 -0.693 1.02 +#> draw V1 V2 V3 V4 V5 +#> 1 -0.203 0.616 -1.770 -0.4751 -0.931 +#> 2 0.077 1.060 0.664 0.3097 1.492 +#> 3 -1.733 -0.511 0.215 -0.4082 0.478 +#> 4 -1.127 -0.084 0.039 -0.0935 1.517 +#> 5 -2.102 -0.152 2.204 0.1133 -0.815 +#> 6 -0.304 0.502 -0.090 -0.1632 1.528 +#> 7 -0.802 -1.780 0.416 0.0023 0.265 +#> 8 -0.459 0.804 0.350 -0.2718 1.313 +#> 9 1.116 -2.127 -1.598 -0.7790 0.038 +#> 10 -1.033 -0.694 0.673 -0.0686 -1.437 summarise_draws(x, "mean", "sd", "median", "mad") #> # A tibble: 5 x 5 -#> variable mean sd median mad -#> -#> 1 V1 0.326 0.755 0.266 0.822 -#> 2 V2 -0.296 0.747 -0.268 0.641 -#> 3 V3 0.602 0.879 0.651 1.05 -#> 4 V4 0.0166 0.949 0.213 1.15 -#> 5 V5 0.403 1.06 0.412 1.06 +#> variable mean sd median mad +#> +#> 1 V1 -0.657 0.924 -0.631 0.685 +#> 2 V2 -0.237 1.07 -0.118 1.00 +#> 3 V3 0.110 1.14 0.283 0.559 +#> 4 V4 -0.183 0.314 -0.128 0.285 +#> 5 V5 0.345 1.12 0.371 1.68 ``` Instead of `as_draws_matrix()` we also could have just used diff --git a/docs/articles/index.html b/docs/articles/index.html index 44dc78cd..49238b1a 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -79,7 +79,7 @@
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      • diff --git a/docs/articles/posterior.html b/docs/articles/posterior.html index d604fc08..7867b25b 100644 --- a/docs/articles/posterior.html +++ b/docs/articles/posterior.html @@ -39,7 +39,7 @@
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          +

          The posterior R package

          @@ -146,9 +146,9 @@

          Installation

          -

          The package is not on CRAN yet, but you can install the latest beta release version via

          +

          You can install the latest official release version via

          -install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
          +install.packages("posterior")

          or the latest development version from GitHub via

           # install.packages("remotes")
@@ -285,17 +285,17 @@ 
          
 print(x)
          ## # A draws_matrix: 10 iterations, 1 chains, and 5 variables
 ##     variable
-## draw    V1    V2     V3     V4    V5
-##   1   0.29 -0.80 -0.884 -1.179 -0.34
-##   2  -1.31  1.11  0.364 -1.202 -0.50
-##   3   1.09  0.40  0.298  1.373  0.90
-##   4   0.51 -0.71 -0.023 -0.086 -0.43
-##   5  -0.56 -0.61  0.614 -0.089  1.19
-##   6   0.93 -0.82 -1.254 -1.884 -1.17
-##   7   1.30  1.77  1.318 -0.831  0.81
-##   8  -0.18  1.21 -0.209 -0.756  0.60
-##   9   1.16 -1.22  0.208  0.291 -0.29
-##   10  0.13  0.53  0.468  1.099  1.37
          +## draw V1 V2 V3 V4 V5 +## 1 -2.10 -0.71 1.38 2.183 0.081 +## 2 -0.87 -0.47 -0.28 0.665 1.820 +## 3 -1.09 0.20 0.79 -0.125 2.872 +## 4 -1.94 0.36 -0.29 -0.611 0.389 +## 5 -1.80 1.82 -1.08 1.230 -1.899 +## 6 -0.79 0.93 0.17 -0.338 -0.483 +## 7 0.24 -1.78 -0.43 -0.576 -0.424 +## 8 0.57 -0.41 -0.62 2.449 0.921 +## 9 -0.41 -0.69 0.59 0.072 -0.102 +## 10 -0.78 1.30 -0.69 1.245 -1.106

          Because the matrix was converted to a draws_matrix, all of the methods for working with draws objects described in subsequent sections of this vignette will now be available.

          Instead of as_draws_matrix() we also could have just used as_draws(), which attempts to find the closest available format to the input object. In this case the result would be a draws_matrix object either way.

          @@ -308,17 +308,17 @@

          print(x)

          ## # A draws_matrix: 50 iterations, 1 chains, and 2 variables
 ##     variable
-## draw alpha  beta
-##   1   1.52  0.59
-##   2  -0.82 -0.51
-##   3   0.19 -0.46
-##   4  -0.89  0.86
-##   5  -0.44 -0.86
-##   6  -1.39  0.35
-##   7   0.26  0.96
-##   8  -0.19 -1.23
-##   9  -0.69 -0.26
-##   10  0.87 -0.23
+## draw alpha   beta
+##   1   0.63 -0.043
+##   2  -0.44 -0.494
+##   3   0.56 -1.099
+##   4  -0.68 -1.160
+##   5  -0.35 -0.860
+##   6  -0.88  1.651
+##   7   0.68  0.814
+##   8  -1.32 -0.556
+##   9   0.56  0.214
+##   10 -1.99 -0.562
 ## # ... with 40 more draws

          Analogous functions exist for the other draws formats and are used similarly.

          @@ -426,11 +426,11 @@ 

          ## # A draws_matrix: 5 iterations, 1 chains, and 3 variables
 ##     variable
 ## draw alpha  beta theta
-##    1 -1.10  0.77  1.21
-##    2  1.36 -0.53  0.56
-##    3  1.14  0.42  0.75
-##    4  2.43  1.16  1.01
-##    5  0.77 -1.58  1.11
          +## 1 0.22 -0.93 0.42 +## 2 -0.24 0.11 1.55 +## 3 -1.17 -0.74 0.51 +## 4 -0.95 -0.74 0.35 +## 5 0.28 0.58 0.62

          Because x1 and x2 have the same variables, we can bind them along the 'draw' dimension to create a single draws_matrix with more draws:

           x5 <- bind_draws(x1, x2, along = "draw")
@@ -438,16 +438,16 @@ 
          
 
          ## # A draws_matrix: 10 iterations, 1 chains, and 2 variables
 ##     variable
 ## draw alpha  beta
-##   1  -1.10  0.77
-##   2   1.36 -0.53
-##   3   1.14  0.42
-##   4   2.43  1.16
-##   5   0.77 -1.58
-##   6  -0.87  0.48
-##   7   2.42 -0.48
-##   8  -1.73  1.96
-##   9   1.00  0.58
-##   10 -0.36  0.87
          
+##   1   0.22 -0.93
+##   2  -0.24  0.11
+##   3  -1.17 -0.74
+##   4  -0.95 -0.74
+##   5   0.28  0.58
+##   6   0.36  1.12
+##   7   1.53  1.60
+##   8   0.79  0.36
+##   9   0.46 -1.08
+##   10 -0.17 -1.22

          As with all posterior methods, bind_draws() can be used with all draws formats and depending on the format different dimensions are available to bind on. For example, we can bind draws_array objects together by iteration, chain, or variable, but a 2-D draws_matrix with the chains combined can only by bound by draw and variable.

          @@ -533,16 +533,16 @@ 

          ## # A tibble: 10 x 2
 ##    variable weighted_mean
 ##    <chr>            <dbl>
-##  1 mu                4.32
-##  2 tau               4.01
-##  3 theta[1]          6.34
-##  4 theta[2]          5.27
-##  5 theta[3]          2.90
-##  6 theta[4]          4.85
-##  7 theta[5]          3.47
-##  8 theta[6]          4.15
-##  9 theta[7]          6.77
-## 10 theta[8]          5.06
          +## 1 mu 4.15 +## 2 tau 4.04 +## 3 theta[1] 6.57 +## 4 theta[2] 5.12 +## 5 theta[3] 2.81 +## 6 theta[4] 4.87 +## 7 theta[5] 3.13 +## 8 theta[6] 4.27 +## 9 theta[7] 6.25 +## 10 theta[8] 4.73

          diff --git a/vignettes/posterior.Rmd b/vignettes/posterior.Rmd index 189e8e44..85584539 100644 --- a/vignettes/posterior.Rmd +++ b/vignettes/posterior.Rmd @@ -27,11 +27,10 @@ from Bayesian models. The primary goals of the package are to: ## Installation -The package is not on CRAN yet, but you can install the latest beta release -version via +You can install the latest official release version via ```{r install, eval=FALSE} -install.packages("posterior", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) +install.packages("posterior") ``` or the latest development version from GitHub via