diff --git a/DESCRIPTION b/DESCRIPTION index 9bbdfb8..5382a86 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: metacal Title: Bias estimation and calibration for metagenomics experiments -Version: 0.0.0.9000 +Version: 0.1.0 Authors@R: person(given = "Michael", family = "McLaren", diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index a036465..e17fb97 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -60,7 +60,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 981bb62..9ae1e37 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -60,7 +60,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/articles/index.html b/docs/articles/index.html index 6c61ab6..e487200 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/articles/tutorial.html b/docs/articles/tutorial.html index a71d1d3..243be15 100644 --- a/docs/articles/tutorial.html +++ b/docs/articles/tutorial.html @@ -30,7 +30,7 @@ metacal - 0.0.0.9000 + 0.1.0 @@ -372,13 +372,13 @@

#> # A tibble: 7 x 4 #> Taxon Bhat Gm_mean Gm_se #> <chr> <dbl> <dbl> <dbl> -#> 1 Ava 0.342 0.340 1.08 -#> 2 Gva 0.179 0.179 1.09 -#> 3 Lcr 2.30 2.31 1.08 +#> 1 Ava 0.342 0.341 1.08 +#> 2 Gva 0.179 0.180 1.10 +#> 3 Lcr 2.30 2.30 1.08 #> 4 Lin 4.51 4.50 1.05 #> 5 Pbi 1.63 1.63 1.07 #> 6 Sam 4.03 4.02 1.06 -#> 7 Sag 0.241 0.241 1.05 +#> 7 Sag 0.241 0.240 1.05

By converting the bootstrap estimates to pairwise estimates, we can also get standard errors for the pairwise bias,

bootreps.pw <- bootreps %>%
     compute_ratios(group_vars = ".id")
@@ -392,14 +392,14 @@ 

 #>    <chr>   <chr>    <dbl> <chr>     <dbl> <dbl>
 #>  1 Ava     Ava     1      Ava:Ava  1       1   
 #>  2 Ava     Gva     1.91   Ava:Gva  1.90    1.08
-#>  3 Ava     Lcr     0.149  Ava:Lcr  0.147   1.16
-#>  4 Ava     Lin     0.0759 Ava:Lin  0.0756  1.13
-#>  5 Ava     Pbi     0.210  Ava:Pbi  0.208   1.13
-#>  6 Ava     Sag     1.42   Ava:Sag  1.41    1.12
-#>  7 Ava     Sam     0.0850 Ava:Sam  0.0847  1.10
-#>  8 Gva     Ava     0.523  Gva:Ava  0.526   1.08
+#>  3 Ava     Lcr     0.149  Ava:Lcr  0.148   1.15
+#>  4 Ava     Lin     0.0759 Ava:Lin  0.0759  1.13
+#>  5 Ava     Pbi     0.210  Ava:Pbi  0.209   1.13
+#>  6 Ava     Sag     1.42   Ava:Sag  1.42    1.12
+#>  7 Ava     Sam     0.0850 Ava:Sam  0.0850  1.10
+#>  8 Gva     Ava     0.523  Gva:Ava  0.527   1.08
 #>  9 Gva     Gva     1      Gva:Gva  1       1   
-#> 10 Gva     Lcr     0.0780 Gva:Lcr  0.0776  1.18
+#> 10 Gva     Lcr     0.0780 Gva:Lcr  0.0780  1.18
 #> # … with 39 more rows
diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-22-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-22-1.png index ef6d338..47c361a 100644 Binary files a/docs/articles/tutorial_files/figure-html/unnamed-chunk-22-1.png and b/docs/articles/tutorial_files/figure-html/unnamed-chunk-22-1.png differ diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-35-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-35-1.png index 37a157c..e9ee773 100644 Binary files a/docs/articles/tutorial_files/figure-html/unnamed-chunk-35-1.png and b/docs/articles/tutorial_files/figure-html/unnamed-chunk-35-1.png differ diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-37-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-37-1.png index 0c00a39..142700e 100644 Binary files a/docs/articles/tutorial_files/figure-html/unnamed-chunk-37-1.png and b/docs/articles/tutorial_files/figure-html/unnamed-chunk-37-1.png differ diff --git a/docs/authors.html b/docs/authors.html index 22563a0..60c3546 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ metacal - 0.0.0.9000 + 0.1.0
diff --git a/docs/index.html b/docs/index.html index d2dfb7a..70268ae 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/anorm.html b/docs/reference/anorm.html index e8e431b..84427e1 100644 --- a/docs/reference/anorm.html +++ b/docs/reference/anorm.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/as_matrix.html b/docs/reference/as_matrix.html index 30fb8a3..976d6a4 100644 --- a/docs/reference/as_matrix.html +++ b/docs/reference/as_matrix.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/bootrep_center.html b/docs/reference/bootrep_center.html index 8f16ec5..1013501 100644 --- a/docs/reference/bootrep_center.html +++ b/docs/reference/bootrep_center.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/build_matrix.html b/docs/reference/build_matrix.html index 7ad60cc..ff4d985 100644 --- a/docs/reference/build_matrix.html +++ b/docs/reference/build_matrix.html @@ -64,7 +64,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/center.html b/docs/reference/center.html index 3bc1ea9..9c00c3c 100644 --- a/docs/reference/center.html +++ b/docs/reference/center.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/center_elts.html b/docs/reference/center_elts.html index 132b397..3e850e0 100644 --- a/docs/reference/center_elts.html +++ b/docs/reference/center_elts.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/close_elts.html b/docs/reference/close_elts.html index cc8e100..7464af9 100644 --- a/docs/reference/close_elts.html +++ b/docs/reference/close_elts.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/clr.html b/docs/reference/clr.html index 77eefb8..393c7a8 100644 --- a/docs/reference/clr.html +++ b/docs/reference/clr.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/compute_ratios.html b/docs/reference/compute_ratios.html index 719f1ab..b67f4b8 100644 --- a/docs/reference/compute_ratios.html +++ b/docs/reference/compute_ratios.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/cooccurrence.html b/docs/reference/cooccurrence.html index b045e0c..7d734ea 100644 --- a/docs/reference/cooccurrence.html +++ b/docs/reference/cooccurrence.html @@ -64,7 +64,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/corner.html b/docs/reference/corner.html index e06706e..a1d3e8c 100644 --- a/docs/reference/corner.html +++ b/docs/reference/corner.html @@ -67,7 +67,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/gm.html b/docs/reference/gm.html index 266ac8c..6243ae4 100644 --- a/docs/reference/gm.html +++ b/docs/reference/gm.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/gm_abs.html b/docs/reference/gm_abs.html index 30269d7..01318de 100644 --- a/docs/reference/gm_abs.html +++ b/docs/reference/gm_abs.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/gm_mean.html b/docs/reference/gm_mean.html index f8a1c9c..190be3f 100644 --- a/docs/reference/gm_mean.html +++ b/docs/reference/gm_mean.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/gm_range.html b/docs/reference/gm_range.html index 4158d74..442723d 100644 --- a/docs/reference/gm_range.html +++ b/docs/reference/gm_range.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/gm_sd.html b/docs/reference/gm_sd.html index 6fab9f6..b686fe4 100644 --- a/docs/reference/gm_sd.html +++ b/docs/reference/gm_sd.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index a3fca1d..7e52a6f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/logit.html b/docs/reference/logit.html index d9837c2..0a8a27f 100644 --- a/docs/reference/logit.html +++ b/docs/reference/logit.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/mutate_by.html b/docs/reference/mutate_by.html index dbd9858..dd89d88 100644 --- a/docs/reference/mutate_by.html +++ b/docs/reference/mutate_by.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/odds.html b/docs/reference/odds.html index a1c8df1..6698da1 100644 --- a/docs/reference/odds.html +++ b/docs/reference/odds.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/proj_mat.html b/docs/reference/proj_mat.html index 1d32a87..9a5db5b 100644 --- a/docs/reference/proj_mat.html +++ b/docs/reference/proj_mat.html @@ -64,7 +64,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/pw_ratios.html b/docs/reference/pw_ratios.html index ac1285e..3097703 100644 --- a/docs/reference/pw_ratios.html +++ b/docs/reference/pw_ratios.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/pw_ratios_matrix.html b/docs/reference/pw_ratios_matrix.html index fccb9f0..2ef37d0 100644 --- a/docs/reference/pw_ratios_matrix.html +++ b/docs/reference/pw_ratios_matrix.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/ratio_matrix.html b/docs/reference/ratio_matrix.html index 0086bcb..ee54ab0 100644 --- a/docs/reference/ratio_matrix.html +++ b/docs/reference/ratio_matrix.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0 diff --git a/docs/reference/xydist.html b/docs/reference/xydist.html index 232d1f8..3ccab9f 100644 --- a/docs/reference/xydist.html +++ b/docs/reference/xydist.html @@ -63,7 +63,7 @@ metacal - 0.0.0.9000 + 0.1.0