diff --git a/pkgdown.yml b/pkgdown.yml
index fd93d5da..ad096618 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
checks: checks.html
bugphyzz: bugphyzz.html
workflow: workflow.html
-last_built: 2024-01-03T21:10Z
+last_built: 2024-01-03T21:47Z
urls:
reference: https://waldronlab.io/bugphyzz/reference
article: https://waldronlab.io/bugphyzz/articles
diff --git a/reference/getBugAnnotations.html b/reference/getBugAnnotations.html
index ed862d05..dfdb07c7 100644
--- a/reference/getBugAnnotations.html
+++ b/reference/getBugAnnotations.html
@@ -100,7 +100,7 @@
Examples
x = c('561', '562'), bp = importBugphyzz(), tax.id.type = 'NCBI_ID'
)
#> Downloading, bugphyzz_export.tsv.
-
#> Using data downloaded on 2024-01-03 21:10:11.
+
#> Using data downloaded on 2024-01-03 21:47:18.
x
#> $`561`
#> $`561`$aerophilicity
diff --git a/reference/getBugphyzzSignatures.html b/reference/getBugphyzzSignatures.html
index 8b38fd8f..e9309d1a 100644
--- a/reference/getBugphyzzSignatures.html
+++ b/reference/getBugphyzzSignatures.html
@@ -135,7 +135,7 @@
Examples
## Create signatures of categorical or binary attributes
bp <- importBugphyzz()
-
#> Using data downloaded on 2024-01-03 21:10:11.
+
#> Using data downloaded on 2024-01-03 21:47:18.
sigs <- sig_fun(bp)
map(sigs, head)
#> $`bugphyzz:COGEM pathogenicity rating|COGEM pathogenicity rating 1|s`
diff --git a/reference/physiologies.html b/reference/physiologies.html
index 01be0af1..c03e36a9 100644
--- a/reference/physiologies.html
+++ b/reference/physiologies.html
@@ -130,6 +130,7 @@
Examples
#> Finished halophily.
#> Finished health associated.
#> Finished hemolysis.
+
#> Finished host-associated.
#> Finished hydrogen gas producing.
#> Finished isolation site.
#> Finished lactate producing.
diff --git a/reference/showPhys.html b/reference/showPhys.html
index 48bd3061..1e17f0dd 100644
--- a/reference/showPhys.html
+++ b/reference/showPhys.html
@@ -114,23 +114,24 @@
Examples
#> [21] "halophily"
#> [22] "health associated"
#> [23] "hemolysis"
-
#> [24] "hydrogen gas producing"
-
#> [25] "isolation site"
-
#> [26] "lactate producing"
-
#> [27] "length"
-
#> [28] "metabolite production"
-
#> [29] "metabolite utilization"
-
#> [30] "motility"
-
#> [31] "mutation rate per site per generation"
-
#> [32] "mutation rate per site per year"
-
#> [33] "optimal ph"
-
#> [34] "pathogenicity human"
-
#> [35] "plant pathogenicity"
-
#> [36] "shape"
-
#> [37] "sphingolipid producing"
-
#> [38] "spore formation"
-
#> [39] "spore shape"
-
#> [40] "width"
+
#> [24] "host-associated"
+
#> [25] "hydrogen gas producing"
+
#> [26] "isolation site"
+
#> [27] "lactate producing"
+
#> [28] "length"
+
#> [29] "metabolite production"
+
#> [30] "metabolite utilization"
+
#> [31] "motility"
+
#> [32] "mutation rate per site per generation"
+
#> [33] "mutation rate per site per year"
+
#> [34] "optimal ph"
+
#> [35] "pathogenicity human"
+
#> [36] "plant pathogenicity"
+
#> [37] "shape"
+
#> [38] "sphingolipid producing"
+
#> [39] "spore formation"
+
#> [40] "spore shape"
+
#> [41] "width"
showPhys('bacdive')
#> [1] "aerophilicity" "animal pathogen" "biosafety level"
#> [4] "country" "growth medium" "geographic location"
@@ -155,20 +156,21 @@
Examples
#> [14] "growth temperature"
#> [15] "habitat"
#> [16] "health associated"
-
#> [17] "hydrogen gas producing"
-
#> [18] "isolation site"
-
#> [19] "lactate producing"
-
#> [20] "length"
-
#> [21] "mutation rate per site per generation"
-
#> [22] "mutation rate per site per year"
-
#> [23] "optimal ph"
-
#> [24] "plant pathogenicity"
-
#> [25] "shape"
-
#> [26] "spore shape"
-
#> [27] "width"
-
#> [28] "genome size"
-
#> [29] "coding genes"
-
#> [30] "sphingolipid producing"
+
#> [17] "host-associated"
+
#> [18] "hydrogen gas producing"
+
#> [19] "isolation site"
+
#> [20] "lactate producing"
+
#> [21] "length"
+
#> [22] "mutation rate per site per generation"
+
#> [23] "mutation rate per site per year"
+
#> [24] "optimal ph"
+
#> [25] "plant pathogenicity"
+
#> [26] "shape"
+
#> [27] "spore shape"
+
#> [28] "width"
+
#> [29] "genome size"
+
#> [30] "coding genes"
+
#> [31] "sphingolipid producing"
bp <- importBugphyzz()
-#> Using data downloaded on 2024-01-03 21:10:11.
+#> Using data downloaded on 2024-01-03 21:47:18.
whichAttr(bp)
#> [1] "Acne--TRUE"
#> [2] "Arthritis--TRUE"
diff --git a/reference/whichAttrGrp.html b/reference/whichAttrGrp.html
index 97c74a78..6ff9c959 100644
--- a/reference/whichAttrGrp.html
+++ b/reference/whichAttrGrp.html
@@ -91,7 +91,7 @@ Value
Examples
bp <- importBugphyzz()
-#> Using data downloaded on 2024-01-03 21:10:11.
+#> Using data downloaded on 2024-01-03 21:47:18.
whichAttrGrp(bp)
#> [1] "COGEM pathogenicity rating"
#> [2] "acetate producing"