Calculate a sample-wise alpha diversity metric from a microbiome_dataset.
Usage
calculate_alpha_diversity(
object,
metric = c("observed", "shannon", "simpson", "pielou")
)Examples
data("global_patterns", package = "microbiomedataset")
x <- calculate_alpha_diversity(global_patterns, metric = "shannon")
class(x)
#> [1] "microbiome_diversity"
#> attr(,"package")
#> [1] "microbiomedataset"
head(x@result)
#> sample_id value Primer Final_Barcode Barcode_truncated_plus_T
#> 1 CL3 6.576517 ILBC_01 AACGCA TGCGTT
#> 2 CC1 6.776603 ILBC_02 AACTCG CGAGTT
#> 3 SV1 6.498494 ILBC_03 AACTGT ACAGTT
#> 4 M31Fcsw 3.828368 ILBC_04 AAGAGA TCTCTT
#> 5 M11Fcsw 3.287666 ILBC_05 AAGCTG CAGCTT
#> 6 M31Plmr 4.289269 ILBC_07 AATCGT ACGATT
#> Barcode_full_length SampleType Description
#> 1 CTAGCGTGCGT Soil Calhoun South Carolina Pine soil, pH 4.9
#> 2 CATCGACGAGT Soil Cedar Creek Minnesota, grassland, pH 6.1
#> 3 GTACGCACAGT Soil Sevilleta new Mexico, desert scrub, pH 8.3
#> 4 TCGACATCTCT Feces M3, Day 1, fecal swab, whole body study
#> 5 CGACTGCAGCT Feces M1, Day 1, fecal swab, whole body study
#> 6 CGAGTCACGAT Skin M3, Day 1, right palm, whole body study
#> class
#> 1 Subject
#> 2 Subject
#> 3 Subject
#> 4 Subject
#> 5 Subject
#> 6 Subject