Man pages for surh/AMOR
Abundance Matrix Operations in R
| AMOR-package | Abundance Matrix Operations in R |
| beta_diversity | Beta diversity |
| bootstrap_glm | Bootstrap estimation of Generalized Linear Models on a matrix... |
| clean | Remove samples and taxons from a Dataset |
| collapse_by_taxonomy | Collapse by taxonomy |
| collapse_matrix | Collapse matrix |
| compare_site_diversity | Compare diversity accross sites and groups of samples. |
| create_dataset | Create Dataset object |
| find_good_samples | Find good samples |
| get_tax_level | Get tax level |
| heatgg | Heatmap with ggplot2 |
| matrix_glm | Fit Generalized Linear Models on a matrix of observations |
| matrix_glmNB | Fit Negative Binomial Generalized Linear Models on a matrix... |
| measurable_taxa | Identify measurable taxa |
| normalize | Normalize |
| PCA | Principal Component Analysis |
| PCO | Principal Coordinates Analysis |
| phylogram | Phylogram |
| plotgg | Make ggplot2 plot |
| plotgg.PCA | Plot a PCA |
| plotgg.PCO | Plotting a PCoA |
| plotgg_rankabun | Make rank abundance plot |
| plotgg_rankabun2 | Make rank abundance plot with Poisson confidence intervals. |
| plotgg.site.diversity | Plot diversity across sites. |
| plotgg_taxon | Plot single taxon. |
| plotgg_var | Plot single variable. |
| pool_samples | Pool samples |
| print.summary.bootglm | Print summary.bootglm object |
| rarefaction | Rarefaction |
| read.am | Read abundance matrix |
| remove_samples | Remove samples from a Dataset object. |
| remove_taxons | Remove taxa from a Dataset object. |
| samples | Get sample names |
| site_diversity | Diversity across sites. |
| subset.Dataset | Subset samples from a Dataset object. |
| summary.bootglm | Summarize bootstrap_glm model fits |
| summary.matrix.glm | Summarize matrix GLM results |
| taxa | Get taxa names |
| theme_blackbox | Blackbox theme |
| total_richness | Calculate richness of an abundance table. |
| variables | Get metadata variables |
| write.qiime | Write a QIIME abundance table file |
