Man pages for adsteen/Lloyd.et.al.Cell.abundance.metaanalysis
Package to reproduce analysis from Lloyd et al (2013), Applied and Environmental Microbiology
| AIC_lik | Returns liklihood of models relative to the best (based on... |
| aov_perm_test | AOV permutation test |
| boxplots_by_perm | Creates boxplots of yield and Also runs statistics on those... |
| calc_cn_ratio | Calculates the copy number ratio |
| gld | Generates labels based on Tukey HSD post hoc testing |
| intertidal_yield_fig | Makes a supplemental figure of FISH yield in intertidal... |
| Lloyd.et.al.Cell.abundance.metaanalysis-package | Lloyd.et.al.Cell.abundance.metaanalysis |
| lm_stats | Returns statistics for linear regressions (e.g. slope,... |
| make_qPCR_plots | Creates Fig 4, the qPCR plots |
| make_sed_yield_boxplots | Make boxplots of yield for sediments data, split by various... |
| make_sw_yield_boxplots | Create boxplots of yield in seawater, split by various... |
| merge_seds_and_sw | Merges the sediments and sw data frames into a single allData... |
| plot_cell_vs_fish | Make a plot of totalcells vs CARDFISH (or other FISH) counts... |
| plot_depth_trends | plots depth trends |
| qPCR_516_evaluation | Makes plot and calculates summary stats for qPCR using or not... |
| read_data | Reads and formats cell abundance database |
| reproduce_research | Reproduces analysis from Lloyd et al (submitted) |
| sed_bac_and_arc_v_depth | Makes plots and models of sediments bac and arc... |
| sed_depth_trends | plots depth trends |
| sed_percent_arc_v_depth | Make depth profiles and calculate linear models for sediment... |
| significance_labeller | Create 'significance code' based on p values |
| single_sw_yield_boxplot | Make a single yield boxplot (seds and sw, despite the name) |
| sw_depth_profiles | Plots depth profiles of various things in seawater |
| yield_by_core | Create a boxplot of yield (total cells by *-FISH relative to... |
