/Rhizosphere-Nitrogen-Fate

Processed data and R codes Relevant to Management and rhizosphere microbial associations modulate genetic-driven nitrogen fate

Primary LanguageR

Management and rhizosphere microbial associations modulate genetic-driven nitrogen fate

Mitra Ghotbi1,2*, Marjan Ghotbi3, Yakov Kuzyakov4,5, William R. Horwath6

Affiliations:

Mitra Ghotbi

  • 1 Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, IL, USA
  • 2 Department of Biology, Middle Tennessee State University at Murfreesboro, TN, USA

Marjan Ghotbi

  • 3 GEOMAR Helmholtz Centre for Ocean Research at Kiel, Germany

Yakov Kuzyakov

  • 4 Department of Soil Science of Temperate Ecosystems and Department of Agricultural Soil Science, Georg-August-University of Göttingen at Göttingen, Germany
  • 5 Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia

William R. Horwath

  • 6 Plant and Environmental Sciences Building, Department of Land, Air & Water Resources, University of California Davis, at Davis, CA, USA

Corresponding Author:

Mitra Ghotbi, PhD.

N Fate

The R codes relevant to each figure have been published here to assist readers in navigating and reproducing them easily.

Prerequisites: Ensure that the required packages are installed and loaded.

reqpkg <- c("phyloseq", "vegan", "microbiome", "DESeq2", 
            "plyr", "reshape2", "grid", "scales", "cluster", "ape", "dplyr","ggrepel",
            "igraph", "ggnet", "microbiomeutilities", "network", "SpiecEasi",
            "data.table", "decontam", "ggtext","microbiomeMarker", "devtools", "dada2", "ggplot2", "ggpubr",
            "agridat", "lme4", "rstatix", "emmeans", "lmerTest")

# Check against installed packages:
inpkg <- installed.packages()[, "Package"]
neededpkg <- reqpkg[!reqpkg %in% inpkg]

if (length(neededpkg) > 0) {
  cat("The following package(s) need to be installed:", paste(neededpkg, collapse = ", "), "\n")
  cat("Installing package(s)...\n")
  install.packages(neededpkg)
  cat("Package(s) installed successfully.\n")
} else {
  cat("All required packages are already installed.\n")
}

# Load required packages:
cat("Loading required packages...\n")
invisible(lapply(reqpkg, library, character.only = TRUE))
cat("All required packages loaded successfully.\n")

Rhizosphere-nitrogen-fate by Mitra Ghotbi is licensed under Attribution-ShareAlike 4.0 International