@@ -10,14 +10,14 @@ We show how non-specific biomass removal can result in false discoveries or fals
In short, the scripts in this repository:
-Create the conceptual Figure 1
-Assess the significance of relationships between response variables and biomass removed in the gradient (gradient regression)
-When these gradient regressions are significant:
-Adjust response variables to account for the confounding effect of removed biomass
-Simulate variation to assess how variability in the gradient regression
-Analyze the treatment effects on the observed, adjusted or simulated data
-Create Figure 4 to illustrate the procedure and its effect on three response variables
-Create Supplementary Figures S1 and S2
- Create the conceptual Figure 1
- Assess the significance of relationships between response variables and biomass removed in the gradient (gradient regression)
- When these gradient regressions are significant:
- Adjust response variables to account for the confounding effect of removed biomass
- Simulate variation to assess how variability in the gradient regression
- Analyze the treatment effects on the observed, adjusted or simulated data
- Create Figure 4 to illustrate the procedure and its effect on three response variables
- Create Supplementary Figures S1 and S2
## Prerequisites
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@@ -31,27 +31,27 @@ R.
## File description
-Files not contained in `code` or `data` are not necessary to initiate the analysis and are provided for record. Such files will be created and/or overwritten as the scripts are executed.
-`code/`
-`Manuscript_figures.Rmd` and `Manuscript_figures.html` - R-markdown and HTML output of the figure-generation script
-`data/`
-`harmonized_data.csv` - Contains sample information, biomass removed and response variables
- Files not contained in `code` or `data` are not necessary to initiate the analysis and are provided for record. Such files will be created and/or overwritten as the scripts are executed.
-`code/`
-`Manuscript_figures.Rmd` and `Manuscript_figures.html` - R-markdown and HTML output of the figure-generation script
-`data/`
-`harmonized_data.csv` - Contains sample information, biomass removed and response variables
nteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E.J., Lett, S., Pedersen, E.P., and Väisänen, M. (2023). Data analysis for adjusting effects of biomass removal in a mycorrhizal association-based plant removal experiment. Software version 1.0.0. Bolin Centre Code Repository. <https://doi.org/10.57669/monteux-2023-plant-removal-1.0.0>
Monteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E.J., Lett, S., Pedersen, E.P., and Väisänen, M. (2023). Data analysis for adjusting effects of biomass removal in a mycorrhizal association-based plant removal experiment. Software version 1.0.0. Bolin Centre Code Repository. https://doi.org/10.57669/monteux-2023-plant-removal-1.0.0
## References
Monteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E.J., Lett, S., Pedersen, E.P., and Väisänen, M. (2023). Controlling for biases in targeted plant removal experiments. bioRxiv, 2023.08.22.554120. <https://doi.org/10.1101/2023.08.22.554120>
Monteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E.J., Lett, S., Pedersen, E.P., and Väisänen, M. (2023). Controlling for biases in targeted plant removal experiments. bioRxiv, 2023.08.22.554120. https://doi.org/10.1101/2023.08.22.554120
Monteux, S., Blume-Werry, G., Gavazov, K., Kirchhoff, L., Krab, E.J., Lett, S., Pedersen, E.P., and Väisänen, M. (2023). Controlling for biases in targeted plant removal experiments. New Phytologist, Manuscript accepted for publication.
