Initial commit

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

Analysis.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

README.md

-# Monteux 2023 Plant Removal
-
-
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://git.bolin.su.se/monteuxs/monteux-2023-plant-removal.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://git.bolin.su.se/monteuxs/monteux-2023-plant-removal/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
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-## Name
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-
-## Installation
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-
-## Usage
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-## Contributing
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-## Authors and acknowledgment
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-## Project status
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+# Data analysis and figure generation for a gradient design to account for biases in plant removal experiments
+
+## Overview
+
+Code and data underlying "[Controlling biases in targeted plant removal experiments](https://doi.to-do)" by Sylvain Monteux, Gesche Blume-Werry, Konstantin Gavazov, Leah K. Kirchhoff, Eveline J. Krab, Signe Lett, Emily Pickering Pedersen, Maria Vaisanen, New Phytologist, 2023. This repository stores the entire analysis pipeline: statistical analyses and figure generation.
+
+The experimental design consists in 5 spatially-replicated blocks containing each one of the following treatments: undisturbed control (CTL), targeted removal of ericoid- (-ERM), ecto- (-ECM) or both ericoid- and ecto-mycorrhizal plants (-ECM/-ERM) in a subarctic tundra heath at the forest-tundra ecotone in northern Sweden. A gradient of indiscriminate biomass removal based on area was implemented alongside the targeted removal treatments to account for biases induced by the removal of plant biomass. The repository describes how the data was analysed based on results observed in the gradient, and depending on that whether the response variables in the treatment plots were adjusted for potential confounding effects. 
+
+We show how non-specific biomass removal can result in false discoveries or false negatives based on data obtained within this experiment.
+
+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 
+
+## Prerequisites
+
+R scripts were tested on R4.1.3 on Windows 10 and R4.3.1 on Linux Mint 21.2.
+No intensive resource use.
+
+
+## Language
+
+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.
+-   `data/`
+    -   `harmonized_data.csv` - Contains sample information, biomass removed and response variables
+-   `results/` - Final result files
+    -   `Fig1_conceptual.pdf` - Figure 1
+    -   `Fig3_assembled.pdf` - Figure 3
+    -   `SI_Fig_1_biomass_cover.png` - Supplementary Figure S1
+    -   `SI_Fig_2_Bnana_growth_nonegatives.pdf` - Supplementary Figure S2
+-   `code/`
+    -   `Manuscript_figures.Rmd` and `Manuscript_figures.html` - R-markdown and HTML output of the figure-generation script
+-  `sessionInfo.txt` - R environment file
+-  `LICENCE` - Licence file
+-   `./README.md` - This document
+
+## Citation
+
+Monteux S (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.K., Krab E.J., Lett S., Pickering Pedersen E. and Vaisanen M., Controlling for biases in targeted plant removal experiments, journaljournaljournal, vol nr pp. nr. <https://doi.org/placeholder>
+
+## Comments
+
+
+### Acknowledgements
+
+We thank the Swedish Polar Research Secretariat and SITES for the logistical support of the work done at the Abisko Scientific Research Station. 
+
+This study was financially supported by the Bolin Centre for Climate Research, Helge Ax:son Johnsons stiftelse and Arcum (SM); Swiss Polar Institute Exploratory Grant (SPIEG-2020-001) and Swiss National Science Foundation (grant PZ00P2_174047) (KG); Waldemar von Frenckells stiftelse, Oskar Oflunds stiftelse, the Osk. Huttunen Foundation and The University of Oulu & The Academy of Finland PROFI4 (Grant 318930) (MV).
+
+We thank James T. Weedon for critical input on statistical data processing, Anika Mayr for obtaining and processing data on Betula nana growth and isotopic nitrogen content, and Sonia Meller for lending us the SEAR scanner. We also thank Anna Miettinen, Elisa Jung, Henrike Lange, Janne Welling, Lorenzo Masini, Luca Dettmers, Margaux Chadanson, Paul Schulz and Yannick Bernard for their help in the maintenance of the experiment and data collection. 
+
+
+## Creators
+
+Sylvain Monteux
+
+## Contact information
+
+Sylvain Monteux
+
+Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
+
+sylvain.monteux [at] aces.su.se
+
+UiT The Arctic University Museum of Norway, NO-9013 Tromsø, Norway
+
+sylvain.monteux [at] uit.no
+
+## Publisher
+
+Bolin Centre Code Repository
+
+## Version
+
+1.0.0
+
+## Project URL
+
+<https://abisko-lter.weebly.com/>
+
+## DOI
+
+to-do
+
+## License
+
+Distributed under the GNU General Public License v3.0. See LICENSE text for more information.
+
+## Publication date
+
+placeholder

data/harmonized_data.csv

+block;Treatment;plot;Betula_d15N;Betula_growth;MUX;biomass_removed_g;ERM_rem;ECM_rem
+1;gradient;5;-8.823;7.4225;30.2;219.519;NA;NA
+1;gradient;60;-2.644;3.085;31.9;2134.862;NA;NA
+1;gradient;85;-5.801;11.585;27.7;3922.052;NA;NA
+1;gradient;0;;;;0;NA;NA
+1;control;CTL;-6.388;1.6325;;0;FALSE;FALSE
+1;ECM;ECM;;;27.1;262.683;FALSE;TRUE
+1;ERM;ERM;-3.24;6.355;8.6;2885.626;TRUE;FALSE
+1;EE;EE;;;34.1;2847.611;TRUE;TRUE
+2;gradient;20;-6.161;5.93;65.5;1185.274;NA;NA
+2;gradient;40;-4.361;5.7325;39.2;1979.314;NA;NA
+2;gradient;100;;;55.4;5219.143;NA;NA
+2;gradient;0;;;;0;NA;NA
+2;control;CTL;-5.109;6.98;21.7;0;FALSE;FALSE
+2;ECM;ECM;;;34.4;427.594;FALSE;TRUE
+2;ERM;ERM;-3.887;3.964166667;21.4;3253.115;TRUE;FALSE
+2;EE;EE;;;32;4219.464;TRUE;TRUE
+3;gradient;15;-6.826;4.3325;43.1;642.902;NA;NA
+3;gradient;30;-6.458;10.27666667;27;794.885;NA;NA
+3;gradient;65;-4.016;9.935;16.8;2645.798;NA;NA
+3;gradient;0;;;;0;NA;NA
+3;control;CTL;-6.344;6.1975;20.5;0;FALSE;FALSE
+3;ECM;ECM;;;31.4;262.369;FALSE;TRUE
+3;ERM;ERM;-2.998;5.0975;40.8;3103.164;TRUE;FALSE
+3;EE;EE;;;38.2;3081.144;TRUE;TRUE
+4;gradient;10;-7.504;8.2525;;357.771;NA;NA
+4;gradient;45;-4.179;8.5175;17.7;1505.353;NA;NA
+4;gradient;75;-4.639;12.49083333;15.5;3033.943;NA;NA
+4;gradient;0;;;;0;NA;NA
+4;control;CTL;-7.416;4.3175;25.8;0;FALSE;FALSE
+4;ECM;ECM;;;25.9;258.255;FALSE;TRUE
+4;ERM;ERM;-5.045;7.315;21.8;3102.549;TRUE;FALSE
+4;EE;EE;;;36.2;3307.985;TRUE;TRUE
+5;gradient;25;-5.883;4.975833333;19.7;659.288;NA;NA
+5;gradient;50;-6.449;8.013333333;19.8;1128.194;NA;NA
+5;gradient;90;-2.584;11.295;16.1;3543.287;NA;NA
+5;gradient;0;;;;0;NA;NA
+5;control;CTL;-7.294;3.1125;;0;FALSE;FALSE
+5;ECM;ECM;;;38.7;638.59;FALSE;TRUE
+5;ERM;ERM;-4.889;1.916666667;24.7;2270.834;TRUE;FALSE
+5;EE;EE;;;22.3;1847.278;TRUE;TRUE

sessionInfo.txt

+R version 4.3.1 (2023-06-16)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Linux Mint 21.2
+
+Matrix products: default
+BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=sv_SE.UTF-8    LC_MESSAGES=en_US.UTF-8   
+ [7] LC_PAPER=sv_SE.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C       
+
+time zone: Europe/Stockholm
+tzcode source: system (glibc)
+
+attached base packages:
+[1] stats     graphics  grDevices utils     datasets  methods   base     
+
+other attached packages:
+ [1] car_3.1-2       carData_3.0-5   ggside_0.2.2    lmerTest_3.1-3 
+ [5] lme4_1.1-34     Matrix_1.6-0    sciplot_1.2-0   lubridate_1.9.2
+ [9] forcats_1.0.0   stringr_1.5.0   dplyr_1.1.2     purrr_1.0.2    
+[13] readr_2.1.4     tidyr_1.3.0     tibble_3.2.1    tidyverse_2.0.0
+[17] patchwork_1.1.3 ggplot2_3.4.3  
+
+loaded via a namespace (and not attached):
+ [1] sass_0.4.7          utf8_1.2.3          generics_0.1.3     
+ [4] stringi_1.7.12      lattice_0.21-8      hms_1.1.3          
+ [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.21      
+[10] grid_4.3.1          timechange_0.2.0    fastmap_1.1.1      
+[13] jsonlite_1.8.7      fansi_1.0.4         scales_1.2.1       
+[16] numDeriv_2016.8-1.1 jquerylib_0.1.4     abind_1.4-5        
+[19] cli_3.6.1           rlang_1.1.1         munsell_0.5.0      
+[22] splines_4.3.1       withr_2.5.0         cachem_1.0.8       
+[25] yaml_2.3.7          tools_4.3.1         tzdb_0.4.0         
+[28] nloptr_2.0.3        minqa_1.2.5         colorspace_2.1-0   
+[31] boot_1.3-28         vctrs_0.6.3         R6_2.5.1           
+[34] lifecycle_1.0.3     MASS_7.3-60         pkgconfig_2.0.3    
+[37] pillar_1.9.0        bslib_0.5.1         gtable_0.3.4       
+[40] Rcpp_1.0.11         glue_1.6.2          xfun_0.40          
+[43] tidyselect_1.2.0    rstudioapi_0.15.0   knitr_1.43         
+[46] htmltools_0.5.6     nlme_3.1-162        rmarkdown_2.24     
+[49] compiler_4.3.1