Repository to our manuscript "Root-Driven Soil Reduction in Wadden Sea Salt Marshes".
Submitted to Wetlands journal 2024. Accepted Oct 2024
Authors: Julian Mittmann-Goetsch, Monica Wilson, Kai Jensen, Peter Mueller
Link: https://link.springer.com/article/10.1007/s13157-024-01867-8
README
|data # all data frames included in the repository
|- df_optode_ap # raw planar optode data of Atriplex portulacoides @Monica Wilson
|- df_optode_sa # raw planar optode data of Spartina anglica @Monica Wilson
|- df_tt_iris # IRIS data from the tidal-tank experiment @JulianMiGoe
|- df_tt_dchange # IRIS data calculated as delta change values against non-vegetated controls from the tidal-tank experiment @JulianMiGoe
|- df_tt_ph # pH data from the tidal-tank experiment @JulianMiGoe
|- df_field_iris # IRIS data from the field study @JulianMiGoe
|- df_field_dchange # IRIS data calculated as delta change values against non-vegetated controls from the field study @JulianMiGoe
|- df_field_ancillary # ancilliary data from the field study. Calculated as means per plot @JulianMiGoe
|- df_raw_biomass # raw biomass data (above- and belowground) from the field study @JulianMiGoe
|- df_raw_soil # raw soil paramenter data (pH, OM, conductivity) from the field study @JulianMiGoe
|- df_DSK_iris # IRIS data from Diek-Sander-Koog field study (Mueller et al. 2020) @Peter Mueller
|
|code # R code used for the analysis
|- iris_optode.RMD # RMarkdown Skript
CODE structure and processing
| df_optode_ap # L0 raw planar optode data of Atriplex portulacoides @Monica Wilson
|- df_optode_ap_long # L1 processed data (filtered df_optode_sa to long format table, inlcuding only ROI used for the analysis) - Used to create Figure 4b
|-- df_optode_ap_long_filtered # L2 processed data from L1 (filtered df_optode_ap_long two slide numbers with drops below 0, slide 40 & slide 159, filtered to only include slides 155-230) - Used to create Figure 4b subpanel
|
| df_optode_sa # L0 raw planar optode data of Spartina anglica @Monica Wilson
|- df_optode_sa_long # L1 processed data (filtered df_optode_ap to long format table, inlcuding only ROI used for the analysis) - Used to create Figure 4a
|-- df_optode_ap_long_filtered # L2 processed data from L1 (filtered df_optode_sa_long to only include slides 155-230) - USed to create Figure 4a subpanel
|
| df_tt_iris # L0 IRIS data from the tidal-tank experiment @JulianMiGoe
|- df_tt_iris_aov # L1 processed data (filtered df_tt_iris to exclude all NAs) - Used for statistical analysis
|- df_tt_stat_veg # L1 processed data (filtered df_tt_iris to exclude all NAs & filtered to only include non-vegetated controls) - Used for statistical analysis
|- df_tt_a15 # L1 processed data (filtered df_tt_iris, to include all segments from 0-15cm) - Used to create Figure S1
|-- df_tt_a15_sum # L2 processed data (summarised df_tt_a15 to the factor zone)
|- df_tt_15 # L1 processed data (filtered df_tt_iris, to only include bottom segment 15-20 cm)
|-- df_tt_all_sum # L2 processed data (summarised df_tt_15 by factor zone) - Used to create Barplot Figure 3a
|-- df_tt_non_veg # L2 processed data (filtered df_tt_15 to only include non-vegetated controls)
|--- df_tt_non_veg_sum # L3 processed data (summarised df_tt_non_veg by factor zone) - Used to create Barplot Figure 3b
|
|- df_tt_dchange # L1 processed IRIS data calculated (in Excel) as delta change values against non-vegetated controls from the tidal-tank experiment @JulianMiGoe
|-- df_tt_dchange_sum # L2 processed data (summarised df_tt_dchange by factor zone, plant) - Used to create Barplot Figure 3c
|
| df_tt_ph # L0 raw pH data from the tidal-tank experiment @JulianMiGoe
|- df_tt_ph_sum # L1 processed data (summarised df_tt_ph by factor zone, vegetation) - Used to create Figure S2
|
| df_field_iris # L0 raw IRIS data from the field study @JulianMiGoe
|- df_field_iris_long # L1 processed data (transformed df_field_iris to long format)
|-- df_field_iris_aov # L2 processed data (filtered df_field_iris_long to exclude all NAs) - Used for statistical analysis
|-- df_field_elevation # L2 processed data (summarised df_field_iris_long by factors zone & depth) - Used for Figure S3
|-- df_field_all # L2 processed data (summarised df_field_iris_long by factor zone) - Used for Figure 5a
|-- df_field_subset # L2 processed data (filtered df_field_iris_long, intermediate dataframe)
|--- df_field_unplanted # L3 processed data (summarised df_field_subset by factor zone, excluded all vegetated plots) - Used for Figure 5b
|
| df_field_dchange # L1 processed IRIS data calculated (in Excel) as delta change values against non-vegetated controls from the field study @JulianMiGoe
|- df_field_dchange_sum # L2 processed data (summarised df_field_dchange by factor zone, depth) - Used to create Barplot Figure 5c
|
| df_raw_biomass # L0 raw biomass data (above- and belowground) from the field study @JulianMiGoe
| df_raw_soil # L0 raw soil paramenter data (pH, OM, conductivity) from the field study @JulianMiGoe
|- df_field_ancillary # L1 processed ancilliary data from the field study. Calculated as means per plot (in Excel from both df_raw_biomass & df_raw_soil) @JulianMiGoe - Used to create Figure 6a-d
|
| df_DSK_iris # L0 raw IRIS data from Diek-Sander-Koog field study (Mueller et al. 2020) @Peter Mueller
| df_DSK_sum # L1 processed data (summarised df_DSK_iris by factor zone) - Used to create barplot Figure S5a