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+---
+title: "sPlot 3 - Documentation"
+author: "Francesco Maria Sabatini"
+date: "11/30/2020"
+output:
+ html_document:
+ number_sections: true
+ toc: true
+ toc_depth: 2
+---
+
+<center>
+ 
+</center>
+
+**Timestamp:** `r date()`
+**Drafted:** Francesco Maria Sabatini
+**Revised:**
+**version:** 1.0
+
+This reports describes and provides a basic summary of the objects composing the working version of sPlot 3.0.
+
+```{r results="hide", message=F, warning=F}
+library(tidyverse)
+library(knitr)
+library(kableExtra)
+```
+
+# Taxonomic Backbone
+The taxonomic backbone is a resolved list of species names from either sPlot or TRY, which allows to:
+1) Match functional traits to species in sPlot, based on a common nomenclature.
+2) Resolve synonyms and correct spelling mistakes in species names, so to allow matching species across the datasets constituting sPlot.
+The construction of the Backbone is documented at https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/03_TaxonomicBackbone.html (download needed)
+```{r}
+load("../_output/Backbone3.0.RData")
+```
+## Show output
+```{r echo=F}
+knitr::kable(Backbone %>%
+ sample_n(20),
+ caption="Example of Backbone (only 20 randomly selected taxa shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+The Backbone contains `r nrow(Backbone)` taxon names. Of these, `r Backbone %>% filter(sPlot_TRY=="S") %>% nrow()` derive from sPlot.
+
+## Description of fields
+
+The bulk of the taxonomic standardization was done using [TNRS](http://tnrs.iplantcollaborative.org/index.html) or [TPL](http://www.theplantlist.org/), accessed using the package [taxonstand](https://cran.r-project.org/web/packages/Taxonstand/index.html). Below, the list of fields comprised in the Backbone output.
+<br>
+1. `Name_sPlot_TRY`: Taxon names, as derived from the Turboveg version of the original datasets.
+2. `Name_string_corr1`: Taxon name after a first round of manual cleaning (e.g., some types, abbreviations).
+3. `Name_string_corr2`: Taxon name after a second round of manual cleaning.
+4. `sPlot_TRY`: Origin of the taxon name (S = sPlot, T = TRY, A = Alpine dataset, see Testolin et al. 2020).
+<br>
+**The fields below derive from the output of [TNRS](http://tnrs.iplantcollaborative.org/index.html) (or TPL)** - See [here](http://tnrs.iplantcollaborative.org/instructions.html) for additional information.
+5. `Name_submitted`: Taxon name, as submitted to the services of taxonomic resolution, either TNRS or TPL.
+6. `Name_number`: Order of submission to TNRS or TPL.
+7. `Overall_score`: Level of matching in TNRS or TPL (1=perfect match).
+8. `Name_matched`: Scientific name with the highest match score. May be an exact match or a fuzzy match. This score does not include the author score.
+9. `Name_matched_rank`: The lowest taxonomic rank for the name matched.
+10. `Name_score`: Overall score for the name matched based on the TNRS ranking algorithm.
+11. `Name_matched_author`: Standard authority for the matched name.
+12. `Name_matched_url`: Web link for the matched name (where applicable).
+13. `Author_matched`: Standard authority of the name with the highest match score name.
+14. `Author_score`: Score assigned by the TNRS to indicate the level of similarity to the author submitted (where applicable). This field will be blank if the user did not submit an author with the name.
+15. `Family_matched`:The closest matching family in the TNRS database to the family submitted. This field will be blank if you did not submit a family, or the family could not be matched.
+16. `Family_score`: Score assigned by the TNRS to indicate the level of similarity to the family submitted (where applicable).
+17. `Name_matched_accepted_family`: Family of the accepted name.
+18. `Genus_matched`: The closest matching genus in the TNRS database to the genus submitted. This field will be blank if the genus submitted could not be matched.
+19. `Genus_score`: Score assigned by the TNRS to indicate the level of similarity to the genus submitted.
+20. `Specific_epithet_matched`: The specific epithet of closest matching species in the TNRS database to the species submitted. This field will be blank if the species submitted could not be matched.
+21. `Specific_epithet_score`: Score assigned by the TNRS to indicate the level of similarity to the species submitted.
+22. `Infraspecific_rank`: If an infraspecific taxon was submitted (subspecies, variety, etc.), this field provides the standardized rank abbreviation for that taxon (subspecies, variety, etc.).
+23. `Infraspecific_epithet_matched`: The infraspecific epithet of closet matching subspecies or variety in the TNRS database to the subspecies or variety submitted. This field will be blank if no infraspecific taxon was submitted, or if the subspecies or variety could not be matched.
+24. `Infraspecific_epithet_score`: Score assigned by the TNRS to indicate the level of similarity to the infraspecific taxon submitted.
+25. `Infraspecific_rank_2`: If a quadrinomal taxon name was submitted, this field provides the standardized rank abbreviation for that taxon. For example, "Poa annua var. purpurea forma minima" would return "fo.".
+26. `Infraspecific_epithet_2_matched`: The final epithet of closest matching quadrinomial infraspecific taxon in the TNRS database to the quadrinomial infraspecific taxon, for example "Poa annua var. purpurea forma minima". This field will be blank if a quadrinomial was not submitted or if the final epithet could not be matched.
+27. `Infraspecific_epithet_2_score`: Score assigned by the TNRS to indicate the level of similarity to the lower infraspecific taxon (quadrinomial) submitted. This field will be blank if a quadrinomial was not submitted, or if the final epithet of the quadrinomial could not be matched.
+28. `Annotations`: Any standardized botanical annotations of uncertainty embedded within the name, such as "cf." or "aff.", are removed and stored here.
+29. `Unmatched_terms`: The complete trailing portion of the name not matched by the TNRS, minus any annotations.
+30. `Taxonomic_status`: Where the submitted name is *Accepted*, *Synonym*, or not know (e.g., *No opinion*, *Invalid*, *Illegitimate*, *Misapplied*, *Unresolved*).
+31. `Accepted_name`: The accepted (correct) scientific name of the name matched by the TNRS, according to the taxonomic source used. If the name matched is an accepted name, or if the TNRS indicated "No opinion" for the name matched, then acceptedName will be the same as Name_matched. If Name_matched is a synonymy, then Accepted_name will be different.
+32. `Accepted_name_author`: Standard authority of the Accepted_name.
+33. `Accepted_name_rank`: Taxonomic rank of the accepted Accepted_name.
+34. `Accepted_name_url`: Web link for the accepted name (where applicable).
+35. `Accepted_name_species`: The genus+species portion only of the Accepted_name. If the rank of the Accepted_name is species, then Accepted_species will be the same as Accepted_name. If the rank of the Accepted_name is higher than species, for example, if the Accepted_name is a genus, then this field will be blank.
+36. `Accepted_name_family`: The accepted familial classification of the accepted name for the name matched by the TNRS.
+37. `Selected`: Denotes the best match according to either taxonomic or maximum score.
+38. `Source`: Source used for the resolution (for TNRS sources see [](http://tnrs.iplantcollaborative.org/sources.html)).
+39. `Warnings`: If TNRS is unable to uncategorically resolve your submitted name to one best matched name in our database, a red warning flag will appear next to the submitted name.
+40. `Accepted_name_lsid`: As exported by TNRS.
+<br>
+**Below columns added specifically for this backbone** - These fields represent the actual output.
+41. `Status_correct`: Simplification of `Taxonomic_status`.
+42. `Name_correct`: If Accepted_name is non-null, otherwise returns `Name_matched`. This field represent the union of accepted + matched name.
+43. `Genus_correct`: Genus derived from `Name_correct`, but only when `Accepted_name_rank` is lower than family.
+44. `Rank_correct`: Simplification of `Accepted_name_rank`.
+45. `Family_correct`: Family of `Name_correct`. Complements `Accepted_name_family` with multiple sources.
+46. `Name_short`: First two words of `Name_correct`.
+47. `phylum`: As derived from `The Catalogue of Life`.
+48. `is_vascular_species`: TRUE if the species is a vascular plant. It is derived based on selection of `phylum` from `The Catalogue of Life`.
+49. `Taxon group`: Taxon group, as in Turboveg. Five possible entries. *Alga*, *Lichen*, *Moss*, *Vascular plant* or *Unknown*.
+<br><br>
+The object `Backbone3.0.RData` also contains two ancillary vectors, which were use to refine the Backbone. These are:
+`lichen.genera` - a list of genera for lichen species contained in the Backbone; `mushroom` - a list of genera for mushroom species spotted in sPlot species list (and excluded); `mushroom.families` - a list of family names for mushroom spotted in sPlot (and excluded).
+
+# Header
+The *header* object contains all plot-level information, including source and location. The description of its construction can be found at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/04_buildHeader.html (download needed).
+Import data
+```{r}
+load("../_output/header_sPlot3.0.RData")
+```
+
+## Show output
+```{r echo=F}
+knitr::kable(header %>%
+ sample_n(10),
+ caption="Example of header (only 10 randomly selected plots shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+sPlot 3.0 contains `r nrow(header)` Plots.
+
+## Description of fields
+
+1. `PlotObservationID`: Identificator provided by Turboveg 3, unique for each plot.
+2. `Dataset`: Name of source dataset.
+3. `GIVD ID`: [GIVD](https://www.givd.info/) code of source dataset.
+4. `TV2 relevé number`: Original number in the Turboveg 2 version of the source dataset.
+5. `ORIG_NUM`: Original number of the plot in the source dataset.
+6. `GUID`: GUID identifier, as created in Turboveg 2.
+<br>
+**Geographic location**
+7. `Longitude`: Degrees, WGS85.
+8. `Latitude`: Degrees, WGS85.
+9. `Location uncertainty (m)`: Uncertainty of geographic coordinates. Negative if estimated, instead of measured.
+10. `Country`: Original country name in Turboveg 3.
+11. `CONTINENT`: Continent.
+12. `sBiome`: Biome, as defined in [Bruelheide et al. 2019 - JVS](https://onlinelibrary.wiley.com/doi/10.1111/jvs.12710).
+13. `sBiomeID`: Biome ID, as defined in [Bruelheide et al. 2019 - JVS](https://onlinelibrary.wiley.com/doi/10.1111/jvs.12710) (see Appendix 5).
+14. `Ecoregion`: [WWF Ecoregion](https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world)
+15. `EcoregionID`: WWF ecoreigon ID.
+16. `Locality`: As reported in the original data.
+<br>
+**Sampling design**
+17. `Relevé area (m²)`: Size of the sampling plot.
+18. `Cover abundance scale`: Cover\\abundance scale used in the field.
+19. `Date of recording`: Date of sampling.
+20. `Plants recorded`: Group of plants recorded in the field: e.g., "All vascular plants", "Woody plants with DBH > 10cm". In case of NA, it is mostly safe to assume that all vascular plants were recorded.
+21. `Herbs identified (y/n)`: Y if herbs were identified (as opposed to woody species). In case of NA, it is mostly safe to assume that herbs were sampled and identified.
+22. `Mosses identified (y/n)`: Y if mosses were identified. In case of NA, it is safe to assume that Mosses were NOT sampled.
+23. `Lichens identified (y/n)`: Y if lichens were identified. In case of NA, it is safe to assume that lichens were NOT sampled.
+<br>
+**Topogaphy**
+24. `elevation_dem`: Elevation of plot, as derived from geographic coordinates (and averaged based on location uncertainty).
+25. `Altitude (m)`: Elevation of plot, as measured in the field.
+26. `Aspect (°)`: Topographical aspect of plot (in degrees).
+27. `Slope (°)`: Topographical slope of plot (in degrees).
+<br>
+**Vegetation types** - The fields Forest, Shrubland, Grassland, Wetland and Sparse_vegetation are not mutually exclusive. Their combination identifies ecotones and transition vegetation types.
+28. `Forest`: TRUE (=1) or Fals (=0).
+29. `Shrubland`: TRUE (=1) or Fals (=0).
+30. `Grassland`: TRUE (=1) or Fals (=0).
+31. `Wetland`: TRUE (=1) or Fals (=0).
+32. `Sparse.vegetation`: TRUE (=1) or Fals (=0).
+33. `Naturalness`: 1=Natural, 2=Semi-natural, 3=Anthropogenic.
+34. `ESY`: EUNIS Habitat Classification Expert system, as described in [Chytrý et al. (2020)](https://onlinelibrary.wiley.com/doi/full/10.1111/avsc.12519).
+<br>
+**Vegetation structure**
+35. `Cover total (%)`: Total cover of vegetation.
+36. `Cover tree layer (%)`: Total cover of tree layer.
+37. `Cover shrub layer (%)`: Total cover of shrub layer.
+38. `Cover herb layer (%)`: Total cover of herb layer.
+39. `Cover moss layer (%)`: Total cover of moss layer.
+40. `Cover lichen layer (%)`: Total cover of lichen layer.
+41. `Cover algae layer (%)`: Total cover of algae layer.
+42. `Cover litter layer (%)`: Total cover of litter layer.
+43. `Cover open water (%)`: Total cover of open water.
+44. `Cover bare rock (%)`: Total cover of bare rocks.
+45. `Height (highest) trees (m)`: Height of the highest tree layer.
+46. `Height lowest trees (m)`: Height of the lowest tree layer.
+47. `Height (highest) shrubs (m)`: Height of the highest shrub layer.
+48. `Height lowest shrubs (m)`: Height of the lowest shrub layer.
+49. `Aver. height (high) herbs (cm)`: Average height of highest herb layer.
+50. `Aver. height lowest herbs (cm)`: Average height of the lowest herb layer.
+51. `Maximum height herbs (cm)`: Maximum height of herbs.
+52. `Maximum height cryptogams (mm)`: Maximum height of cryptogams.
+<br>
+Additional info on some of the fields is in [Bruelheide et al. 2019 - JVS](https://onlinelibrary.wiley.com/doi/10.1111/jvs.12710).
+
+# DT Table
+The DT table, contains information on which species was recorded in what plot, and with what abundance. The construction of the object `DT_sPlot3.0` is documented at https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/06_buildDT.html (download needed).
+```{r}
+load("../_output/DT_sPlot3.0.RData")
+```
+
+## Show output
+```{r echo=F}
+knitr::kable(DT2 %>%
+ filter(PlotObservationID %in% sample(header$PlotObservationID,3)),
+ caption="Example of DT table (only species from three randomly selected plots shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+The DT table contains `r nrow(DT2)` entries, from `r length(unique(DT2$Species))` species.
+
+## Description of fields
+1. `PlotObservationID`: Plot ID (as in Header).
+2. `Species`: Resolved species name (as derived from the field `name_short` in the Backbone).
+3. `Species_original`: Original species name (before resolution, as in the field `name_sPlot_TRY` in the Backbone).
+4. `Rank_correct`: Taxonomic rank of the corrected name (as in the homonymous field in the Backbone).
+5. `Taxon_group`: Taxon group (as in the homonymous field in the Backbone).
+6. `Layer`: Vegetation layer, as specified in Turboveg: *0*: No layer specified, *1*: Upper tree layer, *2*: Middle tree layer, *3*: Lower tree layer, *4*: Upper shrub layer, *5*: Lower shrub layer, *6*: Herb layer, *7*: Juvenile, *8*: Seedling, *9*: Moss layer.
+7. `Cover_code`: Cover\\abundance code in original data, before transformation to quantitative value or percentage cover.
+8. `Ab_scale`: Abundance scale in original data. Possible values are: *CoverPerc*: Cover Percentage, *pa*: Presence absence, *x_BA*: Basal Area, *x_IC*: Individual count, *x_SC*: Stem count, *x_IV*: Relative Importance, *x_RF*: Relative Frequency.
+9. `Abundance`: Abundance value, in original value, or as transformed from original `Cover code` to quantitative values.
+10. `Relative_cover`: Abundance\\Cover of each species after being normalized to 1 in each plot.
+
+# Functional Traits and Community Weighted Means\\Variances
+The object `Traits_CWMs_sPlot3.RData` contains three data.frames:
+1) data.frame `try.combined.means` - Mean and s.d. of gap-filled functional traits of all species in TRY 5.0.
+2) data.frame `sPlot.traits` - Mean and s.d. of gap-filled functional traits of all species in sPlot.
+3) data.frame `CWM` - Plot Community Weighted means and variances.
+<br>
+
+A detailed description of the construction of this object is available at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/07_buildCWMs.html (download needed)
+```{r}
+load("../_output/Traits_CWMs_sPlot3.RData")
+```
+## Show output
+Object `try.combined.means`.
+```{r echo=F}
+knitr::kable(try.combined.means %>%
+ sample_n(10),
+ caption="Example of trait table of TRY species (only 10 randomly selected species shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+The object `try.combined.means` contains the average and standard deviation of the gap-filled trait values of `r nrow(try.combined.means)` taxa (species or genera) from TRY 5.0.
+<br>
+
+Object `sPlot.traits`.
+```{r echo=F}
+knitr::kable(sPlot.traits %>%
+ sample_n(10),
+ caption="Example of trait table of sPlot species (only 10 randomly selected species shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+The object `sPlot.traits` contains the average and standard deviation of the gap-filled trait values for `r sPlot.traits %>% filter(!is.na(SLA_mean)) %>% nrow()` taxa (species or genera), out of `r nrow(sPlot.traits)` in sPlot. It also contains growth form information for `r sPlot.traits %>% filter(!is.na(GrowthForm)) %>% nrow()` species.
+
+<br>
+Object `CWM`.
+```{r echo=F}
+knitr::kable(CWM %>%
+ sample_n(10),
+ caption="Example of CWM table (only 10 randomly selected plots shown)") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+The CWM table contains `r nrow(CWM)` entries, i.e., the combination between `r CWM %>% distinct(PlotObservationID) %>% nrow()` unique plots, and `r CWM %>% distinct(variable) %>% nrow()`.
+
+
+
+
+## Description of fields
+
+**Legend of traits** used in the data.frame `sPlot.traits` and `try.combined.means`. The number represents the code in TRY dictionary. The abbreviation used is reported after the trait description.
+<br>
+4 Stem specific density (SSD) or wood density (stem dry mass per stem fresh volume)_g/cm3 - `StemDens`
+6 Root rooting depth_m - `RootingDepth`
+11 Leaf area per leaf dry mass (specific leaf area, SLA or 1/LMA) - `SLA`
+13 Leaf carbon (C) content per leaf dry mass_mg/g - `LeafC.perdrymass`
+14 Leaf nitrogen (N) content per leaf dry mass_mg/g - `LeafN`
+15 Leaf phosphorus (P) content per leaf dry mass_mg/g - `LeafP`
+18 Plant height (vegetative + generative) - `PlantHeight`
+21 Stem diameter_m - `StemDiam`
+26 Seed dry mass_mg - `SeedMass`
+27 Seed length_mm - `Seed.length`
+46 Leaf thickness_mm - `LeafThickness`
+47 Leaf dry mass per leaf fresh mass (leaf dry matter content, LDMC)_g g-1 - `LDMC`
+50 Leaf nitrogen (N) content per leaf area_g m-2 - `LeafNperArea`
+55 Leaf dry mass (single leaf)_mg - `LeafDryMass.single`
+78 Leaf nitrogen (N) isotope signature (delta 15N)_per - `Leaf.delta.15N`
+95 Seed germination rate (germination efficiency) % - `SeedGerminationRate`
+138 Seed number per reproducton unit_number - `Seed.num.rep.unit`
+144 Leaf length_mm - `LeafLength`
+145 Leaf width_cm - `LeafWidth`
+146 Leaf carbon/nitrogen (C/N) ratio_g/cm3 - `LeafCN.ratio`
+163 Leaf fresh mass_g - `Leaffreshmass`
+169 Stem conduit density (vessels and tracheids)_mm-2 - `Stem.cond.dens`
+223 Species genotype: chromosome number_dimensionless - `Chromosome.n`
+224 Species genotype: chromosome cDNA content_pg - `Chromosome.cDNAcont`
+237 Dispersal unit length_mm - `Disp.unit.leng`
+281 Stem conduit diameter (vessels, tracheids)_micro m - `StemConduitDiameter`
+282 Wood vessel element length; stem conduit (vessel and tracheids) element length_micro m - `Wood.vessel.length`
+289 Wood fiber lengths_micro m - `WoodFiberLength`
+1080 Root length per root dry mass (specific root length, SRL)_cm/g - `SpecificRootLength`
+3112 Leaf area (in case of compound leaves: leaf, undefined if petiole in- or excluded)_mm2 - `LeafArea.leaf.undef`
+3113 Leaf area (in case of compound leaves: leaflet, undefined if petiole is in- or excluded)_mm2 - `LeafArea.leaflet.undef`
+3114 Leaf area (in case of compound leaves undefined if leaf or leaflet, undefined if petiole is in- or excluded)_mm2 - `LeafArea.undef.undef`
+3120 Leaf water content per leaf dry mass (not saturated)_g(W)/g(DM) - `LeafWaterCont`
+<br>
+<br>
+**List of Fields**
+<br>
+Object `sPlot.traits`
+1. `Species`: Species name, as in the field `Species` of DT2.
+2. `GrowthForm`: Possible values: *herb* , *herb/shrub* , *herb/shrub/tree* , *other* , *shrub* , *shrub/tree* , *tree*.
+3. `is.tree.or.tall.shrub`: TRUE\\FALSE - Defines as tree of tall shrub if Growth Form contains is equal to 'tree', 'shrub/tree' or 'shrub', or if Height > 10 m.
+4. `n`: Number of individual gap-filled entries used for calculating mean and s.d. of the taxon.
+5-37. **Functional traits** means
+38-70. **Functional traits** standard deviations
+<br>
+
+
+Object `try.combined.means`
+1. `Taxon_name`: Species name, as in the field `Species` of DT2.
+2. `Rank_correct`: Rank of taxon name (either "Species", or "Genus"), used for calculating the mean and s.d. of trait values.
+3. `n`: Number of individual gap-filled entries used for calculating mean and s.d. of the taxon.
+4-36. **Functional trait** means
+37-69. **Functional trait** standard deviations
+<br>
+<br>
+
+Object `CWM`
+1. `PlotObservationID`: Plot ID, as in `header`.
+2. `variable`: Functional trait.
+3. `sp.richness`: Number of species in plot.
+4. `prop.sp.with.trait`: Proportion of species with trait information.
+5. `trait.coverage`: Proportion of the species' relative cover for which functional trait is available.
+6. `CWM`: Community Weighted Mean.
+7. `CWV`: Community Weighted Variance.
+
+# Environmental variables
+```{r}
+load("../_output/SoilClim_sPlot3.RData")
+```
+The object `SoilClim_sPlot3` contains data on the environmental conditions of plots, as derived from matching Plots' coordinates with global-scale layers of topography, climate and soil data. Its construction is documented at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/05_ExtractEnvironment.html (download needed).
+Environmental data derive from three sources:
+
+1. Bioclimatic variables (bio01-bio19) derive from [CHELSA](http://chelsa-climate.org/bioclim/).
+2. Soil variables (5 cm depth) derive from the [ISRIC dataset](https://www.isric.org/), downloaded at 250-m resolution.
+3. DEM derive from package [elevatr](https://cran.r-project.org/web/packages/elevatr/vignettes/introduction_to_elevatr.html#get_raster_elevation_data), which uses the [Terrain Tiles on Amazon Web Services](https://registry.opendata.aws/terrain-tiles/).
+
+## Show output
+Example of dataframe `soilclim`.
+```{r echo=F}
+knitr::kable(soilclim %>%
+ sample_n(10),
+ caption="Example of environmental information on 10 randomly selected plots") %>%
+ kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
+ latex_options = "basic",
+ full_width = F, position = "center")
+```
+
+## Description of fields
+1. `PlotObservationID`: Plot ID, as in `header`.
+<br>
+**Elevation data** - median and s.d.
+2. `Elevation_median`: Median elevation in a circle centered on plot location, having a radius of the plot's `location uncertainty` (NA if >50km).
+3. `Elevation_q2.5`: 2.5 percentile of elevation in a circle centered on plot location, having a radius of the plot's `location uncertainty` (NA if >50km).
+4. `Elevation_q97.5`: 97.5 percentile of elevation in a circle centered on plot location, having a radius of the plot's `location uncertainty` (NA if >50km).
+5. `Elevation_DEM.res`: Resolution of Digital Elevation Model used (in m).
+<br>
+**Bioclimatic Variables** - Mean and s.d.
+6. `bio01`: Annual Mean Temperature
+7. `bio02`: Mean Diurnal Range
+8. `bio03`: Isothermality
+9. `bio04`: Temperature Seasonality
+10. `bio05`: Max Temperature of Warmest Month
+11. `bio06`: Min Temperature of Coldest Month
+12. `bio07`: Temperature Annual Range
+13. `bio08`: Mean Temperature of Wettest Quarter
+14. `bio09`: Mean Temperature of Driest Quarter
+15. `bio10`: Mean Temperature of Warmest Quarter
+16. `bio11`: Mean Temperature of Coldest Quarter
+17. `bio12`: Annual Precipitation
+18. `bio13`: Precipitation of Wettest Month
+19. `bio14`: Precipitation of Driest Month
+20. `bio15`: Precipitation Seasonality
+21. `bio16`: Precipitation of Wettest Quarter
+22. `bio17`: Precipitation of Driest Quarter
+23. `bio18`: Precipitation of Warmest Quarter
+24. `bio19`: Precipitation of Coldest Quarter
+25-43 - Same as above, but standard deviations
+<br>
+**Soil Variables** - Mean and s.d.
+44. `BLDFIE`: Bulk Density (fine earth) in kg/m3
+45. `CECSOL`: Cation Exchange capacity of soil
+46. `CLYPPT`: Clay mass fraction in %
+47. `CRFVOL`: Coarse fragments volumetric in %
+48. `ORCDRC`: Soil Organic Carbon Content in g/kg
+49. `PHIHOX`: Soil pH x 10 in H20
+50. `SLTPPT`: Silt mass fraction in %
+51. `SNDPPT`: Sand mass fraction in %
+52-59 - Same as above, but standard deviations
+
+
+# SessionInfo
+```{r}
+sessionInfo()
+```
+
+