Prepare data
In this script we prepared the data for posterior analysis. The data are also deposited at Figshare: doi:10.6084/m9.figshare.21207836.v1 
Code
raw_data <- read_excel(path=here::here("data/rpasfield_alcontar.xlsx"),
sheet = "alcontar") Code
raw_data %>% datatable() Code
spdata <- read_excel(path=here::here("data/rpasfield_alcontar.xlsx"),
sheet = "species_coverage")
table_species <- spdata %>%
mutate(treatment = recode(treatment,
'Prescribed Burn'='PB',
'Pyric Herbivorism'='PH')) %>%
group_by(species_name, treatment) %>%
summarise_at("coverage", list(mean = ~round(mean(., na.rm=TRUE),2),
se = ~round(plotrix::std.error(., na.rm = TRUE),2),
min = ~min(., na.rm = TRUE),
max = ~max(., na.rm = TRUE),
n = ~length(.)
))
table_species %>% kable()| species_name | treatment | mean | se | min | max | n |
|---|---|---|---|---|---|---|
| Alyssum granatense | PH | 0.17 | 0.03 | 0.10 | 0.2 | 3 |
| Androsace maxima | PH | 0.15 | 0.05 | 0.10 | 0.2 | 2 |
| Andryala ragusina | PB | 0.30 | NA | 0.30 | 0.3 | 1 |
| Andryala ragusina | PH | 0.20 | 0.10 | 0.10 | 0.3 | 2 |
| Anthyllis vulneraria | PB | 0.40 | NA | 0.40 | 0.4 | 1 |
| Anthyllis vulneraria | PH | 0.27 | 0.09 | 0.10 | 0.4 | 3 |
| Arabidopsis thaliana | PB | 0.10 | 0.00 | 0.10 | 0.1 | 3 |
| Arabidopsis thaliana | PH | 0.78 | 0.49 | 0.10 | 5.0 | 10 |
| Arabis auriculata | PH | 0.27 | 0.12 | 0.10 | 0.5 | 3 |
| Arabis parvula | PH | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Arenaria leptoclados | PH | 0.31 | 0.10 | 0.10 | 1.0 | 9 |
| Argyrolobium zanonii | PH | 0.50 | NA | 0.50 | 0.5 | 1 |
| Arrhenatherum album | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Artemisia campestris | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Asperula hirsuta | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Asperula hirsuta | PH | 1.90 | 1.68 | 0.20 | 12.0 | 7 |
| Asphodelus albus | PB | 1.42 | 0.46 | 0.10 | 5.0 | 11 |
| Asphodelus albus | PH | 1.82 | 0.81 | 0.10 | 6.0 | 8 |
| Asteraceae | PH | 0.20 | NA | 0.20 | 0.2 | 1 |
| Asterolinon linum-stellatum | PB | 0.10 | 0.00 | 0.10 | 0.1 | 4 |
| Asterolinon linum-stellatum | PH | 0.16 | 0.02 | 0.10 | 0.3 | 11 |
| Astragalus alopecuroides | PB | 5.00 | 1.00 | 4.00 | 6.0 | 2 |
| Astragalus monspessulanus subsp. monspessulanus | PB | 1.05 | 0.45 | 0.60 | 1.5 | 2 |
| Astragalus sesameus | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Avenula bromoides subsp. pauneroi | PB | 0.36 | 0.05 | 0.30 | 0.5 | 4 |
| Avenula bromoides subsp. pauneroi | PH | 0.27 | 0.08 | 0.10 | 0.8 | 8 |
| Biscutella laxa | PH | 0.27 | 0.06 | 0.10 | 0.7 | 13 |
| Bombycilaena | PH | 1.00 | NA | 1.00 | 1.0 | 1 |
| Bromus hordeaceus | PH | 0.50 | NA | 0.50 | 0.5 | 1 |
| Bromus rubens | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Bromus rubens | PH | 0.36 | 0.15 | 0.10 | 1.5 | 9 |
| Bromus tectorum | PH | 0.17 | 0.03 | 0.10 | 0.2 | 3 |
| Bufonia tenuifolia | PH | 0.15 | 0.05 | 0.10 | 0.2 | 2 |
| Bupleurum spinosum | PB | 3.53 | 0.83 | 0.10 | 15.0 | 21 |
| Bupleurum spinosum | PH | 1.13 | 0.19 | 0.10 | 5.5 | 39 |
| Carex hallerana | PB | 4.78 | 3.78 | 0.20 | 16.0 | 4 |
| Carex hallerana | PH | 1.18 | 0.30 | 0.20 | 4.0 | 12 |
| Carlina | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Centaurea gabrielis-blancae | PH | 0.20 | NA | 0.20 | 0.2 | 1 |
| Cerastium brachypetalum | PH | 0.21 | 0.04 | 0.10 | 0.5 | 10 |
| Cerastium gracile | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Chaenorhinum grandiflorum | PH | 0.50 | 0.20 | 0.10 | 1.0 | 5 |
| Chaenorhinum macropodum subsp. macropodum | PH | 0.80 | 0.40 | 0.40 | 1.2 | 2 |
| Chaenorhinum minus | PH | 1.00 | NA | 1.00 | 1.0 | 1 |
| Clypeola jonthlaspi subsp. microcarpa | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Clypeola jonthlaspi subsp. microcarpa | PH | 0.20 | 0.08 | 0.10 | 0.5 | 5 |
| Colutea hispanica | PH | 0.80 | NA | 0.80 | 0.8 | 1 |
| Crepis albida subsp. grosii | PH | 0.72 | 0.20 | 0.10 | 1.3 | 5 |
| Crupina | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Crupina | PH | 0.13 | 0.03 | 0.10 | 0.2 | 3 |
| Dactylis glomerata | PB | 0.27 | 0.12 | 0.10 | 0.5 | 3 |
| Dactylis glomerata | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Desconocida | PH | 0.30 | NA | 0.30 | 0.3 | 2 |
| Digitalis obscura subsp. obscura | PH | 0.30 | NA | 0.30 | 0.3 | 1 |
| Dipcadi serotinum | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Eryngium campestre | PB | 0.37 | 0.13 | 0.10 | 0.5 | 3 |
| Eryngium campestre | PH | 0.56 | 0.36 | 0.10 | 2.0 | 5 |
| Euphorbia segetalis | PH | 1.70 | NA | 1.70 | 1.7 | 1 |
| Euphorbia serrata | PH | 3.80 | NA | 3.80 | 3.8 | 1 |
| Festuca capillifolia | PB | 3.00 | NA | 3.00 | 3.0 | 1 |
| Festuca capillifolia | PH | 3.48 | 1.84 | 0.20 | 25.0 | 13 |
| Filago fuscescens | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Filago fuscescens | PH | 0.12 | 0.03 | 0.10 | 0.2 | 4 |
| Fumaria officinalis subsp. officinalis | PH | 0.20 | NA | 0.20 | 0.2 | 1 |
| Galium parissiense subsp. parissiense | PH | 0.20 | 0.10 | 0.10 | 0.5 | 4 |
| Galium verticillatum | PB | 0.30 | 0.20 | 0.10 | 0.5 | 2 |
| Galium verticillatum | PH | 0.30 | NA | 0.30 | 0.3 | 1 |
| Genista scorpius | PB | 6.45 | 1.29 | 0.20 | 20.0 | 21 |
| Genista scorpius | PH | 6.45 | 1.40 | 0.20 | 55.0 | 49 |
| Helianthemum almeriense | PB | 6.17 | 0.55 | 1.00 | 12.0 | 32 |
| Helianthemum almeriense | PH | 4.13 | 0.66 | 0.20 | 16.0 | 40 |
| Helianthemum appenninum | PH | 2.19 | 0.71 | 0.10 | 8.0 | 11 |
| Helianthemum cinereum subsp. cinereum | PB | 0.50 | 0.17 | 0.10 | 1.6 | 8 |
| Helianthemum cinereum subsp. cinereum | PH | 1.14 | 0.34 | 0.10 | 7.0 | 22 |
| Helianthemum ledifolium | PB | 0.16 | 0.06 | 0.10 | 0.4 | 5 |
| Helianthemum ledifolium | PH | 1.06 | 0.39 | 0.10 | 2.5 | 7 |
| Helianthemum salicifolium | PB | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Helianthemum salicifolium | PH | 0.37 | 0.19 | 0.10 | 2.0 | 10 |
| Helictotrichon filifolium | PB | 3.58 | 1.14 | 0.30 | 14.0 | 11 |
| Helictotrichon filifolium | PH | 5.24 | 1.04 | 0.10 | 24.0 | 31 |
| Hippocrepis bourgaei | PB | 0.97 | 0.26 | 0.10 | 6.0 | 27 |
| Hippocrepis bourgaei | PH | 0.50 | 0.09 | 0.10 | 1.2 | 16 |
| Hippocrepis ciliata | PH | 0.20 | 0.00 | 0.20 | 0.2 | 3 |
| Hornungia petraea | PB | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Hornungia petraea | PH | 0.27 | 0.06 | 0.10 | 1.5 | 22 |
| Inula montana | PH | 1.00 | NA | 1.00 | 1.0 | 1 |
| Koeleria vallesiana | PB | 1.16 | 0.34 | 0.10 | 2.5 | 8 |
| Koeleria vallesiana | PH | 1.29 | 0.23 | 0.10 | 4.0 | 24 |
| Lavandula lanata | PH | 2.03 | 0.96 | 0.10 | 8.0 | 9 |
| Leontodon longirrostris | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Linaria aeruginea subsp. aeruginea | PH | 0.33 | 0.19 | 0.10 | 0.7 | 3 |
| Linaria arvensis | PH | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Linaria simplex | PH | 0.28 | 0.15 | 0.10 | 1.0 | 6 |
| Linum strictum | PB | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Linum suffruticosum | PB | 1.03 | 0.20 | 0.20 | 3.5 | 16 |
| Linum suffruticosum | PH | 0.78 | 0.10 | 0.10 | 4.2 | 48 |
| Lithodora fruticosa | PH | 0.80 | NA | 0.80 | 0.8 | 1 |
| Logfia arvensis | PH | 0.50 | NA | 0.50 | 0.5 | 1 |
| Lomelosia stellata | PH | 0.50 | NA | 0.50 | 0.5 | 1 |
| Macrochloa tenacissima | PB | 16.69 | 3.92 | 0.10 | 60.0 | 23 |
| Macrochloa tenacissima | PH | 26.05 | 5.25 | 0.10 | 80.0 | 28 |
| Malcolmia africana | PH | 0.30 | 0.06 | 0.20 | 0.4 | 3 |
| Medicago minima | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Medicago minima | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Minuartia campestris | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Minuartia hybrida | PB | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Minuartia hybrida | PH | 0.40 | 0.22 | 0.10 | 3.0 | 13 |
| Odontites | PB | 0.50 | NA | 0.50 | 0.5 | 1 |
| Odontites | PH | 0.27 | 0.04 | 0.10 | 0.5 | 12 |
| Ononis natrix | PH | 0.85 | 0.23 | 0.20 | 1.5 | 6 |
| Ononis pusilla | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Ononis pusilla | PH | 0.35 | 0.15 | 0.10 | 0.7 | 4 |
| Ononis reclinata subsp. Mollis | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Ononis reclinata subsp. Mollis | PH | 0.20 | NA | 0.20 | 0.2 | 1 |
| Onopordum acaulon | PB | 0.30 | NA | 0.30 | 0.3 | 1 |
| Onopordum acaulon | PH | 2.50 | NA | 2.50 | 2.5 | 1 |
| Papaver dubium | PH | 0.20 | NA | 0.20 | 0.2 | 1 |
| Paronychia argentea | PH | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Petrorhagia nanteuilii | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Petrorhagia nanteuilii | PH | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Picris hispanica | PB | 0.10 | 0.00 | 0.10 | 0.1 | 2 |
| Picris hispanica | PH | 3.20 | 2.02 | 0.10 | 7.0 | 3 |
| Plantago albicans | PB | 6.00 | NA | 6.00 | 6.0 | 1 |
| Poa bulbosa | PB | 0.30 | NA | 0.30 | 0.3 | 1 |
| Poa bulbosa | PH | 1.21 | 0.55 | 0.10 | 8.0 | 14 |
| Polygala rupestris | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Polygala rupestris | PH | 0.32 | 0.10 | 0.10 | 0.8 | 8 |
| Reseda alba | PB | 1.00 | NA | 1.00 | 1.0 | 1 |
| Reseda alba | PH | 1.00 | 0.00 | 1.00 | 1.0 | 2 |
| Reseda lutea | PB | 0.35 | 0.05 | 0.30 | 0.4 | 2 |
| Reseda lutea | PH | 0.98 | 0.24 | 0.10 | 5.0 | 23 |
| Reseda undata subsp. Undata | PH | 0.25 | 0.15 | 0.10 | 0.4 | 2 |
| Retama sphaerocarpa | PH | 4.00 | NA | 4.00 | 4.0 | 1 |
| Rhaponticum coniferum | PB | 0.40 | NA | 0.40 | 0.4 | 1 |
| Rhaponticum coniferum | PH | 0.40 | 0.30 | 0.10 | 0.7 | 2 |
| Rosmarinus officinalis | PH | 0.23 | 0.09 | 0.10 | 0.4 | 3 |
| Salvia lavandulifolia subsp. vellerea | PB | 1.00 | 0.00 | 1.00 | 1.0 | 2 |
| Salvia lavandulifolia subsp. vellerea | PH | 9.97 | 3.92 | 0.10 | 50.0 | 16 |
| Sanguisorba | PH | 0.48 | 0.19 | 0.20 | 1.0 | 4 |
| Scabiosa turolensis | PH | 0.80 | 0.70 | 0.10 | 1.5 | 2 |
| Scorzonera angustifolia | PB | 0.58 | 0.36 | 0.10 | 2.0 | 5 |
| Scorzonera angustifolia | PH | 0.27 | 0.09 | 0.10 | 0.4 | 3 |
| Sideritis pusilla | PH | 0.88 | 0.38 | 0.10 | 3.0 | 9 |
| Silene conica | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Silene mellifera | PH | 0.32 | 0.10 | 0.10 | 0.5 | 4 |
| Staehelina dubia | PH | 0.71 | 0.43 | 0.25 | 2.0 | 4 |
| Stipa almeriense | PH | 1.50 | NA | 1.50 | 1.5 | 1 |
| Stipa bufensis | PB | 17.00 | 16.00 | 1.00 | 33.0 | 2 |
| Stipa bufensis | PH | 0.70 | 0.26 | 0.10 | 2.0 | 7 |
| Teucrium capitatum subsp. gracillimum | PB | 1.49 | 0.68 | 0.10 | 5.0 | 8 |
| Teucrium capitatum subsp. gracillimum | PH | 0.74 | 0.13 | 0.10 | 2.0 | 27 |
| Thymelaea | PB | 0.40 | NA | 0.40 | 0.4 | 1 |
| Thymus zygis subsp. gracilis | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Thymus zygis subsp. gracilis | PH | 0.50 | NA | 0.50 | 0.5 | 1 |
| Trachynia distachya | PB | 0.20 | NA | 0.20 | 0.2 | 1 |
| Trifolium arvense | PH | 0.30 | NA | 0.30 | 0.3 | 1 |
| Trigonella polyceratia | PB | 0.10 | NA | 0.10 | 0.1 | 1 |
| Valerianella | PH | 0.10 | 0.00 | 0.10 | 0.1 | 4 |
| Velezia rigida | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
| Xeranthemum inapertum | PH | 0.10 | NA | 0.10 | 0.1 | 1 |
Code
# Get the name of the species
#| echo: false
#| eval: false
taxon <- table_species %>%
pull(species_name) %>%
unique() %>%
as_tibble() %>%
rename(scientificName = value)
taxon_names <- rgbif::name_backbone_checklist(taxon)
table_species_normalized <- table_species %>% inner_join(
(taxon_names %>% dplyr::select(scientificName, verbatim_name)),
by=c("species_name"="verbatim_name"))
write_csv(table_species_normalized, file=here::here("output/normalized_gbif.csv"))