library(tidyverse)
library(mudata2)
raw <- read_mudata("data-raw/kellys_lake.mudata")
ages <- raw %>%
select_params(contains("age_ad")) %>%
tbl_data() %>%
select(-dataset, -n, -n_detect, -param) %>%
rename(age_ad = value)
rename_param <- . %>%
str_remove("/SINLAB") %>%
str_remove("/XRF/Vanta") %>%
str_remove("/RelAbund") %>%
str_remove("/MyCore") %>%
str_remove("/CRS") %>%
str_remove("/210Pb") %>%
str_replace("C_N", "C/N") %>%
str_replace("210Pb/Unsupported", "Unsupported 210Pb")
# rename params
raw$params$param <- rename_param(raw$params$param)
raw$data$param <- rename_param(raw$data$param)
# add ages
adm <- tidypaleo::age_depth_model(ages, depth, age_ad)
raw$data$age_ad <- raw$data$depth %>% tidypaleo::predict_age(object = adm)
raw$data <- raw$data %>%
select(dataset, location, param, depth, age_ad, everything()) %>%
arrange(param, depth)
attr(raw, "x_columns") <- c("depth", "age_ad")
# make sure we didn't invalidate the object
validate_mudata(raw)
# use data
kellys_lake <- raw
kellys_lake_geochem <- kellys_lake %>%
select_params(-Fe, -Mn,-age_ad, -`Unsupported 210Pb`, -Zn, -Ti) %>%
select_params(-starts_with("Cladocera")) %>%
tbl_data() %>%
select(-dataset) %>%
filter(!is.na(value))
# ggplot(kellys_lake_geochem, aes(x = value, y = depth)) +
# geom_point() +
# facet_wrap(vars(param), scales = "free_x", nrow = 1)
usethis::use_data(kellys_lake_geochem, overwrite = TRUE)
kellys_lake_cladocera <- kellys_lake %>%
select_params(starts_with("Cladocera")) %>%
tbl_data() %>%
select(-c(dataset, error, error_type, n_detect, n)) %>%
rename(rel_abund = value, taxon = param) %>%
mutate(
taxon = taxon %>%
str_remove("Cladocera/") %>%
str_replace("Acantholebris curvirostris", "Acantholeberis curvirostris")
) %>%
# select only some taxa to include in toy data set
mutate(
taxon = fct_lump(taxon, 12, w = rel_abund) %>%
fct_reorder(rel_abund) %>%
fct_recode("D. pulex-complex" = "D. pulex complex")
) %>%
filter(taxon != "Other")
ggplot(kellys_lake_cladocera, aes(x = rel_abund, y = depth)) +
tidypaleo::geom_col_segsh() +
tidypaleo::facet_abundanceh(vars(taxon))
usethis::use_data(kellys_lake_cladocera, overwrite = TRUE)
kellys_lake_ages <- ages
usethis::use_data(kellys_lake_ages, overwrite = TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.