inst/doc/mudata_create.R

In mudata2: Interchange Tools for Multi-Parameter Spatiotemporal Data

## -----------------------------------------------------------------------------
library(mudata2)
ns_climate %>% tbl_data()

## ---- include=FALSE-----------------------------------------------------------
# this is to avoid depending on tidyverse
library(tidyr)
library(dplyr)
data("pocmaj")
data("pocmajsum")

## ---- eval = FALSE------------------------------------------------------------
#  library(tidyverse)
#  data("pocmaj")
#  data("pocmajsum")

## -----------------------------------------------------------------------------
pocmajwide <- pocmajsum %>%
  select(core, depth, Ca, V, Ti)

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(pocmajwide, row.names = FALSE, digits = 0)

## -----------------------------------------------------------------------------
pocmajwide <- pocmajwide %>%
  rename(location = core)

## -----------------------------------------------------------------------------
pocmajlong <- pocmajwide %>%
  gather(Ca, Ti, V, key = "param", value = "value")

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(pocmajlong), row.names = FALSE, digits = 0)

## -----------------------------------------------------------------------------
md <- mudata(pocmajlong)
md

## ---- results='hide'----------------------------------------------------------
pocmajsum

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(pocmajsum, row.names = FALSE, digits = 0)

## -----------------------------------------------------------------------------
pocmajwide <- pocmajsum %>%
  rename(location = core)

## -----------------------------------------------------------------------------
pocmajlong <- parallel_gather(
  pocmajwide,
  key = "param",
  value = c(Ca, Ti, V),
  sd = c(Ca_sd, Ti_sd, V_sd)
)

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(pocmajlong), row.names = FALSE, digits = 0)

## ---- warning=FALSE-----------------------------------------------------------
md <- mudata(pocmajlong)
md

## -----------------------------------------------------------------------------
# default parameter table
md %>%
  tbl_params()

# parameter table with metadata
md %>%
  update_params(method = "Portable XRF Spectrometer (Olympus X-50)") %>%
  tbl_params()

## -----------------------------------------------------------------------------
# default location table
md %>%
  tbl_locations()

# location table with metadata
md %>%
  update_locations(
    "MAJ-1",
    latitude = -64.298, longitude = 44.819, lake = "Lake Major"
  ) %>%
  update_locations(
    "POC-2",
    latitude = -65.985, longitude = 44.913, lake = "Pockwock Lake"
  ) %>%
  tbl_locations()

## -----------------------------------------------------------------------------
# default datasets table
md %>%
  tbl_datasets()

# datasets table with metadata
md %>%
  update_datasets(source = "R package mudata2") %>%
  tbl_datasets()

## -----------------------------------------------------------------------------
md_doc <- md %>%
  update_params(method = "Portable XRF Spectrometer (Olympus X-50)") %>%
  update_locations(
    "MAJ-1",
    latitude = -63.486, longitude = 44.732, lake = "Lake Major"
  ) %>%
  update_locations(
    "POC-2",
    latitude = -63.839, longitude = 44.794, lake = "Pockwock Lake"
  ) %>%
  update_datasets(source = "R package mudata2")

## -----------------------------------------------------------------------------
md_doc <- md_doc %>%
  update_columns_table()

## -----------------------------------------------------------------------------
# default columns table
md_doc %>%
  tbl_columns()

# columns with metadata
md_doc %>%
  update_columns("depth", description = "Depth in sediment core (cm)") %>%
  update_columns("sd", description = "Standard deviation uncertainty of n=3 values") %>%
  tbl_columns() %>%
  select(dataset, table, column, description, type)

## -----------------------------------------------------------------------------
md_doc <- md %>%
  update_params(method = "Portable XRF Spectrometer (Olympus X-50)") %>%
  update_locations(
    "MAJ-1",
    latitude = -63.486, longitude = 44.732, lake = "Lake Major"
  ) %>%
  update_locations(
    "POC-2",
    latitude = -63.839, longitude = 44.794, lake = "Pockwock Lake"
  ) %>%
  update_datasets(source = "R package mudata2") %>%
  update_columns_table() %>%
  update_columns("depth", description = "Depth in sediment core (cm)") %>%
  update_columns("sd", description = "Standard deviation uncertainty of n=3 values")

## ---- eval = FALSE------------------------------------------------------------
#  # write to directory
#  write_mudata(poc_maj, "poc_maj.mudata")
#  # write to ZIP
#  write_mudata(poc_maj, "poc_maj.mudata.zip")
#  # write to JSON
#  write_mudata(poc_maj, "poc_maj.mudata.json")

## ---- eval = FALSE------------------------------------------------------------
#  # read from directory
#  read_mudata("poc_maj.mudata")
#  # read from ZIP
#  read_mudata("poc_maj.mudata.zip")
#  # read from JSON
#  read_mudata("poc_maj.mudata.json")