#29: Centralize gathering, cleaning and exporting of raw data in data…

…-raw/data.Rmd.

data-raw/data.Rmd

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+---
+title: "Gather raw data,clean it and export it to  data/"
+output: github_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+# Overview
+
+This document exports data. It takes data from data-raw/, cleans it, and places a .rda version of it in data/. To update all exported data you can do either of two things: (1) Click Knit (Ctrl+Shift+K), which will also update data.md, or (2) Run > Run All (Ctrl+Alt+R). You can also update the data in specific code chunks. (Learn more about RMarkdown documents [here](https://rmarkdown.rstudio.com/lesson-1.html).)
+
+# Gather raw master data and clean it
+
+Clean master data
+
+```{r master}
+master <- readr::read_csv(here::here("data-raw/allotemp_main.csv"))
+```
+
+```{r master-clean}
+# FIXME: Remove ambiguity of this code chunk (#29; https://goo.gl/rmuzmH)
+# eliminate rows where fam or sp is unknown #use unique(allo_main$species)
+master <- subset(master, family != "Unkown")
+# chnage name of "equation" column to "equation_form"
+```
+
+# Export subsets of the clean master data
+
+This section exports subsets of the clean master data to data/. Each dataset documented in R/data.R to produce a help file that can be accessed from the R console with `?name-of-the-dataset` and also from the Functions Index tab of the website of __allodb__.
+
+## Dataset `equations`
+
+Allometric equations (doesn't include sites, but sp? not sure)
+
+```{r equations}
+# Needs to include a column after'equation_form' to combine
+# coeficienss+formula so we get "unique" equations, then give unique id
+equations_cols <- c(
+  "equation_id",
+  "model_parameters",
+  "biomass_units_original",
+  "regression_model",
+  "other_equations_tested",
+  "log (biomass)",
+  "d",
+  "dbh_min_cm",
+  "dbh_max_cm",
+  "n_trees",
+  "dbh_units_original",
+  "equation",
+  "equation_grouping",
+  "bias correction _CF"
+)
+equations <- master[equations_cols]
+usethis::use_data(equations, overwrite = TRUE)
+
+equations_metadata <- readr::read_csv(
+  here::here("data-raw/data_equations_metadata.csv")
+)
+usethis::use_data(equations_metadata, overwrite = TRUE)
+```
+
+## Dataset `missing_values`
+
+```{r missing-values}
+missing_values_metadata <- readr::read_csv(
+  here::here("data-raw/data_missing_values_metadata.csv")
+)
+usethis::use_data(missing_values_metadata, overwrite = TRUE)
+```
+
+## Dataset `references`
+
+References (links to wood density table with an id, my raw reference table includes sites for my own sanity!).
+
+```{r}
+# TODO: Add table.
+
+# usethis::use_data(references, overwrite = TRUE)
+
+references_metadata <- readr::read_csv(
+  here::here("data-raw/data_references_metadata.csv")
+)
+usethis::use_data(references_metadata, overwrite = TRUE)
+```
+
+## Dataset `sites_info`
+
+```{r}
+# Basic info ForestGEO sites
+
+# TODO: Add table. See https://goo.gl/ic7uya.
+
+# usethis::use_data(references, overwrite = TRUE)
+```
+
+## Dataset `sitespecies`
+
+Site-species (includes non-tropical sites, links to equation table with eq Id).
+
+```{r}
+sitespecies_cols <- c(
+  "site",
+  "family",
+  "species",
+  "species_code",
+  "life_form",
+  "model_parameters",
+  "allometry_development_method",
+  "equation_id",
+  "regression_model",
+  "wsg",
+  "wsg_id"
+)
+sitespecies <- master[sitespecies_cols]
+usethis::use_data(sitespecies, overwrite = TRUE)
+
+sitespecies_metadata <- readr::read_csv(
+  here::here("data-raw/data_sitespecies_metadata.csv")
+)
+usethis::use_data(sitespecies_metadata, overwrite = TRUE)
+```
+
+## Dataset `wsg`
+
+Wood density (with this scrip and master table we only take wsg for temperate sites, later to be merge with trop).
+
+```{r}
+wsg_cols <- c(
+  "wsg_id",
+  "family",
+  "species",
+  "wsg",
+  "wsg_specificity",
+  "variable",
+  "site"
+)
+wsg <- master[wsg_cols]
+usethis::use_data(wsg, overwrite = TRUE)
+
+wsg_metadata <- readr::read_csv(
+  here::here("data-raw/data_wsg_metadata.csv")
+)
+usethis::use_data(wsg_metadata, overwrite = TRUE)
+```
+