#29: Further improve comments and code organization.

* Remove information that is better recorded via git. Git knows who does what and when. So it's best to avoid recording this info as comments because it is too easy for such comments to become out of sync with changes in the code.

* Describe file more generally so the comment remains up to date. Notice that the description refers to 4 tables; later a comment refers to 5 tables; and finally only 3 tables are exported. So it is best to not refer to how many tables we expect because this may continue to change.

* Remove references to table numbers; instead rely on table names. This is a clearer way to refer to tables because it identifies tables in a unique way (by name as opposed to by name and number). Also, numbers become out of date too easily, as tables are added, removed or their order is changed.

* Group code by table, not by task. This makes it easier to read and maintain the code.

data-raw/Script to build tables.R

@@ -1,37 +1,46 @@
-#Dec 20, 2017
-#Erika Gonzalez-Akre
-#Last update : 01/23/2018
-#This simple script is used to build 4 tables for the ForestGEO allometry datapaper
-
-#read.csv file, which could be modified. allotemp_main.cvs resides in 'data" folder in Git.
-master<-read.csv("allotemp_main.csv")
-#eliminate rows where fam or sp is unknown #use unique(allo_main$species)
-master<-subset(master, master$family !="Unkown")
-#chnage name of "equation" column to "equation_form"
-
-#Currently, we think 5 tables will go to the paper
-#table 1: Basic info ForestGEO sites (could be modified from forestgeo/Site-Data repository)
-#table 2: Site-species (includes non-tropical sites, links to equation table with eq Id)
-#table 3: Allometric equations (doesn't include sites, but sp? not sure)
-#table 4: Wood density (with this scrip and master table we only take wsg for temperate sites, later to be merge with trop)
-#table 5: References (links to wood density table with an id, my raw reference table includes sites for my own sanity!)
-
-#table2 or sitesp
+# Build the core tables of the data paper.
+
+master <- read.csv("allotemp_main.csv")
+# eliminate rows where fam or sp is unknown #use unique(allo_main$species)
+master <- subset(master, master$family != "Unkown")
+# chnage name of "equation" column to "equation_form"
+
+# Basic info ForestGEO sites (could be modified from
+# forestgeo/Site-Data repository).
+
+
+
+# TODO: Add table. See https://goo.gl/ic7uya.
+
+
+
+# Site-species (includes non-tropical sites, links to equation table
+# with eq Id).
 names(master)
-sitespecies<-master[c(1:5,23,19,20,24,6,7)]
+sitespecies <- master[c(1:5, 23, 19, 20, 24, 6, 7)]
 names(sitespecies)
+write.csv(sitespecies, file = "sitespecies.csv", row.names = FALSE)
 
-#table3, needs to include a column after'equation_form' to combine coeficienss+formula so we get
-#..."unique" equations, then give unique id
-equations<-master[c(20,23,18,24,25,26,13:16,17,21,22,28 )]
+# Allometric equations (doesn't include sites, but sp? not sure)
+# Needs to include a column after'equation_form' to combine
+# coeficienss+formula so we get "unique" equations, then give unique id
+equations <- master[c(20, 23, 18, 24, 25, 26, 13:16, 17, 21, 22, 28)]
 names(equations)
+write.csv(equations, file = "equations.csv", row.names = FALSE)
 
-#table4
-#right now this table may look incomplete..
-wsg<-master[c(7,2,3, 6,8,30,1)]
+# Wood density (with this scrip and master table we only take wsg for
+# temperate sites, later to be merge with trop).
+# Right now this table may look incomplete.
+wsg <- master[c(7, 2, 3, 6, 8, 30, 1)]
 names(wsg)
+write.csv(wsg, file = "wood_density.csv", row.names = FALSE)
+
+# References (links to wood density table with an id, my raw reference
+# table includes sites for my own sanity!).
+
+
+
+# TODO: Add table.
+
+
 
-#build tables, load them to github
-write.csv(sitespecies, file="sitespecies.csv", row.names=FALSE)
-write.csv(equations, file="equations.csv", row.names=FALSE)
-write.csv(wsg, file="wood_density.csv", row.names=FALSE)