Add TODOs to Dataset Files

man/ChromHMMiterations.Rd

@@ -12,6 +12,8 @@
 \usage{data("ChromHMMiterations")}
 \format{
   Named list of 3 data.frames: metrics, transition, emission.
+
+  TODO add codebook
   }
 \source{
   https://github.com/tdhock/ChromHMM-viz/blob/master/iterations.R

man/FluView.Rd

@@ -6,6 +6,10 @@
 }
 \description{
   Data about Flu outbreaks.
+
+  TODO need source
+
+  TODO need codebook
 }
 \usage{data("FluView")}
 \format{

man/FunctionalPruning.Rd

@@ -9,6 +9,8 @@
 }
 \usage{data("FunctionalPruning")}
 \format{
+  TODO add codebook
+
   a named list of 4 data.frames
 }
 \source{

man/PeakConsistency.Rd

@@ -10,7 +10,10 @@
   the peak.
 }
 \usage{data("PeakConsistency")}
-\format{A list of four data.frames: model, truth, signal, guess.
+\format{
+TODO add codebook
+
+A list of four data.frames: model, truth, signal, guess.
 }
 \source{
   https://github.com/tdhock/PeakSegJoint-paper/blob/master/figure-consistency.R

man/TestROC.Rd

@@ -9,6 +9,8 @@ Five peak detection models were evaluated.
 }
 \usage{data("TestROC")}
 \format{
+  TODO add codebook
+
   A list of two data frames.
 }
 \source{

man/UStornadoes.Rd

@@ -9,6 +9,8 @@ Tornadoes in the United States from 1950 to 2012
 }
 \usage{data(UStornadoes)}
 \format{
+  TODO add codebook
+
   A data frame with 41620 observations on the following 32 variables.
   \describe{
     \item{\code{fips}}{a numeric vector}

man/VariantModels.Rd

@@ -5,6 +5,8 @@
   Error rates of supervised learning methods for variant calling
 }
 \description{
+  TODO add codebook
+
   Several supervised machine learning models were applied to the binary
   classification task of predicting True Positive or False Positive
   variants, using several filtering scores as input.

man/WorldBank.Rd

@@ -9,6 +9,8 @@
 }
 \usage{data(WorldBank)}
 \format{
+  TODO add codebook
+
   A data frame with 11342 observations on the following 15 variables.
   \describe{
     \item{\code{iso2c}}{a character vector}

man/climate.Rd

@@ -13,6 +13,8 @@ Temperatures are given in degrees celsius (original data had Kelvin).
 }
 \usage{data(climate)}
 \format{
+  TODO add codebook
+
   A data frame with 41472 observations on the following 16 variables.
   \describe{
     \item{\code{time}}{a numeric vector}

man/compare.Rd

@@ -15,6 +15,8 @@ level curves of the learned functions.
 }
 \usage{data(compare)}
 \format{
+TODO add codebook
+
 List of 4 data.frames: error contains the test error of the learned
 models, bayes contains the Bayes classification error of the latent
 ranking function applied to the test data, rank contains the ranking

man/generation.loci.Rd

@@ -10,6 +10,8 @@ Evolution simulation
 }
 \usage{data(generation.loci)}
 \format{
+  TODO add codebook
+
   A data frame with 120000 observations on the following 4 variables.
   \describe{
     \item{\code{locus}}{a numeric vector}

man/intreg.Rd

@@ -10,6 +10,10 @@ observed several noisy piecewise constant signals, and we have
 weak labels about how many change-points occur in several regions. Max
 margin interval regression is an algorithm that uses this information to
 learn a penalty function for accurate change-point detection.
+
+TODO need source
+
+TODO need codebook
 }
 \usage{data(intreg)}
 \format{There are 7 related data.frames: signals contains the noisy

man/malaria.Rd

@@ -14,6 +14,8 @@
 }
 \usage{data("malaria")}
 \format{
+TODO add codebook
+
 List of 8 data.frames:
  $ error.variants  :'data.frame':	18800 obs. of  19 variables:
  $ regions         :'data.frame':	14 obs. of  6 variables:

man/mixtureKNN.Rd

@@ -9,6 +9,8 @@
 }
 \usage{data("mixtureKNN")}
 \format{
+  TODO add codebook
+
   Named list of 9 data.frames.
 }
 \source{

man/montreal.bikes.Rd

@@ -8,7 +8,10 @@
   Data on montreal bike usage, paths, and accidents, 2009-2014.
 }
 \usage{data("montreal.bikes")}
-\format{A named list of four data.frames. counter.counts contains dates
+\format{
+  TODO add codebook
+
+  A named list of four data.frames. counter.counts contains dates
   and counts of bikes at several locations in
   Montreal. counter.locations has the geographical coordinates of the
   counter locations. path.locations has the geographical coordinates of

man/pirates.Rd

@@ -10,6 +10,8 @@
 }
 \usage{data(pirates)}
 \format{
+  TODO add codebook
+
   A data frame with 6636 observations on the following 14 variables.
   \describe{
     \item{\code{Reference}}{factor}

man/prior.Rd

@@ -10,6 +10,8 @@ data sets.
 }
 \usage{data(prior)}
 \format{
+TODO add codebook
+
 List of 2 data.frames: accuracy contains the mean and standard error of
 the performance measures (sqErr and accuracy), data.set.info contains
 meta-data about the dimension and number of positive and negative

man/prostateLasso.Rd

@@ -9,6 +9,8 @@
 }
 \usage{data("prostateLasso")}
 \format{
+  TODO add codebook
+
   A list of 4 data.frames: path for the piecewise linear coefficient
   path, residuals for the prediction error of every model at every data
   point, models with one row per regularization parameter, error for

man/todo.md

@@ -0,0 +1,54 @@
+## About
+
+This file explains why there are all these TODOs scattered
+about some of the `.Rd` files in `man/`. There are 2 kinds
+of TODOs:
+
+1. TODO add source
+2. TODO add codebook
+
+The 1st appears only in 2 files: `FluView.Rd` and `intreg.Rd`.
+It means that the source for the file is missing.
+
+The 2nd appears in all of the files that contain a TODO. 
+It means that an explanation for each column's variable is
+missing. Since variable names are often either truncated or
+not obvious, having a brief explanation of each variable
+helps the reader use the dataset.
+
+A good example of a dataset with a good-enough codebook is
+`diamonds.Rd`. It gives enough information to make the
+dataset useable. Good-enough is probably good enough. I
+reckon most people don't Animint2 for its datasets.
+
+Sorry in advance if some of this writing seems condescending.
+You probably know all of this already. I write like this cuz
+I forget things a lot, and documentation helps future me.
+
+
+## Files with TODOs
+
+Here's the list of files that have at least one TODO 
+in them:
+
+- ChromHMMiterations
+- climate
+- compare
+- FluView
+- FunctionalPruning
+- generation.loci
+- intreg
+- malaria
+- mixtureKNN
+- montreal.bikes
+- PeakConsistency
+- pirates
+- presidential
+- prior
+- prostateLasso
+- seals
+- TestROC
+- UStornadoes
+- VariantModels
+- vervet
+- WorldBank

man/vervet.Rd

@@ -15,6 +15,8 @@ bacterium.
 }
 \usage{data(vervet)}
 \format{
+  TODO add codebook
+
   The format is a named list of data.frames: samples contains 64 rows
   with sample-specific info, counts contains 1190208 rows with counts of
   55mers observed in each sample, and monkeys contains 23 rows with