fix or remove broken links

Author: brymz

exercises/Higher-order-functions-dna-Python.md

@@ -7,7 +7,7 @@ language: Python
 
 Write a function to determine the GC-content of a DNA sequence and another
 function to download this list of sequences from the web.
-[Download the data](http://www.programmingforbiologists.org/sites/programmingforbiologists.org/files/dna_sequences.csv)
+[Download the data]({{ site.baseurl }}/data/dna-sequences-1.txt)
 using your function and then use map() to calculate the value of the GC-content
 for all of the sequences. Print the results to the screen.
 

exercises/Lists-nested-lists-2-Python.md

@@ -6,7 +6,7 @@ language: Python
 ---
 
 One of your collaborators has posted [a comma-delimited text
-file](http://www.programmingforbiologists.org/sites/programmingforbiologists.org/files/shrub_dimensions.txt)
+file]({{ site.baseurl }}/data/shrub-dimensions.csv)
 online for you to analyze. The file contains dimensions of a series of
 shrubs (ShrubID, Length, Width, Height) and they need you to determine
 their volumes. You could do this using a spreadsheet, but the project

exercises/Neon-neon-raster-R.md

@@ -5,7 +5,7 @@ title: NEON Raster
 language: R
 ---
 
-Jane just got a job working to develop data products for [NEON](neoninc.org). 
+Jane just got a job working to develop data products for [NEON](http://www.neonscience.org/). 
 She's got to familiarize herself with working with LiDAR data and seeks out the 
 great 'Work with Data' [tutorial for raster data](http://neondataskills.org/lidar-data/lidar-data-rasters-in-R/). 
 Help Jane take the next step and develop a few additional products from the 

exercises/Problem-decomposition-exponential-growth-2-Python.md

@@ -5,7 +5,9 @@ title: Exponential Growth 2
 language: Python
 ---
 
-One of you lab mates (you may remember them from the For Loops 2
+*The data for this problem is no longer available.*
+
+One of your lab mates (you may remember them from the For Loops 2
 problem) is busy working on insect population dynamics. Initial results
 suggested that exponential growth was too simplistic for understanding
 the observed dynamics, so now they need to look at logistic growth.
@@ -26,10 +28,8 @@ ceil function in the math module.
 Your lab mate has compiled data from literature on the reproductive
 rates and carrying capacity for a number of different individuals for a
 variety of species. You've been teaching them about database structure
-so they have broken the data into two tables: an [individuals
-table](http://www.programmingforbiologists.org/sites/programmingforbiologists.org/files/individuals_table.csv)
-and [species
-table](http://www.programmingforbiologists.org/sites/programmingforbiologists.org/files/species_table.csv).
+so they have broken the data into two tables: an *individuals
+table* and *species table*.
 The database has information on several different taxonomic groups, but
 for this project your lab mate is only interested in the data for the
 insects.
@@ -41,10 +41,7 @@ population size of 10. Once you've determined the value for each
 species, plot the time to equilibrium as a function of the reproductive
 rate and (on a separate graph) the carrying capacity.
 
-You can either break this problem down into manageable parts yourself
-(you can use the [problem decomposition
-steps](http://www.programmingforbiologists.org/problem-decomposition-steps)
-to help) or follow [this
-approach](http://www.programmingforbiologists.org/problem-decomposition-problem-decomposition).
+Break this problem down into manageable parts yourself using the [problem
+decomposition steps]({{ site.baseurl }}/materials/problem-decomposition).
 Turn in the Python code and (if you use one) a database file with any
 queries that you use.

exercises/Scientific-dna-complement-2-Python.md

@@ -5,8 +5,9 @@ title: DNA Complement 2
 language: Python
 ---
 
-Download the file
-[sequence_data_complete.txt](http://www.programmingforbiologists.org/sites/programmingforbiologists.org/files/sequence_data_complete.txt)
+*The data for this problem is no longer available.*
+
+Download the file *sequence_data_complete.txt*
 from the website. This file consists of three columns separate by
 commas: 1) A sequence ID (like the primary keys we've using in our
 database work); 2) The length of the sequence; and 3) The sequence

exercises/Sets-species-composition-1-Python.md

@@ -58,7 +58,7 @@ readable, and most computationally efficient ways to solve this problem.
 
 When tackling a broad problem like this it is always important to
 think about how you are going to [decompose the
-problem]({{ site.baseurl }}/material/problem-decomposition) into manageable pieces. Take a few
+problem]({{ site.baseurl }}/materials/problem-decomposition) into manageable pieces. Take a few
 minutes to think about how you would approach this problem before
 following the steps outlined below. Sketch them out in a text file, or
 by writing out just the final commands you will use (i.e., none of the

materials/data-structures-R.md

@@ -108,7 +108,7 @@ shrub_data <- read.csv('./data/shrub-dimensions-labeled.csv')
 
 > DO NOT USE setwd() FOR THIS CLASS
 
-> Do [Exercise 10 - Shrub Volume Data Frame]({{ site.baseurl }}/exercises/Data-frames-shrub-volue-data-frame-R).
+> Do [Exercise 10 - Shrub Volume Data Frame]({{ site.baseurl }}/exercises/Data-frames-shrub-volume-data-frame-R).
 
 ### Project structure
 

materials/index.md

@@ -64,7 +64,7 @@ title: Lecture Materials
 - [`tidyr`]({{ site.baseurl }}/materials/tidyr)
 - [Project Structure]({{ site.baseurl }}/materials/project-structure)
 - [Debugging]({{ site.baseurl }}/materials/debugging-R)
-- [`knitr`]({{ site.baseurl }}/materials/knitr) ([Example `RMD`]({{ site.baseurl }}/materials/knitr-examp.Rmd))
+- [`knitr`]({{ site.baseurl }}/materials/knitr)
 - [R Cheat Sheet]({{ site.baseurl }}/materials/Walkthrough-R)
 - [Projects]({{ site.baseurl }}/materials/projects)