diff --git a/docs/reference/index.qmd b/docs/reference/index.qmd
index 06d16ae..d09d86a 100644
--- a/docs/reference/index.qmd
+++ b/docs/reference/index.qmd
@@ -12,7 +12,7 @@ Functions for processing data.
 | [coords_to_sample_dict](coords_to_sample_dict.qmd#spaceprime.coords_to_sample_dict) | Convert sample coordinates to sample dictionaries for simulation and analysis. Can optionally include empirical data, which is accepted as a path to a VCF file. |
 | [create_raster](create_raster.qmd#spaceprime.create_raster) | Creates a raster dataset from a numpy array and reference raster and writes it to a new GeoTiff file. |
 | [mtp_thresh_from_coords](mtp_thresh_from_coords.qmd#spaceprime.mtp_thresh_from_coords) | This function takes the coordinates of empirical sampling localities, finds which raster cells they belong to, extracts the values of the first layer for those localities, and finds the minimum value. |
-| [raster_to_demes](raster_to_demes.qmd#spaceprime.raster_to_demes) | Converts a raster to a 2D np.ndarray of deme sizes using either linear, threshold, or sigmoid transformation functions. For more detail about transformation functions, see [this brief overview](background/trans-fns.md). |
+| [raster_to_demes](raster_to_demes.qmd#spaceprime.raster_to_demes) | Converts a raster to a 2D np.ndarray of deme sizes using either linear, threshold, or sigmoid transformation functions. For more detail about transformation functions, see [this brief overview](transformation-functions.qmd). |
 | [split_landscape_by_pop](split_landscape_by_pop.qmd#spaceprime.split_landscape_by_pop) | Uses nearest-neighbor interpolation to classify a landscape raster based on the ancestral population assigned to sampled individuals. |
 
 ## Demography
diff --git a/docs/reference/raster_to_demes.qmd b/docs/reference/raster_to_demes.qmd
index 9ad3256..666da7f 100644
--- a/docs/reference/raster_to_demes.qmd
+++ b/docs/reference/raster_to_demes.qmd
@@ -2,7 +2,7 @@
 
 `raster_to_demes(raster, transformation='linear', max_local_size=1000, normalize=False, threshold=None, thresh_norm=False, inflection_point=0.5, slope=0.05)`
 
-Converts a raster to a 2D np.ndarray of deme sizes using either linear, threshold, or sigmoid transformation functions. For more detail about transformation functions, see [this brief overview](background/trans-fns.md).
+Converts a raster to a 2D np.ndarray of deme sizes using either linear, threshold, or sigmoid transformation functions. For more detail about transformation functions, see [this brief overview](transformation-functions.qmd).
 Raster data should be continuous and positive.
 This function was created with the idea of taking in habitat suitability rasters scaled from 0 to 1, where 0 is no suitability and 1 is the highest suitability.
 However, it is flexible enough to accommodate other continuous rasters that can be coaxed to a 0 to 1 scale with the operation `(data - np.min(data)) / (np.max(data) - np.min(data))` by setting the `normalize` flag to `True`.
diff --git a/mkdocs.yml b/mkdocs.yml
deleted file mode 100644
index 56fcbf4..0000000
--- a/mkdocs.yml
+++ /dev/null
@@ -1,100 +0,0 @@
-site_name: spaceprime
-site_description: A python package to facilitate spatially explicit coalescent modeling in msprime
-site_author: connor-french
-site_url: https://connor-french.github.io/spaceprime
-repo_url: https://github.com/connor-french/spaceprime
-
-copyright: "Copyright © 2024 - 2024 Connor French"
-
-theme:
-    palette:
-        - scheme: default
-          #   primary: blue
-          #   accent: indigo
-          toggle:
-              icon: material/toggle-switch-off-outline
-              name: Switch to dark mode
-        - scheme: slate
-          primary: indigo
-          accent: indigo
-          toggle:
-              icon: material/toggle-switch
-              name: Switch to light mode
-    name: material
-    icon:
-        repo: fontawesome/brands/github
-    # logo: assets/logo.png
-    # favicon: assets/favicon.png
-    features:
-        - navigation.instant
-        - navigation.tracking
-        - navigation.top
-        - search.highlight
-        - search.share
-    custom_dir: "docs/overrides"
-    font:
-        text: Google Sans
-        code: Regular
-
-plugins:
-    - search
-    - mkdocstrings:
-        handlers:
-            python:
-                options:
-                    paths: [spaceprime]
-                    docstring_style: google
-                    docstring_section_style: table
-
-    - git-revision-date
-    - git-revision-date-localized:
-          enable_creation_date: true
-          type: timeago
-    # - pdf-export
-    - mkdocs-jupyter:
-          include_source: True
-          ignore_h1_titles: True
-          execute: True
-          allow_errors: false
-          ignore: ["conf.py"]
-          execute_ignore: ["*ignore.ipynb"]
-    - callouts
-          
-markdown_extensions:
-    - admonition
-    - abbr
-    - attr_list
-    - def_list
-    - footnotes
-    - meta
-    - md_in_html
-    - nl2br
-    - admonition
-    - pymdownx.superfences
-    - pymdownx.details
-    - pymdownx.highlight:
-          linenums: true
-    - toc:
-          permalink: true
-
-# extra:
-#     analytics:
-#         provider: google
-#         property: UA-XXXXXXXXX-X
-
-nav:
-    - Home: index.md
-    - Vignettes:
-        - examples/intro.ipynb
-        - Suitability to deme size transformation functions: trans-fns.md    
-    - Reference:
-        - utilities module: utilities.md
-        - demography module: demography.md
-        - analysis module: analysis.md
-    - Contributing: contributing.md
-    - Changelog: changelog.md
-    
-    #- Installation: installation.md
-    #- Usage: usage.md
-    #- FAQ: faq.md
-    #- Report Issues: https://github.com/connor-french/spaceprime/issues
\ No newline at end of file