docs: remove last absolute links

docs/index.md

@@ -114,7 +114,7 @@ With these minimal arguments, taxpasta produces a two column output consisting o
 You can count on the second column being integers :wink: Having such a simple
 and tidy table should make your downstream analysis much smoother to start out
 with. Please, have a look at the full [getting
-started](/tutorials/getting-started) tutorial for a more thorough
+started](tutorials/getting-started.md) tutorial for a more thorough
 introduction.
 
 ### Merge

docs/supported_profilers/index.md

@@ -7,7 +7,7 @@ each taxonomic profiler can be standardised by taxpasta.
 
     In particular, when comparing results between various tools, please be very
     aware of their differences.  In the document on
-    [terminology](terminology), we describe how we think about the different
+    [terminology](terminology.md), we describe how we think about the different
     tools. Spending some time on considering the consequences now, will save
     you a lot of headache and prevent potentially wrong results later.
 

docs/tutorials/deepdive.md

@@ -270,7 +270,7 @@ names](../how-tos/how-to-add-names.md).
 !!! tip
 
     Carefully read our [background
-    documentation](/supported_profilers/terminology) on terminology and
+    documentation](../supported_profilers/terminology.md) on terminology and
     considerations for comparing results from different metagenomic profilers.
 
 You may have noticed that when "standardising" the output from each profiler

docs/tutorials/tutorial_python_snippets.qmd

@@ -8,7 +8,7 @@ execute:
 <!-- --8<-- [start:software] -->
 
 - Unix terminal (e.g., `bash`)
-- [Python environment with taxpasta](/#install)
+- [Python environment with taxpasta](../index.md#install)
 - No additional requirements, since we will make use of [pandas](https://pandas.pydata.org/) which is already part of the taxpasta installation.
 
 <!-- --8<-- [end:software] -->

docs/tutorials/tutorial_r_snippets.md

@@ -1,31 +1,30 @@
-
 <!-- --8<-- [start:software] -->
 
-- Unix terminal (e.g., `bash`)
+-   Unix terminal (e.g., `bash`)
 
-- [Python environment with taxpasta](/#install)
+-   [Python environment with taxpasta](../index.md#install)
 
-- [R](https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r)
+-   [R](https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r)
 
-- Package dependencies
+-   Package dependencies
 
-  ``` r
-  install.packages(c("readr", "dplyr"), dependencies = TRUE)
-  ```
+    ```r
+    install.packages(c("readr", "dplyr"), dependencies = TRUE)
+    ```
 
 <!-- --8<-- [end:software] -->
 <!-- --8<-- [start:raw-motus] -->
 
 We can try loading a mOTUs profile into R using the common table reading
 function `read_tsv()` from the `readr` package with default arguments.
 
-``` r
+```r
 requireNamespace("readr")
 ```
 
     Loading required namespace: readr
 
-``` r
+```r
 profile_motus <- readr::read_tsv("2612_pe-ERR5766176-db_mOTU.out")
 ```
 
@@ -52,7 +51,7 @@ into software expecting ‘true’ tabular data, we have to instead add
 extra options to the function, which makes loading the table less than
 smooth for downstream analyses.
 
-``` r
+```r
 profile_motus <- readr::read_tsv("2612_pe-ERR5766176-db_mOTU.out", comment = "#")
 ```
 
@@ -70,11 +69,11 @@ profile_motus <- readr::read_tsv("2612_pe-ERR5766176-db_mOTU.out", comment = "#"
     ℹ Use `spec()` to retrieve the full column specification for this data.
     ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 
-However, once again we hit another error: the column headers are *also*
+However, once again we hit another error: the column headers are _also_
 specified as a comment line… Instead we can try to skip the first two
 lines entirely.
 
-``` r
+```r
 profile_motus <- readr::read_tsv("2612_pe-ERR5766176-db_mOTU.out", skip = 2)
 ```
 
@@ -87,7 +86,7 @@ profile_motus <- readr::read_tsv("2612_pe-ERR5766176-db_mOTU.out", skip = 2)
     ℹ Use `spec()` to retrieve the full column specification for this data.
     ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 
-``` r
+```r
 profile_motus
 ```
 
@@ -110,7 +109,7 @@ profile_motus
 <!-- --8<-- [end:raw-motus] -->
 <!-- --8<-- [start:raw-kraken2] -->
 
-``` r
+```r
 profile_kraken2 <- readr::read_tsv("2612_pe-ERR5766176-db1.kraken2.report.txt")
 ```
 
@@ -124,30 +123,30 @@ profile_kraken2 <- readr::read_tsv("2612_pe-ERR5766176-db1.kraken2.report.txt")
     • `627680` -> `627680...2`
     • `627680` -> `627680...3`
 
-``` r
+```r
 profile_kraken2
 ```
 
     # A tibble: 43 × 6
-       `99.97` `627680...2` `627680...3` U        `0` unclassified      
-         <dbl>        <dbl>        <dbl> <chr>  <dbl> <chr>             
-     1    0.03          168            0 R          1 root              
+       `99.97` `627680...2` `627680...3` U        `0` unclassified
+         <dbl>        <dbl>        <dbl> <chr>  <dbl> <chr>
+     1    0.03          168            0 R          1 root
      2    0.03          168            0 R1    131567 cellular organisms
-     3    0.03          168            0 D       2759 Eukaryota         
-     4    0.03          168            0 D1     33154 Opisthokonta      
-     5    0.02          152            0 K      33208 Metazoa           
-     6    0.02          152            0 K1      6072 Eumetazoa         
-     7    0.02          152            0 K2     33213 Bilateria         
-     8    0.02          152            0 K3     33511 Deuterostomia     
-     9    0.02          152            0 P       7711 Chordata          
-    10    0.02          152            0 P1     89593 Craniata          
+     3    0.03          168            0 D       2759 Eukaryota
+     4    0.03          168            0 D1     33154 Opisthokonta
+     5    0.02          152            0 K      33208 Metazoa
+     6    0.02          152            0 K1      6072 Eumetazoa
+     7    0.02          152            0 K2     33213 Bilateria
+     8    0.02          152            0 K3     33511 Deuterostomia
+     9    0.02          152            0 P       7711 Chordata
+    10    0.02          152            0 P1     89593 Craniata
     # … with 33 more rows
 
 This doesn’t fail to load but unfortunately the column headers look a
 bit weird. It seems the Kraken2 file does not include a column header!
 In this case we have to specify these ourselves.
 
-``` r
+```r
 profile_kraken2 <- readr::read_tsv(
     "2612_pe-ERR5766176-db1.kraken2.report.txt",
     col_names = c(
@@ -170,15 +169,15 @@ profile_kraken2 <- readr::read_tsv(
     ℹ Use `spec()` to retrieve the full column specification for this data.
     ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 
-``` r
+```r
 profile_kraken2
 ```
 
     # A tibble: 44 × 6
-       percent clade_assigned_reads direct_assigned_reads taxonomy_lvl taxon…¹ name 
+       percent clade_assigned_reads direct_assigned_reads taxonomy_lvl taxon…¹ name
          <dbl>                <dbl>                 <dbl> <chr>          <dbl> <chr>
      1  100.                 627680                627680 U                  0 uncl…
-     2    0.03                  168                     0 R                  1 root 
+     2    0.03                  168                     0 R                  1 root
      3    0.03                  168                     0 R1            131567 cell…
      4    0.03                  168                     0 D               2759 Euka…
      5    0.03                  168                     0 D1             33154 Opis…
@@ -196,13 +195,13 @@ In the tidyverse flavour of R, we can do this with the `full_join`
 function of the `dplyr` package. This form of joining tables includes
 all rows both from the left and right table in the resulting table.
 
-``` r
+```r
 requireNamespace("dplyr")
 ```
 
     Loading required namespace: dplyr
 
-``` r
+```r
 dplyr::full_join(profile_motus, profile_kraken2)
 ```
 
@@ -217,24 +216,24 @@ for the different profilers’ outputs.
 We need to specify which column of the left table should be joined with
 what column of the right table.
 
-``` r
+```r
 raw_merged_table <- dplyr::full_join(profile_motus, profile_kraken2, by = c("NCBI_tax_id" = "taxonomy_id"))
 raw_merged_table
 ```
 
     # A tibble: 33,615 × 8
-       `#consensus_taxonomy`   NCBI_…¹ 2612_…² percent clade…³ direc…⁴ taxon…⁵ name 
+       `#consensus_taxonomy`   NCBI_…¹ 2612_…² percent clade…³ direc…⁴ taxon…⁵ name
        <chr>                     <dbl>   <dbl>   <dbl>   <dbl>   <dbl> <chr>   <chr>
-     1 Leptospira alexanderi …  100053       0      NA      NA      NA <NA>    <NA> 
-     2 Leptospira weilii [ref…   28184       0      NA      NA      NA <NA>    <NA> 
-     3 Chryseobacterium sp. […      NA       0      NA      NA      NA <NA>    <NA> 
-     4 Chryseobacterium galli… 1324352       0      NA      NA      NA <NA>    <NA> 
-     5 Chryseobacterium indol…     253       0      NA      NA      NA <NA>    <NA> 
-     6 Chryseobacterium artoc…      NA       0      NA      NA      NA <NA>    <NA> 
-     7 Chryseobacterium jejue…  445960       0      NA      NA      NA <NA>    <NA> 
-     8 Chryseobacterium sp. G… 1805473       0      NA      NA      NA <NA>    <NA> 
-     9 Chryseobacterium conta… 1423959       0      NA      NA      NA <NA>    <NA> 
-    10 Chryseobacterium indol…     253       0      NA      NA      NA <NA>    <NA> 
+     1 Leptospira alexanderi …  100053       0      NA      NA      NA <NA>    <NA>
+     2 Leptospira weilii [ref…   28184       0      NA      NA      NA <NA>    <NA>
+     3 Chryseobacterium sp. […      NA       0      NA      NA      NA <NA>    <NA>
+     4 Chryseobacterium galli… 1324352       0      NA      NA      NA <NA>    <NA>
+     5 Chryseobacterium indol…     253       0      NA      NA      NA <NA>    <NA>
+     6 Chryseobacterium artoc…      NA       0      NA      NA      NA <NA>    <NA>
+     7 Chryseobacterium jejue…  445960       0      NA      NA      NA <NA>    <NA>
+     8 Chryseobacterium sp. G… 1805473       0      NA      NA      NA <NA>    <NA>
+     9 Chryseobacterium conta… 1423959       0      NA      NA      NA <NA>    <NA>
+    10 Chryseobacterium indol…     253       0      NA      NA      NA <NA>    <NA>
     # … with 33,605 more rows, and abbreviated variable names ¹​NCBI_tax_id,
     #   ²​`2612_pe-ERR5766176-db_mOTU`, ³​clade_assigned_reads,
     #   ⁴​direct_assigned_reads, ⁵​taxonomy_lvl
@@ -245,7 +244,7 @@ raw_merged_table
 Now let’s try to load the taxpasta standardised Kraken2 result into R
 again.
 
-``` r
+```r
 profile_kraken2_std <- readr::read_tsv("2612_pe-ERR5766176-db1_kraken2.tsv")
 ```
 
@@ -257,7 +256,7 @@ profile_kraken2_std <- readr::read_tsv("2612_pe-ERR5766176-db1_kraken2.tsv")
     ℹ Use `spec()` to retrieve the full column specification for this data.
     ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 
-``` r
+```r
 profile_kraken2_std
 ```
 
@@ -282,7 +281,7 @@ profile_kraken2_std
 Once again, let’s try loading the standardised and merged mOTUs result
 into R.
 
-``` r
+```r
 profile_motus_merged <- readr::read_tsv("dbMOTUs_motus.tsv")
 ```
 
@@ -294,7 +293,7 @@ profile_motus_merged <- readr::read_tsv("dbMOTUs_motus.tsv")
     ℹ Use `spec()` to retrieve the full column specification for this data.
     ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 
-``` r
+```r
 profile_motus_merged
 ```
 

docs/tutorials/tutorial_r_snippets.qmd

@@ -8,7 +8,7 @@ execute:
 <!-- --8<-- [start:software] -->
 
 - Unix terminal (e.g., `bash`)
-- [Python environment with taxpasta](/#install)
+- [Python environment with taxpasta](../index.md#install)
 - [R](https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r)
 - Package dependencies