book: fix calls to extdata/

js2264 · Nov 15, 2023 · 04b0151 · 04b0151
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diff --git a/inst/pages/01_intro.qmd b/inst/pages/01_intro.qmd
@@ -1,4 +1,4 @@
-# Preamble {#preamble}
+# Preamble {-}
 
 ```{r setup, echo=FALSE, results="asis"}
 library(rebook)

diff --git a/inst/pages/04_containers.qmd b/inst/pages/04_containers.qmd
@@ -241,7 +241,7 @@ List the [available
 datasets](https://microbiome.github.io/mia/reference/mia-datasets.html) in
 the `mia` package:
 
-```{r, message=FALSE, eval=FALSE}
+```{r, message=FALSE}
 library(mia)
 data(package="mia")
 ```
@@ -350,8 +350,8 @@ You can find full workflow script without further explanations and comments from
 
 ```{r dada2_1, include=FALSE}
 # Load objects
-seqtab.nochim <- readRDS(system.file("data", "dada2_seqtab.nochim", package = "OMA"))
-taxa <- readRDS(system.file("data", "dada2_taxa", package = "OMA"))
+seqtab.nochim <- readRDS(system.file("extdata", "dada2_seqtab.nochim", package = "OMA"))
+taxa <- readRDS(system.file("extdata", "dada2_taxa", package = "OMA"))
 ```
 
 Load required packages.
@@ -454,9 +454,9 @@ arbitrary; we refer here to the same names as in the examples:
 After you have set up the CSV files, you can read them in R:
 
 ```{r importingcsv1, message=FALSE}
-count_file  <- system.file("data", "assay_taxa.csv", package = "OMA")
-tax_file    <- system.file("data", "rowdata_taxa.csv", package = "OMA")
-sample_file <- system.file("data", "coldata.csv", package = "OMA")
+count_file  <- system.file("extdata", "assay_taxa.csv", package = "OMA")
+tax_file    <- system.file("extdata", "rowdata_taxa.csv", package = "OMA")
+sample_file <- system.file("extdata", "coldata.csv", package = "OMA")
 
 # Load files
 counts  <- read.csv(count_file, row.names=1)   # Abundance table (e.g. ASV data; to assay data)
@@ -544,8 +544,8 @@ To construct a _MultiAssayExperiment_ object, just combine multiple _TreeSE_ dat
 Here we import metabolite data from the same study.
 
 ```{r importingcsv4, message=FALSE}
-count_file <- system.file("data", "assay_metabolites.csv", package = "OMA")
-sample_file <- system.file("data", "coldata.csv", package = "OMA")
+count_file <- system.file("extdata", "assay_metabolites.csv", package = "OMA")
+sample_file <- system.file("extdata", "coldata.csv", package = "OMA")
 
 # Load files
 counts  <- read.csv(count_file, row.names=1)  
@@ -594,9 +594,9 @@ To begin with, we store the data in a local directory within the working
 directory, such as _data/_, and define the source file paths.
 
 ```{r}
-biom_file_path <- system.file("data", "Aggregated_humanization2.biom", package = "OMA")
-sample_meta_file_path <- system.file("data", "Mapping_file_ADHD_aggregated.csv", package = "OMA")
-tree_file_path <- system.file("data", "Data_humanization_phylo_aggregation.tre", package = "OMA")
+biom_file_path <- system.file("extdata", "Aggregated_humanization2.biom", package = "OMA")
+sample_meta_file_path <- system.file("extdata", "Mapping_file_ADHD_aggregated.csv", package = "OMA")
+tree_file_path <- system.file("extdata", "Data_humanization_phylo_aggregation.tre", package = "OMA")
 ```  
 
 Now we can read in the biom file and convert it into a TreeSE object. In addition, we retrieve the rank names from the prefixes of the feature names and then remove them with the `rankFromPrefix` and `removeTaxaPrefixes` optional arguments.
@@ -728,7 +728,8 @@ GlobalPatterns_phyloseq2
 ```
 
 Conversion is possible between other data formats. Interested readers can refer to the following functions:
-* [makeTreeSummarizedExperimentFromDADA2](https://microbiome.github.io/mia/reference/makeTreeSummarizedExperimentFromDADA2.html)
-* [makeSummarizedExperimentFromBiom](https://microbiome.github.io/mia/reference/makeSummarizedExperimentFromBiom.html)
-* [loadFromMetaphlan](https://microbiome.github.io/mia/reference/loadFromMetaphlan.html)
+
+* [makeTreeSummarizedExperimentFromDADA2](https://microbiome.github.io/mia/reference/makeTreeSummarizedExperimentFromDADA2.html)  
+* [makeSummarizedExperimentFromBiom](https://microbiome.github.io/mia/reference/makeSummarizedExperimentFromBiom.html)  
+* [loadFromMetaphlan](https://microbiome.github.io/mia/reference/loadFromMetaphlan.html)  
 * [readQZA](https://microbiome.github.io/mia/reference/loadFromQIIME2.html)
diff --git a/inst/pages/90_acknowledgments.qmd b/inst/pages/90_acknowledgments.qmd
@@ -1,4 +1,4 @@
-# Developers {-}
+# Contributions
 
 ```{r setup, echo=FALSE, results="asis"}
 library(rebook)

diff --git a/inst/pages/97_extra_materials.qmd b/inst/pages/97_extra_materials.qmd
@@ -1,4 +1,4 @@
-# Extra material {#extras}
+# Extra material {#extras} 
 
 ```{r}
 knitr::opts_chunk$set(eval=FALSE)
@@ -124,7 +124,7 @@ tse <- SprockettTHData()
 ```{r, message=FALSE, warning=FALSE, echo=FALSE}
 # saveRDS(tse, file="data/SprockettTHData.Rds")
 # Hidden reading of the saved data
-tse <- readRDS("data/SprockettTHData.Rds")
+tse <- readRDS(system.file("extdata", "SprockettTHData.Rds", package = "OMA"))
 ```
 
 We pick three covariates ("Sex","Age_Years","Delivery_Mode") during this

diff --git a/inst/pages/Session_info.qmd b/inst/pages/Session_info.qmd
@@ -1,4 +1,4 @@
-# Sessioninfo {-}
+# Session info 
 
 ```{r "session info"}
 #| cache: false