fix vignettes

- replace MetMasheR with MetMashR in system.file calls
computational-metabolomics · Jan 19, 2024 · a11617f · a11617f
1 parent 54f5c69
commit a11617f
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Showing 4 changed files with 30 additions and 30 deletions.
diff --git a/vignettes/Extending_MetMashR.Rmd b/vignettes/Extending_MetMashR.Rmd
@@ -88,7 +88,7 @@ we have cached the first 10 rows and stored them in the package.
 
 ```{r, include=FALSE,eval=TRUE}
 AN = readRDS(
-    system.file('extdata/AN000465_subset.rds',package='MetMasheR')
+    system.file('extdata/AN000465_subset.rds',package='MetMashR')
 )
 ```
 
@@ -217,7 +217,7 @@ setMethod(f = "read_database",
               
               ## for vignette use locally cached subset
               AN = readRDS(
-                  system.file('extdata/AN000465_subset.rds',package='MetMasheR')
+                  system.file('extdata/AN000465_subset.rds',package='MetMashR')
               )
 
               return(AN)
@@ -447,26 +447,26 @@ refmet = mwb_refmet_database()
 # pubchem caches
 pubchem_cid_cache = rds_database(
     source = system.file('cached/pubchem_cid_cache.rds',
-                       package='MetMasheR')
+                       package='MetMashR')
 )
 pubchem_smile_cache = rds_database(
     source = system.file('cached/pubchem_smiles_cache.rds',
-                       package='MetMasheR')
+                       package='MetMashR')
 )
 ```
 
 ```{r, eval=TRUE,include=FALSE}
 refmet = rds_database(
-    source = system.file('cached/refmet_cache.rds',package = 'MetMasheR')
+    source = system.file('cached/refmet_cache.rds',package = 'MetMashR')
 )
 pubchem_cid_cache = rds_database(
     source = file.path(
-        system.file('cached',package='MetMasheR'),
+        system.file('cached',package='MetMashR'),
         'pubchem_cid_cache.rds')
 )
 pubchem_smile_cache = rds_database(
     source = file.path(
-        system.file('cached',package='MetMasheR'),
+        system.file('cached',package='MetMashR'),
         'pubchem_smiles_cache.rds')
 )
 

diff --git a/vignettes/annotate_mixtures.Rmd b/vignettes/annotate_mixtures.Rmd
@@ -182,10 +182,10 @@ for (assay in c('HILIC_NEG','HILIC_POS','LIPIDS_NEG','LIPIDS_POS')) {
         source = c(
             system.file(
                 paste0('extdata/MTox/CD/',assay,'.xlsx'),
-                package = 'MetMasheR'),
+                package = 'MetMashR'),
             system.file(
                 paste0('extdata/MTox/CD/',assay,'_comp.xlsx'),
-                package = 'MetMasheR')),
+                package = 'MetMashR')),
         tag = paste0('CD_',assay))
     
     # update labels in workflow
@@ -338,7 +338,7 @@ for (assay in c('HILIC_NEG','HILIC_POS','LIPIDS_NEG','LIPIDS_POS')) {
     AT = ls_source(
         source = system.file(
             paste0('extdata/MTox/LS/MTox_2023_',assay,'.txt'),
-            package = 'MetMasheR'),
+            package = 'MetMashR'),
         tag = paste0('LS_',assay)) 
     
     # update labels in workflow
@@ -537,7 +537,7 @@ in practice you would create your own (see [TODO]).
 # import cached results
 inchikey_cache = rds_database(
     source = file.path(
-        system.file('cached',package='MetMasheR'),
+        system.file('cached',package='MetMashR'),
         'pubchem_inchikey_mtox_cache.rds'),
     .writable = FALSE
 )
@@ -604,13 +604,13 @@ non-normalised names.
 # prepare cached results for vignette
 inchikey_cache2 = rds_database(
     source = file.path(
-        system.file('cached',package='MetMasheR'),
+        system.file('cached',package='MetMashR'),
         'pubchem_inchikey_mtox_cache2.rds'),
     .writable = FALSE
 )
 inchikey_cache3 = rds_database(
     source = file.path(
-        system.file('cached',package='MetMasheR'),
+        system.file('cached',package='MetMashR'),
         'pubchem_inchikey_mtox_cache3.rds'),
     .writable=FALSE
 )
@@ -751,7 +751,7 @@ has ready been saved as an RDS file so we can use `rds_database` to import it.
 # prepare object
 R = rds_database(
     source = file.path(
-        system.file('extdata',package='MetMasheR'),
+        system.file('extdata',package='MetMashR'),
         'standard_mixtures.rds'
     ),
     .writable = FALSE

diff --git a/vignettes/daphnia_example.Rmd b/vignettes/daphnia_example.Rmd
@@ -65,7 +65,7 @@ TODO
 # import HILIC_POS
 HP = openxlsx::read.xlsx(
         system.file("extdata/daphnia/daphnia_example.xlsx",
-                package = 'MetMasheR'),
+                package = 'MetMashR'),
         sheet='HILIC_POS',
         rowNames=FALSE,
         colNames=TRUE)
@@ -80,7 +80,7 @@ HP$rsd_sample=as.numeric(HP$rsd_sample)
 # import LIPIDS_POS
 LP = openxlsx::read.xlsx(
         system.file("extdata/daphnia/daphnia_example.xlsx",
-                package = 'MetMasheR'),
+                package = 'MetMashR'),
         sheet='LIPIDS_POS',
         rowNames=FALSE,
         colNames=TRUE)
@@ -157,20 +157,20 @@ cd_sources = list(
         source = c(
             system.file(
                 'extdata/daphnia/HILIC_POS_EL_CD.xlsx',
-                package = 'MetMasheR'),
+                package = 'MetMashR'),
             system.file(
             'extdata/daphnia/HILIC_POS_EL_CD_comp.xlsx',
-            package = 'MetMasheR')),
+            package = 'MetMashR')),
         sheets = c('Compounds','Compounds')
     ),
     LIPIDS_POS = cd_source(
         source = c(
             system.file(
                 'extdata/daphnia/LIPIDS_POS_EL_CD.xlsx',
-                package = 'MetMasheR'),
+                package = 'MetMashR'),
             system.file(
             'extdata/daphnia/LIPIDS_POS_EL_CD_comp.xlsx',
-            package = 'MetMasheR')),
+            package = 'MetMashR')),
         sheets = c('Compounds','Compounds')
     )
 )
@@ -311,13 +311,13 @@ ls_sources = list(
         source = 
             system.file(
                 'extdata/daphnia/HILIC_POS_EL_LS.txt',
-                package = 'MetMasheR')
+                package = 'MetMashR')
     ),
     LIPIDS_POS = ls_source(
         source = 
             system.file(
                 'extdata/daphnia/LIPIDS_POS_EL_LS.txt',
-                package = 'MetMasheR')
+                package = 'MetMashR')
     )
 )
 ```
@@ -401,16 +401,16 @@ For the vignette we used cached results, which we prepare now.
 ```{r}
 cache1=rds_database(
     source=file.path(
-        system.file('cached',package='MetMasheR'),'cache1.rds'))
+        system.file('cached',package='MetMashR'),'cache1.rds'))
 cache2=rds_database(    
  source=file.path(
-        system.file('cached',package='MetMasheR'),'cache2.rds'))
+        system.file('cached',package='MetMashR'),'cache2.rds'))
 cache3=rds_database(
  source=file.path(
-        system.file('cached',package='MetMasheR'),'cache3.rds'))
+        system.file('cached',package='MetMashR'),'cache3.rds'))
 cache4=rds_database(
  source=file.path(
-        system.file('cached',package='MetMasheR'),'cache4.rds'))
+        system.file('cached',package='MetMashR'),'cache4.rds'))
 ```
 
 Next we prepare the workflow and then apply it.

diff --git a/vignettes/using_MetMashR.Rmd b/vignettes/using_MetMashR.Rmd
@@ -158,7 +158,7 @@ rest of the file into a table.
 AT = ls_source(
     source = system.file(
         paste0('extdata/MTox/LS/MTox_2023_HILIC_POS.txt'),
-        package = 'MetMasheR')
+        package = 'MetMashR')
 )
 
 # read source
@@ -243,7 +243,7 @@ to be used as the first step in a workflow.
 AT = ls_source(
     source = system.file(
         paste0('extdata/MTox/LS/MTox_2023_HILIC_POS.txt'),
-        package = 'MetMasheR')
+        package = 'MetMashR')
 )
 
 # prepare workflow
@@ -280,7 +280,7 @@ apply a filtering step to remove records with a lower Grading.
 AT = ls_source(
     source = system.file(
         paste0('extdata/MTox/LS/MTox_2023_HILIC_POS.txt'),
-        package = 'MetMasheR')
+        package = 'MetMashR')
 )
 
 # prepare workflow
@@ -378,7 +378,7 @@ be included in a workflow and updated as more results are collected over time.
 AT = ls_source(
     source = system.file(
         paste0('extdata/MTox/LS/MTox_2023_HILIC_POS.txt'),
-        package = 'MetMasheR')
+        package = 'MetMashR')
 )
 
 # prepare cache