dmu-summary v0.4

- implement parameter for custom cache files - other minor adjustments - update README/NASIS instructions
ncss-tech · Nov 15, 2024 · 263e8a6 · 263e8a6
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diff --git a/inst/reports/region2/dmu-summary/README.md b/inst/reports/region2/dmu-summary/README.md
@@ -1,16 +1,9 @@
 # DMU Summary Report
-PENDING
 
-## Typical Usage
-This report requires setting up a selected set in your local NASIS database:
-
-   * load legend by area symbol
-   * load related MU (approved / provisional only)
-   * load related DMU (rep DMU only)
-   * load related component pedons
-   * load related site observation
+## Usage
 
 Run the following commands to setup the report template.
+
 ```r
 # load this library
 library(soilReports)
@@ -22,9 +15,10 @@ reportSetup(reportName='region2/dmu-summary')
 reportInit(reportName='region2/dmu-summary', outputDir='dmu-summary')
 ```
 
-TODO: Setup `cached.rds`.
+This report requires loading several related objects into your NASIS Selected Set, including Area, Legend Mapunit, Correlation, Component Pedon, Pedon and Site Observation. 
 
-TODO: specification of map unit symbol via `params`
+A useful NASIS query that gets all of the necessary objects is **_NSSC Pangaea_: _Area/Legend/Mapunit/DMU/Pedon/Site by areasymbol_**.
 
-Open `report.Rmd` and then click "knit".
+ - This query has detailed instructions for loading necessary data, and includes only representative data map units. Several other variants of this same query can be used to obtain data based on component or pedon information rather than area symbol.
 
+Open `report.Rmd`, review the "params" section of the YAML header to select target mapunit and cache file name, then click "knit". You can cache the data for many map units (e.g. a whole soil survey area) once, then re-run the report several times with different `musym` values. To force new data to be loaded from the database, delete the .rda file specified in `cache_file` in the document directory.
diff --git a/inst/reports/region2/dmu-summary/cache-data.R b/inst/reports/region2/dmu-summary/cache-data.R
@@ -80,6 +80,6 @@ cm <- cm[, c('.label', 'comppct_r', cm.names)]
 # TODO: re-level component names based on mean comppct
 
 ## save
-save(co, cm, p, cp, osds, cotx, geom, pm, file = 'data.rda')
+save(co, cm, p, cp, osds, cotx, geom, pm, file = params$cache_file)
 
 
diff --git a/inst/reports/region2/dmu-summary/config.R b/inst/reports/region2/dmu-summary/config.R
@@ -15,12 +15,17 @@
   .label = 'CA792',
   variable = factor(
     c('elev', 'ffd', 'maat', 'map', 'slope'),
-    labels = c('Elevation (m)', 'Frost-Free Days', 'MAAT (deg C)', 'MAP (mm)', 'Slope (%)')
+    labels = c(
+      'Elevation (m)',
+      'Frost-Free Days',
+      'MAAT (deg C)',
+      'MAP (mm)',
+      'Slope (%)'
+    )
   ),
   rv = c(3005, 83, 3.28, 984, 43),
   low = c(1469, 40, -1.02, 583, 8),
   high = c(3728, 193, 12.01, 1381, 99)
-
 )
 
 
diff --git a/inst/reports/region2/dmu-summary/custom.R b/inst/reports/region2/dmu-summary/custom.R
@@ -16,23 +16,23 @@
 #' 
 #' # simplest case, use a SPC
 #' data("jacobs2000")
-#' emtpySPC(jacobs2000)
+#' emptySPC(jacobs2000)
 #' 
 #' # convert to SPC with data.table internals
 #' x <- jacobs2000
 #' aqp_df_class(x) <- 'data.table'
 #' x <- rebuildSPC(x)
 #' 
-#' emtpySPC(x)
+#' emptySPC(x)
 #' 
 #' # convert to SPC with tibble internals
 #' x <- jacobs2000
 #' aqp_df_class(x) <- 'tibble'
 #' x <- rebuildSPC(x)
 #' 
-#' emtpySPC(x)
+#' emptySPC(x)
 #' 
-emtpySPC <- function(x, fakeID = 'MISSING', top = 0, bottom = max(x)) {
+emptySPC <- function(x, fakeID = 'MISSING', top = 0, bottom = max(x)) {
 
   # use the first profile / horizon
   # as template