Rd2roxygen #162
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Rd2roxygen #162
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* Convert NASIS-related queries from RODBC->DBI #146 * remove require RODBC * roxygen for fetchNASIS * Color data NA moist state handling * use_sqlite = FALSE is the default for .openNASISchannel * Move VARCHAR(MAX) fields to end of query, per MSSQL specs * fix getHzErrorsNASIS * Validations and tests RE: #149 #146 * Move to fetchNASIS tests (skip on remote) * Add skip() and better handling of missing DB/no data * Use local_NASIS_defined everywhere w/ odbc::odbcListDataSources * cherry-pick: make a proper interface to sqlite NASIS queries cherry-pick: 🧬 Stitch SQLite data source API up to fetchNASIS cherry-pick: Update demo cherry-pick: Default code use 25cm, as proposed Validate/fix NASIS methods * Change name of path argument * fetchNASIS: Remove RIGHT JOIN in geomorphic features query and turn off the MSSQL specific syntax used for `d.rf.data.v2` * Method for cloning local NASIS tables into static SQLite file (#154) * Method for cloning local NASIS tables into static SQLite file #149 * local_NASIS_defined: add static_path arg and use RSQLite::dbCanConnect * Add selected set and static path to getHzErrorsNASIS * get_cosoilmoist / get_vegplot should use selected set argument * Special handling for local_NASIS_defined (does not take SS arg) * Add static_path to local_NASIS_defined * Roxygen: markdown = TRUE Broken docs md-doc: Fix single bracket semantics * Update docs * forgot to commit this one * NEWS / version 2.6.x * Rd2roxygen initial conversion; old in ./manbak * fix \href{} * passing check_man * Rd2roxygen (#162) * Rd2roxygen initial conversion; old in ./manbak * fix \href{} * passing check_man * fixes for R CMD check * deprecate old manpages * Revert existing roxygen back to human-made * get_extended_data_from_NASIS_db: artifact data query should respect SS=FALSE * get extended NASIS photo text notes: check for paths >260 chars * proper sequence to get SQLite pedon snapshot fetchNASIS-ready * Use checkHzDepthLogic (fast=TRUE) in fetchNASIS_pedons * .fetchNASIS_pedons: Use data.table for extended data processing * get_extended_data_from_NASIS_db: Replace plyr::join * dbQueryNASIS: vectorize/test; dbConnectNASIS: add NASIS() alias * docs * Add test for local NASIS DBI issues * Fix for get_cosoilmoist_from_NASISWebReport example * Fix for list output of createStaticNASIS * Close RODBC connection used in tests * Testing some pedon_table_column checks @jskovlin * aqp::union has been removed from namespace * test-fetchKSSL: hide txtProgressBar when running tests * Refactoring utils.R for data.table in fetchNASIS flattening * Docs * Oops DBI/odbc/RSQLite back in Imports * Missing comma * Docs * Mopping up * Move driver packages (odbc, RSQLite) to Suggests * get_cotext_from_NASIS_db: Add support for static_path argument and use dbQueryNASIS * get_cotext_from_NASIS_db: check for try-error * .formatParentMaterialString: Return NA_character_ for conformal data.frame with NULL data * Remove dangling require RODBC * fetchNASIS: extended data flattening handle NULL table contents * createStaticNASIS: better default arguments * Fixes for selected set argument (found by drop all _View_1 tables in a static DB) * Updates to nasisDBI "demo" that runs all the NASIS methods by all the methods * Remove requireNamespace("RODBC")--merge artifact? * demo createStaticNASIS workflow * Add WCS/SDA viz to demo * Fix bug in decoding of horizon data; thanks @dylanbeaudette * Pass through static_path argument to uncode() * Fix get_comonth_from_NASIS_db fill=TRUE * Update demos * Small adjustments to default args for demo/comparisons * Rename static_path arg to dsn * Rename static_path arg to dsn (docs) * Version bump + update README * Update NEWS.md
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Implements several documentation fixes for nasisDBI -- as well as converts to Roxygen markdown format -- by converting legacy .Rd to Roxygen in source .R files.
There are quite a few things that need to be resolved before this can merge into nasisDBI.