Migrating from TSGenerator 1.x to 2.0

Why 2.0 changes the workflow

TSGenerator 1.x combined workflows for VI products, QFLAG2 preprocessing, raster-stack construction, polygon extraction, imputation, and interactive missing-data analysis. Several assumptions no longer fit the current HR-VPP ecosystem.

TSGenerator 2.0 therefore focuses on supported ST/VPP products and separates acquisition, geospatial processing, product quality, temporal completeness, imputation, and modelling.

Function migration table

1.x	2.0	Status
`Download.STPPI()`	`download_st()`	deprecated wrapper retained
`Download.HRVPP()`	`download_vpp()`	deprecated wrapper retained
`Download.VI()`	none	discontinued workflow; migration guard
`get.Stack()`	none	legacy VI/QFLAG2 workflow
`get.Clean.IV()`	`mask_quality()` where applicable	old QFLAG2 workflow retired
`QFLAG2.Mask()`	`mask_quality()`	use only with current ST/VPP QFLAG semantics
`get.Series.mean()`	`extract_ts(..., fun = "mean")`	deprecated wrapper retained
`get.Series.median()`	`extract_ts(..., fun = "median")`	deprecated wrapper retained
`get.Series.VPP()`	`extract_vpp()`	old generic scaling retired
`renames.image.VPP()`	none	filenames preserved for provenance
`quality.Series()`	`assess_ts_quality()`	legacy algorithm retired
`general.Quality()`	`assess_ts_quality()`	legacy algorithm retired
`count_missing()`	`summarize_missingness()`	phenology-specific Plotly workflow retired
`TsImpute()`	`impute_ts()`	deprecated wrapper retained
`GAM.missing()`	`model_missingness()`	deprecated wrapper retained
`GAM.plot()`	`plot_missingness()`	deprecated wrapper retained

Acquisition

Old scripts may contain Python/reticulate setup. Remove it.

Instead of:

# 1.x concept
Download.STPPI(...)

use:

download_st(...)

and replace Download.HRVPP() with download_vpp().

Raster extraction

Replace separate mean/median functions with one API:

extract_ts(
  x = rasters,
  polygons = parcels,
  id_col = "Parcel_ID",
  fun = "median"
)

The 2.0 core uses terra, validates CRS, and uses explicit feature IDs instead of row names.

VPP extraction

Do not migrate get.Series.VPP() by reproducing a global factorR. VPP parameters have different encodings and units. Use:

extract_vpp(
  x = vpp_files,
  polygons = parcels,
  id_col = "Parcel_ID"
)

Preserve original CLMS filenames; 2.0 parses provenance from them.

Quality

The discontinued VI/QFLAG2 workflow is not equivalent to current ST-QFLAG or VPP-QFLAG. Use the 2.0 product-quality functions:

quality_info("ST")
quality_info("VPP")
classify_quality(...)
summarize_quality(...)
mask_quality(...)

Do not bilinearly resample categorical QFLAG rasters.

Missingness and completeness

Replace legacy whole-series quality classification with assess_ts_quality(). Use summarize_missingness() alongside it when a diagnostic breakdown of absent expected dates, explicit NA values, and usable observations is required:

plan <- temporal_plan(series, expected_step = 10)
summarize_missingness(plan)
assess_ts_quality(plan)

This distinguishes absent dates from rows containing NA while keeping assess_ts_quality() as the primary replacement for general.Quality().

Imputation

Use impute_ts() rather than TsImpute(). The original value is retained, imputed values are flagged, long gaps can be protected, and ST re-imputation is blocked by default.

Legacy policy

TSGenerator 2.0 retains selected deprecated wrappers to ease migration. Functions tied only to discontinued VI/QFLAG2 behaviour act as migration guards or remain archived under legacy/. They should not be used for new analyses and are candidates for removal in a future major release.