Try guessing starting parameters for model_params and model_ndvi.
model_start(DT, id = "id", year = "yr")filtered and scaled data.table of NDVI time series. Expects columns 'scaled' and 't' are present.
id column. default is 'id'. See details.
year column name. default is 'yr'.
The input DT data.table appended with xmidS_start and xmidA_start columns. Note - we curently do not attempt to guess appropriate starting values for scalS and scalA.
The id argument is used to split between sampling units. This may be a point id, polygon id, pixel id, etc. depending on your analysis. This should match the id provided to filtering functions.
Other model:
model_ndvi(),
model_params()
# Load data.table
library(data.table)
# Read in example data
ndvi <- fread(system.file("extdata", "sampled-ndvi-MODIS-MOD13Q1.csv", package = "irg"))
# Filter and scale NDVI time series
filter_ndvi(ndvi)
#> id NDVI SummaryQA DayOfYear yr filtered winter rolled top
#> 1: 0 0.1864 3 11 2015 0.3076500 0.3076500 0.3076500 0.8735000
#> 2: 1 0.0541 2 3 2015 0.3163400 0.3163400 0.3163400 0.8632175
#> 3: 2 0.1781 3 11 2015 0.2649875 0.2649875 0.2649875 0.8707500
#> 4: 3 0.1024 2 5 2015 0.2301750 0.2301750 0.2301750 0.8635525
#> 5: 4 0.0898 2 3 2015 0.2177150 0.2177150 0.2177150 0.8476000
#> ---
#> 801: 2 0.1179 2 364 2019 0.2649875 0.2649875 0.2649875 0.8707500
#> 802: 3 0.0789 2 364 2019 0.2301750 0.2301750 0.2301750 0.8635525
#> 803: 4 0.1572 2 364 2019 0.2177150 0.2177150 0.2177150 0.8476000
#> 804: 5 0.0763 2 364 2019 0.3163400 0.3163400 0.3163400 0.8632175
#> 805: 6 0.1197 2 362 2019 0.3149325 0.3149325 0.3149325 0.8632000
scale_doy(ndvi)
#> id NDVI SummaryQA DayOfYear yr filtered winter rolled top
#> 1: 0 0.1864 3 11 2015 0.3076500 0.3076500 0.3076500 0.8735000
#> 2: 1 0.0541 2 3 2015 0.3163400 0.3163400 0.3163400 0.8632175
#> 3: 2 0.1781 3 11 2015 0.2649875 0.2649875 0.2649875 0.8707500
#> 4: 3 0.1024 2 5 2015 0.2301750 0.2301750 0.2301750 0.8635525
#> 5: 4 0.0898 2 3 2015 0.2177150 0.2177150 0.2177150 0.8476000
#> ---
#> 801: 2 0.1179 2 364 2019 0.2649875 0.2649875 0.2649875 0.8707500
#> 802: 3 0.0789 2 364 2019 0.2301750 0.2301750 0.2301750 0.8635525
#> 803: 4 0.1572 2 364 2019 0.2177150 0.2177150 0.2177150 0.8476000
#> 804: 5 0.0763 2 364 2019 0.3163400 0.3163400 0.3163400 0.8632175
#> 805: 6 0.1197 2 362 2019 0.3149325 0.3149325 0.3149325 0.8632000
#> t
#> 1: 0.027397260
#> 2: 0.005479452
#> 3: 0.027397260
#> 4: 0.010958904
#> 5: 0.005479452
#> ---
#> 801: 0.994520548
#> 802: 0.994520548
#> 803: 0.994520548
#> 804: 0.994520548
#> 805: 0.989041096
scale_ndvi(ndvi)
#> id NDVI SummaryQA DayOfYear yr filtered winter rolled top
#> 1: 0 0.1864 3 11 2015 0.3076500 0.3076500 0.3076500 0.8735000
#> 2: 1 0.0541 2 3 2015 0.3163400 0.3163400 0.3163400 0.8632175
#> 3: 2 0.1781 3 11 2015 0.2649875 0.2649875 0.2649875 0.8707500
#> 4: 3 0.1024 2 5 2015 0.2301750 0.2301750 0.2301750 0.8635525
#> 5: 4 0.0898 2 3 2015 0.2177150 0.2177150 0.2177150 0.8476000
#> ---
#> 801: 2 0.1179 2 364 2019 0.2649875 0.2649875 0.2649875 0.8707500
#> 802: 3 0.0789 2 364 2019 0.2301750 0.2301750 0.2301750 0.8635525
#> 803: 4 0.1572 2 364 2019 0.2177150 0.2177150 0.2177150 0.8476000
#> 804: 5 0.0763 2 364 2019 0.3163400 0.3163400 0.3163400 0.8632175
#> 805: 6 0.1197 2 362 2019 0.3149325 0.3149325 0.3149325 0.8632000
#> t scaled
#> 1: 0.027397260 0
#> 2: 0.005479452 0
#> 3: 0.027397260 0
#> 4: 0.010958904 0
#> 5: 0.005479452 0
#> ---
#> 801: 0.994520548 0
#> 802: 0.994520548 0
#> 803: 0.994520548 0
#> 804: 0.994520548 0
#> 805: 0.989041096 0
# Guess starting parameters for xmidS and xmidA
model_start(ndvi)
#> id NDVI SummaryQA DayOfYear yr filtered winter rolled top
#> 1: 0 0.0791 2 61 2016 NA 0.3076500 NA 0.8735000
#> 2: 1 0.0526 2 61 2016 NA 0.3163400 NA 0.8632175
#> 3: 2 0.0707 2 61 2016 NA 0.2649875 NA 0.8707500
#> 4: 3 0.0456 2 61 2016 NA 0.2301750 NA 0.8635525
#> 5: 5 0.0526 2 61 2016 NA 0.3163400 NA 0.8632175
#> ---
#> 801: 1 0.8755 1 225 2015 0.8755 0.3163400 0.8671 0.8632175
#> 802: 2 0.8740 1 225 2015 0.8740 0.2649875 0.8732 0.8707500
#> 803: 3 0.8643 1 225 2015 0.8643 0.2301750 0.8643 0.8635525
#> 804: 5 0.8755 1 225 2015 0.8755 0.3163400 0.8671 0.8632175
#> 805: 6 0.8729 1 225 2015 0.8729 0.3149325 0.8688 0.8632000
#> t scaled xmidS_start xmidA_start
#> 1: 0.1643836 NA 0.3452055 0.7095890
#> 2: 0.1643836 NA 0.3452055 0.7095890
#> 3: 0.1643836 NA 0.3452055 0.7095890
#> 4: 0.1643836 NA 0.3452055 0.7095890
#> 5: 0.1643836 NA 0.3452055 0.7095890
#> ---
#> 801: 0.6136986 1 0.4000000 0.7123288
#> 802: 0.6136986 1 0.3808219 0.7123288
#> 803: 0.6136986 1 0.3808219 0.7808219
#> 804: 0.6136986 1 0.4000000 0.7123288
#> 805: 0.6136986 1 0.3808219 0.7808219