Add functions that can extract and update phenological status based on MODIS data and enable monthly SDA #3249
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Merge Dongchen's branch
…velop Merge from the upstream.
| ##read data | ||
| leafphdata <- utils::read.csv(leaf_pheno_data) | ||
| leafOnDay <- leafphdata$leafonday[leafphdata$year == obs_year & leafphdata$site_id==settings$run$site$id] | ||
| leafOffDay<- leafphdata$leafoffday[leafphdata$year== obs_year & leafphdata$site_id==settings$run$site$id] |
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not required for this PR, but for future reference (1) I suspect dplyr::filter would have been more clear here and (2) it would be good to return a warning to the user if the start.date and end.date are not in the same year, since the current approach doesn't implement any way to update the phenology dates in multi-year runs. Indeed, even in a short term run you could get unexpected results if, for example, you start.date is Dec 31 2023 and your leaf out is in Jan 2024 -- the code as implemented would use the 2023 leaf out date, not the 2024 one.
| if (!(lubridate::month(settings$run$start.date) %in% seq(5,9))){ #Growing seasons are coarsely defined as months from May to September for non-conifers in the US | ||
| site_pft <- utils::read.csv(settings$run$inputs$pft.site$path) | ||
| site.pft.name <- site_pft$pft[site_pft$site == settings$run$site$id] | ||
| if (site.pft.name!="boreal.coniferous") { #Currently only excluding boreal conifers. Other evergreen PFTs could be added here later. |
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Not going to hold up this PR, but this chunk of code here needs updating before it's used more broadly. Even for North American runs, there's has to be a better way of knowing the phenology of a PFT than hard coding it (e.g. adding to the <model> or <pft> configs. Similarly, why hard code the LAI initialization uniformly based on months if we've got a model file that prescribes the leaf-on and leaf-off dates?
| @@ -240,7 +241,8 @@ template <- PEcAn.settings::Settings(list( | |||
| revision = "ssr", | |||
| delete.raw = FALSE, | |||
| binary = model_binary, | |||
| jobtemplate = "~/sipnet_geo.job" | |||
| jobtemplate = "~/sipnet_geo.job", | |||
| leaf_phenology= TRUE | |||
…sda_monthly_local Merge from the upstream.
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Co-authored-by: Chris Black <[email protected]>
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