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Merge pull request #22 from inbo/bugfix
Improvements on imputed data
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| .Rproj.user | ||
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| *.Rproj |
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| Version: 1.0 | ||
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| PackageCheckArgs: --as-cran | ||
| PackageRoxygenize: rd,collate,namespace | ||
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| Original file line number | Diff line number | Diff line change |
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| context("model imputed") | ||
| test_that("model imputation works", { | ||
| this.result.datasource.id <- sha1(letters) | ||
| this.scheme.id <- sha1(letters) | ||
| this.species.group.id <- sha1(letters) | ||
| this.location.group.id <- sha1(letters) | ||
| this.analysis.date <- Sys.time() | ||
| this.model.type <- "inla poisson: A * (B + C) + C:D" | ||
| this.first.imported.year <- 1990L | ||
| this.last.imported.year <- 2015L | ||
| this.last.analysed.year <- 2014L | ||
| this.duration <- 1L | ||
| dataset <- test_data(missing = 0.2) | ||
| base <- tempdir() | ||
| project <- "imputation" | ||
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| imputation <- n2k_inla( | ||
| data = dataset, scheme.id = this.scheme.id, | ||
| result.datasource.id = this.result.datasource.id, | ||
| species.group.id = this.species.group.id, | ||
| location.group.id = this.location.group.id, model.type = this.model.type, | ||
| first.imported.year = this.first.imported.year, imputation.size = 100, | ||
| last.imported.year = this.last.imported.year, family = "poisson", | ||
| last.analyses.year = this.last.analysed.year, duration = this.duration, | ||
| formula = "Count ~ A * (B + C) + f(E, model = \"iid\")", | ||
| analysis.date = Sys.time(), | ||
| ) | ||
| aggregation <- n2k_aggregate( | ||
| scheme.id = this.scheme.id, | ||
| result.datasource.id = this.result.datasource.id, formula = "~ A + B", | ||
| species.group.id = this.species.group.id, | ||
| location.group.id = this.location.group.id, model.type = this.model.type, | ||
| first.imported.year = this.first.imported.year, analysis.date = Sys.time(), | ||
| last.imported.year = this.last.imported.year, fun = sum, | ||
| last.analyses.year = this.last.analysed.year, duration = this.duration, | ||
| parent = get_file_fingerprint(imputation) | ||
| ) | ||
| aggregation2 <- n2k_aggregate( | ||
| scheme.id = this.scheme.id, | ||
| result.datasource.id = this.result.datasource.id, formula = "~ A", | ||
| species.group.id = this.species.group.id, | ||
| location.group.id = this.location.group.id, model.type = this.model.type, | ||
| first.imported.year = this.first.imported.year, analysis.date = Sys.time(), | ||
| last.imported.year = this.last.imported.year, fun = sum, | ||
| last.analyses.year = this.last.analysed.year, duration = this.duration, | ||
| parent = get_file_fingerprint(aggregation) | ||
| ) | ||
| extractor <- function(model) { | ||
| model$summary.fixed[, c("mean", "sd")] | ||
| } | ||
| mi <- n2k_model_imputed( | ||
| scheme.id = this.scheme.id, model.args = list(family = "poisson"), | ||
| result.datasource.id = this.result.datasource.id, model.fun = INLA::inla, | ||
| species.group.id = this.species.group.id, extractor = extractor, | ||
| location.group.id = this.location.group.id, model.type = this.model.type, | ||
| first.imported.year = this.first.imported.year, analysis.date = Sys.time(), | ||
| last.imported.year = this.last.imported.year, formula = "~ A", | ||
| last.analyses.year = this.last.analysed.year, duration = this.duration, | ||
| parent = get_file_fingerprint(aggregation) | ||
| ) | ||
| pma <- list( function(x) { | ||
| return(list(family = "poisson")) | ||
| } ) | ||
| mi2 <- n2k_model_imputed( | ||
| scheme.id = this.scheme.id, model.args = list(), | ||
| result.datasource.id = this.result.datasource.id, model.fun = INLA::inla, | ||
| species.group.id = this.species.group.id, extractor = extractor, | ||
| location.group.id = this.location.group.id, model.type = this.model.type, | ||
| first.imported.year = this.first.imported.year, analysis.date = Sys.time(), | ||
| last.imported.year = this.last.imported.year, formula = "~ A", | ||
| last.analyses.year = this.last.analysed.year, duration = this.duration, | ||
| parent = get_file_fingerprint(aggregation), prepare.model.args = pma | ||
| ) | ||
| store_model(imputation, base, project) | ||
| store_model(aggregation, base, project) | ||
| store_model(mi, base, project) | ||
| store_model(aggregation2, base, project) | ||
| store_model(mi2, base, project) | ||
| fit_model(get_file_fingerprint(imputation), base, project) | ||
| fit_model(get_file_fingerprint(aggregation), base, project) | ||
| fit_model(get_file_fingerprint(mi), base, project) | ||
| fit_model(get_file_fingerprint(aggregation2), base, project) | ||
| fit_model(get_file_fingerprint(mi2), base, project) | ||
| }) |