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Diffstat (limited to 'R/read_spreadsheet.R')
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diff --git a/R/read_spreadsheet.R b/R/read_spreadsheet.R new file mode 100644 index 00000000..a20af6db --- /dev/null +++ b/R/read_spreadsheet.R @@ -0,0 +1,113 @@ +#' Read datasets and relevant meta information from a spreadsheet file +#' +#' This function imports one dataset from each sheet of a spreadsheet file. +#' These sheets are selected based on the contents of a sheet 'Datasets', with +#' a column called 'Dataset Number', containing numbers identifying the dataset +#' sheets to be read in. In the second column there must be a grouping +#' variable, which will often be named 'Soil'. Optionally, time normalization +#' factors can be given in columns named 'Temperature' and 'Moisture'. +#' +#' There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. +#' The first row read after the header read in from this sheet is assumed +#' to contain name and acronym of the parent compound. +#' +#' The dataset sheets should be named using the dataset numbers read in from +#' the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, name +#' of the observed variable (e.g. the acronym of the parent compound or +#' one of its transformation products) should be in the first column, +#' the time values should be in the second colum, and the observed value +#' in the third column. +#' +#' In case relevant covariate data are available, they should be given +#' in a sheet 'Covariates', containing one line for each value of the grouping +#' variable specified in 'Datasets'. These values should be in the first +#' column and the column must have the same name as the second column in +#' 'Datasets'. Covariates will be read in from columns four and higher. +#' Their names should preferably not contain special characters like spaces, +#' so they can be easily used for specifying covariate models. +#' +#' An similar data structure is defined as the R6 class [mkindsg], but +#' is probably more complicated to use. +#' +#' @param path Absolute or relative path to the spreadsheet file +#' @param valid_datasets Optional numeric index of the valid datasets, default is +#' to use all datasets +#' @param parent_only Should only the parent data be used? +#' @param normalize Should the time scale be normalized using temperature +#' and moisture normalisation factors in the sheet 'Datasets'? +#' @export +read_spreadsheet <- function(path, valid_datasets = "all", + parent_only = TRUE, normalize = TRUE) +{ + if (!requireNamespace("readxl", quietly = TRUE)) + stop("Please install the readxl package to use this function") + + # Read the compound table + compounds <- readxl::read_excel(path, sheet = "Compounds") + parent <- compounds[1, ]$Acronym + + # Read in meta information + ds_meta <- readxl::read_excel(path, sheet = "Datasets") + ds_meta["Dataset Number"] <- as.character(ds_meta[["Dataset Number"]]) + + # Select valid datasets + if (valid_datasets[1] == "all") valid_datasets <- 1:nrow(ds_meta) + ds_numbers_valid <- ds_meta[valid_datasets, ]$`Dataset Number` + grouping_factor <- names(ds_meta[2]) # Often "Soil" + + # Read in valid datasets + ds_raw <- lapply(ds_numbers_valid, + function(dsn) readxl::read_excel(path, sheet = as.character(dsn))) + + # Make data frames compatible with mmkin + ds_tmp <- lapply(ds_raw, function(x) { + ds_ret <- x[1:3] |> + rlang::set_names(c("name", "time", "value")) |> + transform(value = as.numeric(value)) + }) + names(ds_tmp) <- ds_numbers_valid + + # Normalize with temperature and moisture correction factors + if (normalize) { + ds_norm <- lapply(ds_numbers_valid, function(ds_number) { + f_corr <- as.numeric(ds_meta[ds_number, c("Temperature", "Moisture")]) + ds_corr <- ds_tmp[[ds_number]] |> + transform(time = time * f_corr[1] * f_corr[2]) + return(ds_corr) + }) + } else { + ds_norm <- ds_tmp + } + names(ds_norm) <- ds_numbers_valid + + # Select parent data only if requested + if (parent_only) { + ds_norm <- lapply(ds_norm, function(x) subset(x, name == parent)) + compounds <- compounds[1, ] + } + + # Create a single long table to combine datasets with the same group name + ds_all <- vctrs::vec_rbind(!!!ds_norm, .names_to = "Dataset Number") + ds_all_group <- merge(ds_all, ds_meta[c("Dataset Number", grouping_factor)]) + groups <- unique(ds_meta[valid_datasets, ][[grouping_factor]]) + + ds <- lapply(groups, function(x) { + ret <- ds_all_group[ds_all_group[[grouping_factor]] == x, ] + ret[c("name", "time", "value")] + } + ) + names(ds) <- groups + + # Get covariates + covariates_raw <- readxl::read_excel(path, sheet = "Covariates") + covariates <- as.data.frame(covariates_raw[4:ncol(covariates_raw)]) + rownames(covariates) <- covariates_raw[[1]] + covariates <- covariates[which(colnames(covariates) != "Remarks")] + + # Attach the compound list to support automatic model building + attr(ds, "compounds") <- as.data.frame(compounds) + + # Attach covariate data + attr(ds, "covariates") <- covariates[groups, , drop = FALSE] + return(ds) +} |