diff --git a/R/ga_api_all_data.R b/R/ga_api_all_data.R index fe8c574..369778a 100644 --- a/R/ga_api_all_data.R +++ b/R/ga_api_all_data.R @@ -54,7 +54,8 @@ ga_api_all_data <- function(token, synthesis_id, dir, include_zeros = FALSE, fil relief <- ga_api_relief(synthesis_id = synthesis_id, token = token) %>% dplyr::semi_join(metadata, by = "sample_url") - + + if (nrow(benthos > 0)) { benthos_summarised <- benthos %>% dplyr::mutate(habitat = case_when(level_2 %in% "Macroalgae" ~ level_2, level_2 %in% "Seagrasses" ~ level_2, @@ -81,7 +82,11 @@ ga_api_all_data <- function(token, synthesis_id, dir, include_zeros = FALSE, fil .fns = ~ .x / total_points_annotated, .names = "{.col}_percent" )) + + assign("benthos_summarised", benthos_summarised, envir = .GlobalEnv) + } + if (nrow(relief > 0)) { relief_summarised <- relief %>% uncount(count) %>% group_by(sample_url) %>% @@ -89,14 +94,17 @@ ga_api_all_data <- function(token, synthesis_id, dir, include_zeros = FALSE, fil ungroup() %>% dplyr::left_join(samples) %>% dplyr::select(sample_url, campaignid, sample, everything()) + + assign("relief_summarised", relief_summarised, envir = .GlobalEnv) + } if (nrow(metadata) > 0) {assign("metadata", metadata, envir = .GlobalEnv)} if (nrow(count > 0)) {assign("count", count, envir = .GlobalEnv)} if (nrow(length > 0)) {assign("length", length, envir = .GlobalEnv)} if (nrow(benthos > 0)) {assign("benthos_raw", benthos, envir = .GlobalEnv)} if (nrow(relief > 0)) {assign("relief_raw", relief, envir = .GlobalEnv)} - if (nrow(benthos_summarised > 0)) {assign("benthos_summarised", benthos_summarised, envir = .GlobalEnv)} - if (nrow(relief_summarised) > 0) {assign("relief_summarised", relief_summarised, envir = .GlobalEnv)} + # if (nrow(benthos_summarised > 0)) {assign("benthos_summarised", benthos_summarised, envir = .GlobalEnv)} + # if (nrow(relief_summarised) > 0) {assign("relief_summarised", relief_summarised, envir = .GlobalEnv)} # Save processed data as RDS files