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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,56 +1,62 @@ | ||
| #' Loads the OTN receiver deployment metadata sheet to prepare it for use in | ||
| #' `convert_otn_to_att` | ||
| #' | ||
| #' @param path the path to the deployment sheet | ||
| #' | ||
| #' @param header_line what line the headers are on | ||
| #' | ||
| #' @param sheet_name the sheet name or number containing the metadata | ||
| #' | ||
| #' @param combine_arr_stn whether or not to to join the station and array columns. Format depends on OTN node | ||
| #' | ||
| #' | ||
| #' @details The function takes the path to the deployment sheet, what line to start | ||
| #' reading from, and what sheet in the excel file to use. It converts column names | ||
| #' to be used by `convert_otn_to_att`. | ||
| #' | ||
| #' @author Ryan Gosse | ||
| #' | ||
| #' @return a data.frame created from the excel file. | ||
| #' | ||
| #' @examples | ||
| #' | ||
| #' #-------------------------------------------------- | ||
| #' # EXAMPLE #1 - loading from NSBS simplified Deployments | ||
| #' | ||
| #' library(glatos) | ||
| #' deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx", | ||
| #' package = "glatos") | ||
| #' | ||
| #' deploy <- prepare_deploy_sheet(header_line, 5, 1) | ||
| #' | ||
| #' @export | ||
|
|
||
| prepare_deploy_sheet <- function(path, header_line = 5, sheet_name = 1, combine_arr_stn = TRUE) { | ||
| deploy_sheet <- readxl::read_excel(path, sheet = sheet_name, skip = header_line) | ||
| deploy_sheet <- deploy_sheet %>% dplyr::rename( | ||
| deploy_lat = DEPLOY_LAT, | ||
| deploy_long = DEPLOY_LONG, | ||
| ins_model_no = INS_MODEL_NO, | ||
| deploy_date_time = `DEPLOY_DATE_TIME (yyyy-mm-ddThh:mm:ss)`, | ||
| recover_date_time = `RECOVER_DATE_TIME (yyyy-mm-ddThh:mm:ss)`, | ||
| station = STATION_NO | ||
|
|
||
| ) | ||
| if (combine_arr_stn) { | ||
| deploy_sheet <- deploy_sheet %>% dplyr::mutate( | ||
| station = paste(OTN_ARRAY, station, sep = '') | ||
| ) | ||
| } | ||
| deploy_sheet <- deploy_sheet %>% dplyr::select( | ||
| station, ins_model_no, deploy_lat, deploy_long, | ||
| deploy_date_time, recover_date_time | ||
| ) | ||
| return(deploy_sheet) | ||
|
|
||
| } | ||
| #' Loads the OTN receiver deployment metadata sheet to prepare it for use in | ||
| #' \code{convert_otn_to_att} | ||
| #' | ||
| #' @param path the path to the deployment sheet | ||
| #' | ||
| #' @param header_line what line the headers are on | ||
| #' | ||
| #' @param sheet_name the sheet name or number containing the metadata | ||
| #' | ||
| #' @param combine_arr_stn whether or not to to join the station and array columns. Format depends on OTN node | ||
| #' | ||
| #' | ||
| #' @details The function takes the path to the deployment sheet, what line to start | ||
| #' reading from, and what sheet in the excel file to use. It converts column names | ||
| #' to be used by \code{convert_otn_to_att}. | ||
| #' | ||
| #' @author Ryan Gosse | ||
| #' | ||
| #' @return a data.frame created from the excel file. | ||
| #' | ||
| #' @examples | ||
| #' | ||
| #' #-------------------------------------------------- | ||
| #' # EXAMPLE #1 - loading from NSBS simplified Deployments | ||
| #' | ||
| #' library(glatos) | ||
| #' deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx", | ||
| #' package = "glatos") | ||
| #' | ||
| #' deploy <- prepare_deploy_sheet(deploy_path, | ||
| #' header_line = 1, | ||
| #' sheet_name = 1) | ||
| #' | ||
| #' @export | ||
|
|
||
| prepare_deploy_sheet <- function(path, header_line = 5, sheet_name = 1, combine_arr_stn = TRUE) { | ||
| deploy_sheet <- readxl::read_excel(path, | ||
| sheet = sheet_name, | ||
| skip = header_line - 1, | ||
| col_names = TRUE) | ||
|
|
||
| deploy_sheet <- deploy_sheet %>% dplyr::rename( | ||
| deploy_lat = DEPLOY_LAT, | ||
| deploy_long = DEPLOY_LONG, | ||
| ins_model_no = INS_MODEL_NO, | ||
| deploy_date_time = `DEPLOY_DATE_TIME (yyyy-mm-ddThh:mm:ss)`, | ||
| recover_date_time = `RECOVER_DATE_TIME (yyyy-mm-ddThh:mm:ss)`, | ||
| station = STATION_NO | ||
|
|
||
| ) | ||
| if (combine_arr_stn) { | ||
| deploy_sheet <- deploy_sheet %>% dplyr::mutate( | ||
| station = paste(OTN_ARRAY, station, sep = '') | ||
| ) | ||
| } | ||
| deploy_sheet <- deploy_sheet %>% dplyr::select( | ||
| station, ins_model_no, deploy_lat, deploy_long, | ||
| deploy_date_time, recover_date_time | ||
| ) | ||
| return(deploy_sheet) | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| #' Defunct functions in glatos | ||
| #' | ||
| #' These functions are gone, no longer available. | ||
| #' | ||
| #' \itemize{ | ||
|
|
||
| #' \item \code{check_dependencies}: Removed in glatos 0.7.0. | ||
| #' | ||
| #' \item \code{install_ffmpeg}: Removed in glatos 0.7.0. | ||
| #' | ||
| #' \item \code{make_video_ffmpeg}: Removed in glatos 0.7.0. | ||
| #' Use \code{\link{make_video}} instead. | ||
| #' | ||
| #' } | ||
| #' | ||
| #' | ||
| #' @name glatos-defunct | ||
| #' @aliases check_dependencies make_video_ffmpeg install_ffmpeg | ||
| NULL |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,72 +1,8 @@ | ||
| ##' Check system dependencies necessary for package 'glatos' | ||
| ##' | ||
| ##' Checks to make sure external dependencies required by functions in | ||
| ##' 'glatos' are installed and available to R. | ||
| ##' | ||
| ##' @details `check_dependencies` checks that ffmpeg (cross platform software | ||
| ##' for manipulating video content) software are installed on your | ||
| ##' computer and accessible to R. FFmpeg is required to create or modify video | ||
| ##' animations of fish movement using the `make_frames`, | ||
| ##' `make_video`, and `adjust_video_playback` functions. | ||
| ##' | ||
| ##' @details When `check_dependencies` is executed, R attempts to | ||
| ##' sequentially access the external libraries. If the libraries | ||
| ##' are installed and accessible, a message is returned to the | ||
| ##' terminal stating that the check was successful. Failed attempts | ||
| ##' to access the external libraries are printed to the terminal. | ||
| ##' | ||
| ##' @details The simplest way to install FFMPEG for use by the 'glatos' package | ||
| ##' functions is to use the `install_ffmpeg` function, which downloads | ||
| ##' the excecutable from one of the websites listed below (depending on | ||
| ##' operating system) and places it in the 'glatos' package directory. | ||
| ##' `make_video` and other `glatos` functions that call ffmpeg will | ||
| ##' from that location. The downside to this method is that | ||
| ##' `install_ffmpeg` will need to be run each time the `glatos` | ||
| ##' package is re-installed. For more permanent installations of FFMPEG, see | ||
| ##' directions below, by operating system. | ||
| ##' | ||
| ##' @details Full installation of the ffmpeg library on windows is | ||
| ##' accomplished by downloading the recent 'static' build from | ||
| ##' <http://ffmpeg.zeranoe.com/builds/>. After the download is | ||
| ##' complete, use your favorite compression utility to extract the | ||
| ##' downloaded folder. Decompress the package and store contents on | ||
| ##' your computer. Last, edit your system path variable to include | ||
| ##' the path to the directory containing ffmpeg.exe | ||
| ##' | ||
| ##' @details Full installation of ffmpeg on Mac is similar to | ||
| ##' windows. First, download most recent build from | ||
| ##' <http://www.evermeet.cx/ffmpeg/>. The binary files are | ||
| ##' compressed with 7zip so may need toinstall an unarchiving | ||
| ##' utility (<http://wakaba.c3.cx/s/apps/unarchiver.html>) to | ||
| ##' extract the program folder. After the folder is extracted, copy | ||
| ##' the ffmpeg folder to /usr/local/bin/ffmpeg on your machine. | ||
| ##' | ||
| ##' @return A message is printed to the console. | ||
| ##' | ||
| ##' @author Todd Hayden, Chris Holbrook | ||
| ##' | ||
| ##' @examples | ||
| ##'\dontrun{ | ||
| ##' # run check | ||
| ##' check_dependencies() | ||
| ##' } | ||
| ##' | ||
| ##' @export | ||
|
|
||
|
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||
| check_dependencies <- function(){ | ||
| #' @export | ||
| check_dependencies <- function(...){ | ||
|
|
||
| # check for ffmpeg | ||
| message("Checking for ffmpeg...") | ||
| ffmpeg <- tryCatch(list(found = TRUE, value = glatos:::get_ffmpeg_path(NA)), | ||
| error = function(e) list(found = FALSE, value = e$message)) | ||
|
|
||
|
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||
| # print message with result | ||
| if(ffmpeg$found) { | ||
| message(" OK... FFmpeg is installed at \n ", ffmpeg$value, ".", "\n") | ||
| } else { | ||
| message(ffmpeg$value, "\n") | ||
| } | ||
| # FFmpeg is no longer needed. Function is now defunct | ||
| .Defunct(new = NA, | ||
| msg = "ffmpeg dependency is no longer needed by glatos package") | ||
|
|
||
| } |
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