spell checking

R/getters.R

@@ -72,7 +72,7 @@ read_sfn_data <- function(site_codes, folder = '.') {
 #' @param folder Route to the folder containing the data. Default to working
 #'   directory
 #'
-#' @param .dry Dry run. Metadata is loaded and readed, but no cache is written
+#' @param .dry Dry run. Metadata is loaded and read, but no cache is written
 #' 
 #' @examples
 #' # Let's access the data in "folder". This typically is the folder where the
@@ -213,12 +213,12 @@ read_sfn_metadata <- function(folder = '.', .write_cache = FALSE) {
 #'
 #' \code{filter_sites_by_md} function takes logical expressions for the metadata
 #' variables (i.e. \code{pl_sens_meth == 'HR'}), and list the sites that met
-#' the criteria from thos supplied
+#' the criteria from those supplied
 #'
 #' \code{.join} argument indicates how sites must be filtered between metadata
 #' classes. \code{'and'} indicates only sites meeting all conditions for all
 #' metadata classes are returned. \code{'or'} indicates all sites meeting any
-#' condition between classes are returned. For two or more filtes of the same
+#' condition between classes are returned. For two or more filters of the same
 #' metadata class, they are combined as 'and'.
 #' 
 #' @param sites character vector with the sites codes to filter, generally the
@@ -272,7 +272,7 @@ read_sfn_metadata <- function(folder = '.', .write_cache = FALSE) {
 #'   .join = 'or'
 #' )
 #'
-#' @return A character vector with the sites fullfilling the premises
+#' @return A character vector with the sites fulfilling the premises
 #'
 #' @export
 

R/helpers.R

@@ -4,7 +4,7 @@
 #'
 #' This helper function calculates the coverage percentage in a vector, and is
 #' designed to be used inside a dplyr summarise statement. It calculates the
-#' coverage as the percentage of no NAs in the expected lenght of the summarising
+#' coverage as the percentage of no NAs in the expected length of the summarising
 #' period stated by the timestep.
 #'
 #' @param x a vector, usually a variable in the sapflow or environmental data.
@@ -157,7 +157,7 @@ min_time <- function(x, time) {
 #'
 #' The code for this function has been kindly provided by Jacob Nelson in python
 #' (see https://github.com/jnelson18/FluxnetTools/blob/master/FileS3.py) and has
-#' been translated to a tidy data phylosophy in R to be used inside a
+#' been translated to a tidy data philosophy in R to be used inside a
 #' \code{\link[dplyr]{summarise}} statement.
 #'
 #' @section Diurnal centroid algorithm:
@@ -226,7 +226,7 @@ diurnal_centroid <- function(variable) {
 #'
 #' The code for this function has been kindly provided by Jacob Nelson in python
 #' (see https://github.com/jnelson18/FluxnetTools/blob/master/FileS3.py) and has
-#' been translated to a tidy data phylosophy in R to be used inside a
+#' been translated to a tidy data philosophy in R to be used inside a
 #' \code{\link[dplyr]{summarise}} statement.
 #'
 #' @section Normalized diurnal centroid algorithm:
@@ -291,7 +291,7 @@ norm_diurnal_centroid <- function(sapf_var, rad_var) {
 
 #' Timezones dictionary
 #'
-#' Tranforms timezone ISO code to character vector compatible with lubridate and
+#' Transforms timezone ISO code to character vector compatible with lubridate and
 #' POSIXct
 #'
 #' GMT time zones are used, as they are day saving light time (DST) agnostic,
@@ -1302,7 +1302,7 @@ describe_md_variable <- function(variable) {
 #' 
 #' sum for summarise_all aware of POSIX objects
 #' 
-#' @param variable the variable as it is pased to the .fixed_metrics function
+#' @param variable the variable as it is passed to the .fixed_metrics function
 #' @param na.rm logical to pass to na.rm argument from sum
 #' 
 #' @examples 
@@ -1320,4 +1320,4 @@ describe_md_variable <- function(variable) {
   }
 
   return(res)
-}
+}

R/metrics.R

@@ -369,7 +369,7 @@ sfn_metrics <- function(
     # progress to not scare seeming like freezed in large datasets
     print(paste0('Nighttime data for ', get_si_code(sfn_data)))
 
-    # period_minutes modification especific for night intervals calculations
+    # period_minutes modification specific for night intervals calculations
     new_period_minutes <- lubridate::as.duration(
       lubridate::hours(24 - (int_start - int_end))
     )@.Data / 60
@@ -442,7 +442,7 @@ sfn_metrics <- function(
       # progress to not scare seeming like freezed
       print(paste0(interval, ' data for ', get_si_code(sfn_data)))
 
-      # period_minutes modification especific for daytime intervals calculations
+      # period_minutes modification specific for daytime intervals calculations
       new_period_minutes <- lubridate::as.duration(
         lubridate::hours(int_end - int_start)
       )@.Data / 60
@@ -524,7 +524,7 @@ sfn_metrics <- function(
 #'   \item{mean: Mean value for the selected period}
 #'   \item{sd: Standard deviation for the selected period}
 #'   \item{coverage: Percentage of coverage as the percentage of no NAs in the
-#'   expected legth of the period, stated by the site timestep}
+#'   expected length of the period, stated by the site timestep}
 #'   \item{q*: q95 by default. Quantile value for the selected period. Quantiles to
 #'   calculate are stated in the probs argument}
 #'   \item{accumulated: Accumulated value on the selected period}
@@ -598,7 +598,7 @@ sfn_metrics <- function(
 #' \itemize{
 #'   \item{mean: mean of variable (tree or environmental variable) for the
 #'         given period. NAs are removed}
-#'   \item{sd: standard deviation of the variable for the givn period. NAs are
+#'   \item{sd: standard deviation of the variable for the given period. NAs are
 #'         removed}
 #'   \item{coverage: Data coverage percentage (percentage of measures without
 #'         NAs)}
@@ -1213,7 +1213,7 @@ metrics_tidyfier <- function(
     dplyr::filter(.data$si_code %in% sites_codes)
 
 
-  # we start modifing the sapflow data
+  # we start modifying the sapflow data
   whole_data <- sapf_data %>%
     purrr::map(.sapflow_tidy) %>%
 
@@ -1425,4 +1425,4 @@ metrics_tidyfier <- function(
     tidyr::fill(.data$custom_dates) %>%
     dplyr::pull(.data$custom_dates) %>%
     lubridate::floor_date(unit = 'hour')
-}
+}

R/sfn_data_methods.R

@@ -5,10 +5,10 @@
 #'
 #' Validation checks for generating sfn_data class objects
 #'
-#' This method is used internally when creating and/or modifing sfn_data class
+#' This method is used internally when creating and/or modifying sfn_data class
 #' objects to ensure that the object returned is correct in terms of content
 #' classes and dimensions (i.e. sapflow data and environmental data has the
-#' same lenght)
+#' same length)
 #'
 #' @name sfn_data_validity
 
@@ -107,7 +107,7 @@ setValidity(
 #'
 #' Validation checks for generating sfn_data_multi class objects
 #'
-#' This method is used internally to ensure the correctnes of the sfn_data_multi
+#' This method is used internally to ensure the correctness of the sfn_data_multi
 #' object. Basically ensures that the object returned is a list of sfn_data
 #' class objects
 #'
@@ -1037,7 +1037,7 @@ setMethod(
 #'         vector of length == nrow(sapf/env_data)}
 #'   \item{For \code{get_si_code} a character vector}
 #' }
-#' Validity is automatically checked before modifing the sfn_data object, and
+#' Validity is automatically checked before modifying the sfn_data object, and
 #' an error is raised if not valid
 #'
 #' @param object sfn_data containing the slot to replace

R/sfn_dplyr.R

@@ -158,7 +158,7 @@ sfn_filter <- function(sfn_data, ..., solar = FALSE) {
 #' sapflow and environmental measures (i.e. mutate sapflow when wind is high or
 #' radiation is zero). Due to this, at the moment any new variable is dropped
 #' when building the final results, so this is ONLY intended to mutate
-#' exisiting variables without changing the names.
+#' existing variables without changing the names.
 #'
 #' @param sfn_data \code{sfn_data} or \code{sfn_data_multi} object to subset
 #'
@@ -284,7 +284,7 @@ sfn_mutate <- function(sfn_data, ..., solar = FALSE) {
 #' `sfn_mutate_at` function will maintain the same number of rows before and
 #' after the modification, so it is well suited to modify variables without
 #' creating TIMESTAMP gaps (i.e. to change variable units). For mutating
-#' indiviudal variables see \code{\link{sfn_mutate}}.
+#' individual variables see \code{\link{sfn_mutate}}.
 #'
 #' @param sfn_data \code{sfn_data} or \code{sfn_data_multi} object to subset
 #'

R/visualizations.R

@@ -27,7 +27,7 @@
 #'
 #' @section Formula:
 #'   \code{formula} argument can be used to select an environmental variable to
-#'   plot versus all the sapflow measurements. Any envirinmental variable is
+#'   plot versus all the sapflow measurements. Any environmental variable is
 #'   allowed, if it exist in the site provided.
 #'
 #' @section Geometry:

README.Rmd

@@ -2,7 +2,7 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
+<!-- README.md is generated from README.Rmd. Please edit thet file -->
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(

README.md

@@ -1,5 +1,5 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
+<!-- README.md is generated from README.Rmd. Please edit thet file -->
 
 # sapfluxnetr