Merge pull request #16 from wendtke/siqi_scratch

Siqi_scratch

.Rbuildignore

@@ -1,3 +1,4 @@
-^psyr\.Rproj$
+^psyphr\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^README\.Rmd$

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(rename_hrv_editing_columns)
-export(transform_editing_sheet)
-export(transform_hrv_sheet)
-export(transform_settings_sheet)
+export(bare_name)
+export(read_MW_EDA)
+export(read_MW_workbook)
+export(rename_hrv_stats_columns)
+export(tidy_MW_EDA)

R/rename.R

@@ -1,12 +1,13 @@
 #' Rename sheet columns after the sheet has been transformed.
 #'
-#' Functions to change the column names to be easier to use by later analysis scripts.
+#' Functions to change the column names to be easier to use by later analysis
+#' scripts.
 #' They should only be called after transform_* has already been used.
 #'
-#' TODO: add error handling in case this is run before transform_* has been run,
-#' and the column names are not as expected. I.e., detect whether the second
-#' column name is a number, and if so,
-#' exit out gracefully with a message to run transform_* function first.
+#' TODO: Add error handling in case this is run before transform_* has been run,
+#' and the column names are not as expected - i.e., detect whether the second
+#' column name is a number, and if so, exit out gracefully with a message
+#' to run transform_* function first.
 #'
 #' @param sheet
 #'
@@ -19,94 +20,79 @@
 #' rename_eda_stats_columns(sheet_data)
 #' rename_hrv_editing_columns(sheet_data)
 #'
-#'
-#'
-
-
-
 rename_hrv_stats_columns <- function(sheet){
-  sheet <- sheet %>%
-    dplyr::rename(segment = segment,
-                  start_time = `Start Time`,
-                  end_time = `End Time`,
-                  seg_length = `Segment Duration`,
-                  mean_hr = `Mean Heart Rate`,
-                  rsa = RSA,
-                  mean_ibi = `Mean IBI`,
-                  r_peaks = `# of R's Found`,
-                  resp_rate = `Respiration Rate`,
-                  resp_amp = `Respiration Amplitude`,
-                  resp_peak_freq = `Respiration Peak Frequency`,
-                  resp_power = `Respiration Power`,
-                  first_r_time = `First ECG R Time`,
-                  last_r_time = `Last ECG R Time`,
-                  r_r_duration = `First R to Last R Duration`,
-                  sdnn = SDNN,
-                  avnn = AVNN,
-                  rmssd = RMSSD,
-                  nn50 = NN50,
-                  pnn50 = pNN50)
-
-  sheet
-
+  sheet %>%
+  dplyr::rename(segment = `Segment Number`,
+                start_time = `Start Time`,
+                end_time = `End Time`,
+                seg_length = `Segment Duration`,
+                mean_hr = `Mean Heart Rate`,
+                rsa = RSA,
+                mean_ibi = `Mean IBI`,
+                r_peaks = `# of R's Found`,
+                resp_rate = `Respiration Rate`,
+                resp_amp = `Respiration Amplitude`,
+                resp_peak_freq = `Respiration Peak Frequency`,
+                resp_power = `Respiration Power`,
+                first_r_time = `First ECG R Time`,
+                last_r_time = `Last ECG R Time`,
+                r_r_duration = `First R to Last R Duration`,
+                sdnn = SDNN,
+                avnn = AVNN,
+                rmssd = RMSSD,
+                nn50 = NN50,
+                pnn50 = pNN50)
 }
 
 
 
 rename_hrv_editing_columns <- function(sheet) {
-  sheet <- sheet %>%
-    dplyr::rename(segment = segment,
-                  ecg_sec_cut = `ECG : Seconds Removed`,
-                  ecg_perc_cut = `ECG : Percentage Removed`,
-                  ecg_sec_est = `ECG : Seconds Estimated`,
-                  ecg_perc_est = `ECG : Percentage Estimated`,
-                  resp_sec_cut = `Resp : Seconds Removed`,
-                  resp_perc_cut = `Resp : Percentage Removed`,
-                  resp_sec_est = `Resp : Seconds Estimated`,
-                  resp_perc_est = `Resp : Percentage Estimated`,
-                  total_r_peaks = `Total Peaks`,
-                  norm_r_peaks = `Normal Peaks`,
-                  norm_r_perc = `% Normal Peaks`,
-                  est_r_peaks = `Estimated Peaks`,
-                  est_r_peaks_perc = `% Estimated Peaks`,
-                  art_r_peaks = `Artifact Peaks`,
-                  art_r_peaks_perc = `% Artifact Peaks`,
-                  dur_est_r_r = `Duration of Estimated R-R Intervals`,
-                  est_r_r_perc = `% of Estimated R-R Intervals`)
-
-  sheet
-
+  sheet %>%
+  dplyr::rename(segment = `Segment Number`,
+                ecg_sec_cut = `ECG : Seconds Removed`,
+                ecg_perc_cut = `ECG : Percentage Removed`,
+                ecg_sec_est = `ECG : Seconds Estimated`,
+                ecg_perc_est = `ECG : Percentage Estimated`,
+                resp_sec_cut = `Resp : Seconds Removed`,
+                resp_perc_cut = `Resp : Percentage Removed`,
+                resp_sec_est = `Resp : Seconds Estimated`,
+                resp_perc_est = `Resp : Percentage Estimated`,
+                total_r_peaks = `Total Peaks`,
+                norm_r_peaks = `Normal Peaks`,
+                norm_r_perc = `% Normal Peaks`,
+                est_r_peaks = `Estimated Peaks`,
+                est_r_peaks_perc = `% Estimated Peaks`,
+                art_r_peaks = `Artifact Peaks`,
+                art_r_peaks_perc = `% Artifact Peaks`,
+                dur_est_r_r = `Duration of Estimated R-R Intervals`,
+                est_r_r_perc = `% of Estimated R-R Intervals`)
 }
 
 
 rename_eda_stats_columns <- function(sheet){
-  sheet <- sheet %>%
-    dpylr::rename(segment = segment,
-                  start_time = `Start Time`,
-                  end_time = `End Time`,
-                  seg_length = `Segment Duration`,
-                  total_scr = `Total SCRs`,
-                  er_scr = `ER-SCRs`,
-                  ns_scrs = `NS-SCRs`,
-                  tonic_scl = `Tonic SCL`,
-                  mean_sc = `Mean SC`,
-                  tonic_period = `Tonic Period`)
-
-  sheet
-
+  sheet %>%
+  dplyr::rename(segment = `Segment Number`,
+                start_time = `Start Time`,
+                end_time = `End Time`,
+                seg_length = `Segment Duration`,
+                total_scr = `Total SCRs`,
+                er_scr = `ER-SCRs`,
+                ns_scrs = `NS-SCRs`,
+                tonic_scl = `Tonic SCL`,
+                mean_sc = `Mean SC`,
+                tonic_period = `Tonic Period`)
 }
 
 
-
 rename_eda_editing_columns <- function(sheet){
-  sheet <- sheet %>%
-    dplyr::rename(segment = segment,
-                  eda_sec_cut = `EDA : Seconds Removed`,
-                  eda_perc_cut = `EDA : Percentage Removed`,
-                  eda_sec_est = `EDA : Seconds Estimated`,
-                  eda_perc_est = `EDA : Percentage Estimated`,
-                  resp_sec_cut = `Resp : Seconds Removed`,
-                  resp_perc_cut = `Resp : Percentage Removed`,
-                  resp_sec_est = `Resp : Seconds Estimated`,
-                  resp_perc_est = `Resp : Percentage Estimated`)
+  sheet %>%
+  dplyr::rename(segment = `Segment Number`,
+                eda_sec_cut = `EDA : Seconds Removed`,
+                eda_perc_cut = `EDA : Percentage Removed`,
+                eda_sec_est = `EDA : Seconds Estimated`,
+                eda_perc_est = `EDA : Percentage Estimated`,
+                resp_sec_cut = `Resp : Seconds Removed`,
+                resp_perc_cut = `Resp : Percentage Removed`,
+                resp_sec_est = `Resp : Seconds Estimated`,
+                resp_perc_est = `Resp : Percentage Estimated`)
 }