Working: co,sx,dx,pi,pwa,ri,mx,prx and cvr

Next action: TFA, ARI and CPPopt

NAMESPACE

@@ -7,3 +7,4 @@ export(cm_prx)
 export(cm_pwa)
 export(cm_ri)
 export(cm_cvr)
+export(cm_co)

R/cm_co.R

@@ -1,6 +1,36 @@
-#Co - https ://www.ncbi.nlm.nih.gov/ pmc / articles /PMC5317099/
-# CO (EST) = PP / (SBP+DBP) * HR
+globalVariables(c("block","epoch","n","period","overlapping"))
 
-cm_co <- function() {
-   print("Hello, world!")
+cm_co <- function(
+   #Dataframes
+   df, del_1 = NULL, del_2 = NULL, trigger = NULL,
+   #Calculation settings
+   blocksize = 3, freq = 1000,
+   #Data Quality
+   blockmin = 0.5,
+   #Output
+   output = "period"
+){
+   df_cols <- colnames(df)
+
+   #Global functions
+   z_validation(df, "recording", 3)
+   z_validation(del_1, "first deleter", 2)
+   z_validation(del_2, "second deleter", 2)
+   z_validation(trigger, "trigger", 2)
+
+   colnames(df) <- c("time","val1","val2")
+   df$n <- c(1:nrow(df))
+
+   df <- z_trigger(df,trigger)
+   df <- z_deleter(df,del_1)
+   df <- z_deleter(df,del_2)
+   df <- z_blocks(df,freq,blocksize)
+
+   df_agg <- z_agg(df,freq,blocksize,blockmin,by_type=c("max","min","mean"),n_vars=2)
+
+   results <- cm_co_output(df, df_agg, by_type=c("val1_max","val1_min","val2_mean"),freq, blocksize, output)
+
+   #FUNCTIONS ----
+   return(results)
 }
+

R/z_functions_co.R

@@ -0,0 +1,46 @@
+#Output creation
+cm_co_output <- function(df, df_agg, by_type, freq, blocksize, output){
+   if(output == "period"){
+
+      results <- NULL
+      for(i in unique(df_agg$period)){
+
+         temp <- cbind(i,
+                       length(unique(df_agg$block[df_agg$period == i])),
+                       min(df$time[df$period == i]),
+                       max(df$time[df$period == i]),
+                       mean(df_agg[df_agg$period == i,c(by_type[1])]),
+                       mean(df_agg[df_agg$period == i,c(by_type[2])]),
+                       mean(df_agg[df_agg$period == i,c(by_type[3])]),
+                       mean(df_agg[df_agg$period == i,c(by_type[4])]),
+                       round(100-sum(df_agg$length[df_agg$period == i])/
+                                (freq*(max(df$time[df$period == i])-
+                                          min(df$time[df$period == i])))*100, digits=1),
+                       mean((df_agg[df_agg$period == i,c(by_type[1])]-df_agg[df_agg$period == i,c(by_type[2])])/
+                            (df_agg[df_agg$period == i,c(by_type[1])]+df_agg[df_agg$period == i,c(by_type[2])])*
+                               df_agg[df_agg$period == i,c(by_type[3])])
+         )
+         results <- rbind(results,temp)
+
+      }
+
+   }else if(output == "block"){
+      results <- NULL
+      for(i in c(1:nrow(df_agg))){
+         temp <- cbind(df_agg[i,c("period","block")],
+                       min(df$time[df$period == df_agg$period[i] & df$block == df_agg$block[i]]),
+                       max(df$time[df$period == df_agg$period[i] & df$block == df_agg$block[i]]),
+                        df_agg[i,c("val1_max","val1_min")],
+                       round(100-df_agg$length[i]/(freq*blocksize)*100, digits=1),
+                        (df_agg$val1_max[i]-df_agg$val1_min[i])/(df_agg$val1_max[i]+df_agg$val1_min[i])*
+                          df_agg$val2_mean[i])
+         results <- rbind(results,temp)
+      }
+
+   }else{
+      stop("\'output\' must be left blank, 'period' or 'block'")
+   }
+   results <- as.data.frame(results)
+   colnames(results) <- c("period","blocks","time.min","time.max","val1_max","val1_min","val2_mean","missing.perc","cvr")
+   return(results)
+}

man/cm_co.Rd

@@ -0,0 +1,27 @@
+\name{cm_co}
+\alias{cm_co}
+\title{Cardiovascular resistance}
+\description{
+Calculates the co, and further described in following publication ...
+[clinmon: An R package for calculation of clinical monitoring indices (2019)]
+Co - https ://www.ncbi.nlm.nih.gov/ pmc / articles /PMC5317099/
+ CO (EST) = PP / (SBP+DBP) * HR
+}
+\usage{
+cm_co(df, del_1, del_2, trigger, blocksize, freq, blockmin, output)
+}
+\arguments{
+  \item{df}{Data imported with 2 columns: time (in seconds), physiological measurement (raw measurement).}
+  \item{del_1}{Deleter periods for pressure with two columns, first column is start of deletion period and last column is end of deletion period, every row is a deletion period. (dataframe) }
+  \item{del_2}{Deleter periods for pressure with two columns, first column is start of deletion period and last column is end of deletion period, every row is a deletion period. (dataframe) }
+  \item{trigger}{Trigger periods with two columns, first column is start of analysed period and last column is end of analysed period, every row is a period for analysis. (dataframe)}
+  \item{blocksize}{Size of blocks created in seconds, default is 3 s. (numeric)}
+  \item{freq}{Frequency of recorded data, default is 1000 Hz. (numeric)}
+  \item{blockmin}{Minimum measurements ratio in every block, default is 0.5 (numeric)}
+  \item{output}{select the resolution of output, either 'period' or 'block' (boolian)}
+}
+\examples{
+data <- data.frame(time=seq(7, 918, 0.001), pres=rnorm(911001),
+                    hr=rnorm(911001))
+cm_co(df=data)
+}

man/cm_cvr.Rd

@@ -4,6 +4,8 @@
 \description{
 Calculates the cvr, and further described in following publication ...
 [clinmon: An R package for calculation of clinical monitoring indices (2019)]
+Cvr formel - https://europepmc.org/article/pmc/pmc6054990
+CVR = mean BP/mean MCAv
 }
 \usage{
 cm_cvr(df, del_1, del_2, trigger, blocksize, freq, blockmin, output)