version 1.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bioC.logs
 Type: Package
 Title: BioConductor Package Downloads Stats
-Version: 1.0
-Date: 2020-01-30
+Version: 1.1
+Date: 2020-02-10
 Author: Marcelo Ponce [aut, cre]
 Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
 Description: Download stats reports from the BioConductor.org stats website.
@@ -14,6 +14,6 @@ BugReports: https://github.com/mponce0/bioC.logs/issues
 RoxygenNote: 6.1.99.9001
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2020-01-29 17:35:25 UTC; marcelo
+Packaged: 2020-02-12 17:03:11 UTC; marcelo
 Repository: CRAN
-Date/Publication: 2020-02-09 16:50:09 UTC
+Date/Publication: 2020-02-13 15:30:07 UTC

MD5

@@ -1,10 +1,23 @@
-db052d72f4bcfc140af23549ba03869a *DESCRIPTION
-04745393c053f4bdc0ee97deb4e3c010 *NAMESPACE
-88120b57df9509f28d27ed96b6537da3 *R/bioC_logs.R
-5bddfb0fc14039966bc23db9a3e1b016 *README.md
+cec4d32abf0e3d070a0b76b14394256f *DESCRIPTION
+742ae3d1e47c80c1faf14b35923ae165 *NAMESPACE
+6d593c08f881f2ef265bdab68ab34f03 *NEWS
+99a5693c331121b6f5ba8e4139d53dc0 *R/auxs-utils.R
+9ea96fcb093cadae59642a10cc8baafd *R/bioC_logs.R
+857fe7fc8e1ff3ee0ed826625d077bcb *README.md
 c24c7ae9e7bbb60722f5c5fdd6d7841c *build/vignette.rds
 3c9e2d06e8560272e30c98b0c827478b *inst/doc/bioC.logs.R
 5110dbd41904072d7d9d356009f9f177 *inst/doc/bioC.logs.Rmd
-d3eef214a95bea5353ed7eda390e1b9c *inst/doc/bioC.logs.html
-706eb66f1ed2a9b8ea80254cd78e985c *man/bioC_downloads.Rd
+83e74db85b382b6011b9e5e70c8f35f8 *inst/doc/bioC.logs.html
+c2542c3889883ceeb60365696d671b92 *man/Xyear.from.now.Rd
+d939c259b47a3f438d210cb5127527dd *man/bioC_downloads.Rd
+58b7a6c109ebcfdf9d2578aa21bed243 *man/checkDate.Rd
+72e1011f8b3c82df6458a83bdb8b034a *man/checkDates.Rd
+8146f5833d2382c033c3c26239e521d6 *man/checkValidDates.Rd
+206ebc429371876226b03db58715041a *man/daysInMonth.Rd
+b9ed70eb152c62618e6b96e65f73a867 *man/last.day.month.Rd
+0fe5347f1b041d058ec053cfbc9d7180 *man/lst.year.Rd
+87c66280907da3c404fb9a9f095a7ef6 *man/origin.of.times.Rd
+ae5ca6247aff0015022d53fdb964bd00 *man/today.Rd
+0f9e38ce24a066f6e689e4cf66c06b87 *man/year.from.now.Rd
+c1b77474fcefb739d9d48ae274b09d2a *man/year.to.date.Rd
 5110dbd41904072d7d9d356009f9f177 *vignettes/bioC.logs.Rmd

NAMESPACE

@@ -1,4 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bioC_downloads)
+importFrom(stats,na.omit)
 importFrom(utils,read.table)

NEWS

@@ -0,0 +1,2 @@
+February 2020: added options for indicating range of dates (to/from & when); adaptive last day of the month; more checks from CRAN format (remove future dates) _ ver 1.1 
+February 2020: First release of "bioC.logs" package _ ver 1.0

R/auxs-utils.R

@@ -0,0 +1,226 @@
+# auxs-utils.R
+#  -- M.Ponce
+
+
+#################################################################################################
+##	Auxiliary Utilities file for the bioC.logs package
+#
+#	Generic auxiliary functions
+#
+#################################################################################################
+
+
+### date's aux fns
+year.to.date <- function(){
+#' function that returns the range dates for the period year-to-date 
+#' @keywords internal
+	cur.date <- Sys.Date()
+
+	cur.year <- substr(cur.date,1,4)
+	return(list(paste(cur.year,"01","01",sep='-'),as.character(cur.date)))
+}
+
+lst.year <- function() {
+#' function that returns the range dates for the last year 
+#' @keywords internal
+        cur.date <- Sys.Date()
+
+        last.year <- as.integer(substr(cur.date,1,4))-1
+        return(list(paste(last.year,"01","01",sep='-'),paste(last.year+1,"01","01",sep='-')))
+
+}
+
+year.from.now <- function() {
+#' function that returns the date from one year ago
+#' @keywords internal
+        cur.date <- Sys.Date()
+        cur.year <- substr(cur.date,1,4)
+        lst.year <- as.integer(cur.year) - 1
+        t0 <- paste(lst.year,substr(cur.date,5,10),sep="")
+
+        return(list(t0,cur.date))
+}
+
+today <- function() {
+#' function that returns the current date 
+#' @keywords internal
+	t1 <- Sys.Date()
+	# Will substract 1 to do not consider today, but yesterday
+	# this matches the definition from cran_downloads too
+	t1 <- t1 - 1 
+	message("Ending date was not specifed, will assume today: ",t1)
+	return(format(t1,format="%d-%m-%Y"))
+}
+
+origin.of.times <- function() {
+#' function that provides a "beginning of times" default date
+#' @keywords internal
+	t0 <- as.Date("1980-01-01",format="%Y-%m-%d")
+	message("Initial date was not specified, will assume:", t0)
+	return(format(t0,format="%d-%m-%Y"))
+}
+
+
+
+Xyear.from.now <- function() {
+#' function that returns the date from one year ago
+#' @keywords internal
+	cur.date <- Sys.Date()-1
+	cur.year <- substr(cur.date,1,4)
+	lst.year <- as.integer(cur.year) - 1
+	t0 <- paste(lst.year,substr(cur.date,5,10),sep="")
+
+	message("Starting date was not specified, will assume a year from now: ",t0)
+	return(t0)
+}
+
+checkDates <- function(t0,t1) {
+#' function to check dates, ie that t0<t1 and t0!=t1
+#' @param  t0  initial date
+#' @param  t1  final date
+#' @return a list with t0 being [[1]] and t1 being [[2]]
+#'
+#' @keywords internal
+
+	# check if there is any missing date
+	if (is.null(t0)) t0 <- origin.of.times()
+	if (is.null(t1)) t1 <- as.Date(today(),format="%d-%b-%Y")
+
+	# check whether t0 is greater than t1
+	if (as.Date(t0) > as.Date(t1)) {
+		# flip dates, t0 will be set to the older date
+		ttemp <- t0
+		t0 <- t1
+		t1 <- ttemp
+	} else if (as.Date(t0) == as.Date(t1)) {
+		# dates should be different
+		stop(t0," and ", t1," should be different!")       
+	}
+
+	return(list(t0,t1))
+}
+
+checkDate <- function(date.candidate) {
+#' function to check date format for "MM-YYYY"
+#' @param  date.candidate  date candidate
+#' 
+#'
+#' @keywords internal
+
+	# bisecting month and year...
+	MM <- as.integer(substr(date.candidate,1,2))
+	YYYY <- as.integer(substr(date.candidate,4,7))
+
+	if ( !is.numeric(MM) |  ((MM<1) | (MM>12)) )
+		stop(paste("Problem detected with date: ",date.candidate,"\n","Dates should be specified in 'MM-YYYY' format, with MM from '01' to '12'"))
+
+	if (!is.numeric(YYYY))
+		stop(paste("Problem detected with date: ",date.candidate,"\n","Dates should be specified in 'MM-YYYY' format, with MM from '01' to '12'"))
+}
+
+
+checkValidDates <- function(t0,t1) {
+#' function to check dates, ie that t0<t1 and t0 and t1 are in MM-YYYY format
+#' @param  t0  initial date
+#' @param  t1  final date
+#' @return a list with t0 being [[1]] and t1 being [[2]]
+#'
+#' @keywords internal
+
+	# check date structure for t0 & t1
+	if (!is.null(t0)) {
+		checkDate(t0)
+	} else {
+		t0 <- substr(origin.of.times(),4,10)
+	}
+	if (!is.null(t1)) {
+		checkDate(t1)
+	} else {
+		t1 <- substr(today(),4,10)
+	}
+
+	fake.t0 <- as.Date(paste0("01-",t0),format='%d-%m-%Y')
+	fake.t1 <- as.Date(paste0("01-",t1),format='%d-%m-%Y')
+	#fake.t1 <- as.Date(paste0(last.day.month(
+
+	# check candidate dates
+	finalDates <- checkDates(fake.t0,fake.t1)
+
+        #return(list(t0,t1))
+	return(finalDates)
+}
+
+
+
+last.day.month <- function(MonthYear) {
+#' function that returns the number of dates in a given month-year
+#' @param  MonthYear  string containing month and year, ie. MM-YYYY
+#' @return number of days --as characters-- in the given month-year
+#'
+#' @keywords internal
+
+	# convert year to numeric
+	year <- as.numeric(substr(MonthYear,5,8))
+	month <- substr(MonthYear,1,3)
+
+	# check for leap years
+	leap = FALSE
+	if ( (year %% 4 == 0 ) | ( year %% 100 == 0  &  year %% 400 == 0) )
+		leap <-  TRUE
+
+	# obtain number of days
+	nbr.days <- switch(tolower(month),
+			'jan' = 31,
+			'feb' = 28 + leap,  # adds 1 if leap year
+                	'mar' = 31,
+                	'apr' = 30,
+                	'may' = 31,
+                	'jun' = 30,
+                	'jul' = 31,
+                	'aug' = 31,
+                	'sep' = 30,
+                	'oct' = 31,
+                	'nov' = 30,
+                	'dec' = 31 )
+
+	return(as.character(nbr.days))
+}
+
+
+daysInMonth <- function(d = Sys.Date()){
+#' function that returns the number of dates in a given date
+#' @param  d  string containing a date in YYYY-MM-DD format
+#' @return number of days in the given the date 
+#'
+#' @keywords internal
+
+  m = substr((as.character(d)), 6, 7)              # month number as string
+  y = as.numeric(substr((as.character(d)), 1, 4))  # year number as numeric
+
+  # Quick check for leap year
+  leap = 0
+  if ((y %% 4 == 0 & y %% 100 != 0) | y %% 400 == 0)
+    leap = 1
+
+  # Return the number of days in the month
+  return(switch(m,
+                '01' = 31,
+                '02' = 28 + leap,  # adds 1 if leap year
+                '03' = 31,
+                '04' = 30,
+                '05' = 31,
+                '06' = 30,
+                '07' = 31,
+                '08' = 31,
+                '09' = 30,
+                '10' = 31,
+                '11' = 30,
+                '12' = 31))
+}
+
+
+
+##### //////////////////////////////////////////////////////////////////////////// #####
+##### //////////////////////////////////////////////////////////////////////////// #####
+##### //////////////////////////////////////////////////////////////////////////// #####
+