From 5c7679ac453b35da9dfaf2a3b85cfb3981d41e5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cl=C3=A9ment=20Turbelin?= Date: Wed, 5 Dec 2018 17:04:20 +0100 Subject: [PATCH] rename funcs with dots in name, to underscore based name --- NAMESPACE | 20 +++++------ R/templates.R | 1 - man/{axis.week.Rd => axis_week.Rd} | 6 ++-- man/box.sd.Rd | 24 -------------- man/{calc.season.Rd => calc_season.Rd} | 6 ++-- ...c.season.fixed.Rd => calc_season_fixed.Rd} | 6 ++-- man/{format.week.Rd => format_week.Rd} | 6 ++-- man/{graph.colors.Rd => graph_colors.Rd} | 6 ++-- man/{polygon.ic.Rd => polygon_ic.Rd} | 6 ++-- man/{recode.intake.Rd => recode_intake.Rd} | 6 ++-- man/{recode.weekly.Rd => recode_weekly.Rd} | 6 ++-- man/{recode.ynp.Rd => recode_ynp.Rd} | 6 ++-- man/segment.sd.Rd | 33 ------------------- 13 files changed, 36 insertions(+), 96 deletions(-) rename man/{axis.week.Rd => axis_week.Rd} (90%) delete mode 100644 man/box.sd.Rd rename man/{calc.season.Rd => calc_season.Rd} (87%) rename man/{calc.season.fixed.Rd => calc_season_fixed.Rd} (89%) rename man/{format.week.Rd => format_week.Rd} (79%) rename man/{graph.colors.Rd => graph_colors.Rd} (85%) rename man/{polygon.ic.Rd => polygon_ic.Rd} (82%) rename man/{recode.intake.Rd => recode_intake.Rd} (83%) rename man/{recode.weekly.Rd => recode_weekly.Rd} (83%) rename man/{recode.ynp.Rd => recode_ynp.Rd} (90%) delete mode 100644 man/segment.sd.Rd diff --git a/NAMESPACE b/NAMESPACE index 601776c..7c3817e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,5 @@ # Generated by roxygen2: do not edit by hand -S3method(format,week) S3method(i18n,default) S3method(i18n,factor) S3method(merge,list) @@ -9,15 +8,15 @@ export(ISOYearWeek) export(WeekStamp) export(WeekStart) export(YearStart) -export(axis.week) -export(box.sd) +export(axis_week) export(calc.age) -export(calc.season) -export(calc.season.fixed) +export(calc_season) +export(calc_season_fixed) export(check_survey_template) export(create_survey_definition) export(dbConnect) export(dbQuery) +export(format_week) export(geo_base_level) export(geo_base_table) export(geo_column) @@ -31,10 +30,10 @@ export(get_historical_tables) export(get_option) export(get_symptoms_aliases) export(graph.close) -export(graph.colors) export(graph.hook) export(graph.open) export(graph.save) +export(graph_colors) export(graph_get_last) export(i18n) export(i18n_inflect) @@ -58,16 +57,15 @@ export(platform_geographic_levels) export(platform_geographic_tables) export(platform_options) export(platform_season_history) -export(polygon.ic) +export(polygon_ic) export(random_string) -export(recode.intake) -export(recode.weekly) -export(recode.ynp) export(recode_alias) +export(recode_intake) +export(recode_weekly) +export(recode_ynp) export(regroup.syndrome) export(replace.names) export(season.def) -export(segment.sd) export(select_columns) export(select_df) export(share.cache.path) diff --git a/R/templates.R b/R/templates.R index 4b09a94..a70b6f5 100644 --- a/R/templates.R +++ b/R/templates.R @@ -1,4 +1,3 @@ - #' Survey Template definitions #' #' Templates of Surveys diff --git a/man/axis.week.Rd b/man/axis_week.Rd similarity index 90% rename from man/axis.week.Rd rename to man/axis_week.Rd index 32497aa..d807ecc 100644 --- a/man/axis.week.Rd +++ b/man/axis_week.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/graph.r -\name{axis.week} -\alias{axis.week} +\name{axis_week} +\alias{axis_week} \title{Axis for yearweek data} \usage{ -axis.week(side, ww, mode = c("ticks", "year", "week", "weeks", "\%\%"), +axis_week(side, ww, mode = c("ticks", "year", "week", "weeks", "\%\%"), format = "yw", col.yw = "yw", sep = "s", century = T, ticks = NULL, ...) } diff --git a/man/box.sd.Rd b/man/box.sd.Rd deleted file mode 100644 index acfdef9..0000000 --- a/man/box.sd.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/graph.r -\name{box.sd} -\alias{box.sd} -\title{Make a rectangle usefull for boxplot} -\usage{ -box.sd(x, up, low, k = 0.25, col = "grey", border = NA) -} -\arguments{ -\item{x}{x value} - -\item{up}{upper value} - -\item{low}{lower value} - -\item{k}{rectangle width around the x} - -\item{col}{color value} - -\item{border}{border color} -} -\description{ -Make a rectangle usefull for boxplot -} diff --git a/man/calc.season.Rd b/man/calc_season.Rd similarity index 87% rename from man/calc.season.Rd rename to man/calc_season.Rd index 7551f13..fd63a40 100644 --- a/man/calc.season.Rd +++ b/man/calc_season.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/week.r -\name{calc.season} -\alias{calc.season} +\name{calc_season} +\alias{calc_season} \title{Return the season number of a yearweek or a Date} \usage{ -calc.season(d) +calc_season(d) } \arguments{ \item{d}{date to compute season number from} diff --git a/man/calc.season.fixed.Rd b/man/calc_season_fixed.Rd similarity index 89% rename from man/calc.season.fixed.Rd rename to man/calc_season_fixed.Rd index 0f83c6c..6821e5a 100644 --- a/man/calc.season.fixed.Rd +++ b/man/calc_season_fixed.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/week.r -\name{calc.season.fixed} -\alias{calc.season.fixed} +\name{calc_season_fixed} +\alias{calc_season_fixed} \title{Compute a season index of each year week} \usage{ -calc.season.fixed(inc, col.yw = "yw", col.stamp = NULL, +calc_season_fixed(inc, col.yw = "yw", col.stamp = NULL, date.start = "09-01", calc.index = TRUE) } \arguments{ diff --git a/man/format.week.Rd b/man/format_week.Rd similarity index 79% rename from man/format.week.Rd rename to man/format_week.Rd index ad3a43c..7eb9c94 100644 --- a/man/format.week.Rd +++ b/man/format_week.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/week.r -\name{format.week} -\alias{format.week} +\name{format_week} +\alias{format_week} \title{Format a yearweek value to a human readable format} \usage{ -\method{format}{week}(w, sep = "s", century = T) +format_week(w, sep = "s", century = T) } \arguments{ \item{w}{vector of yearweek values} diff --git a/man/graph.colors.Rd b/man/graph_colors.Rd similarity index 85% rename from man/graph.colors.Rd rename to man/graph_colors.Rd index 237d643..3b0ceb1 100644 --- a/man/graph.colors.Rd +++ b/man/graph_colors.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/graph.r -\name{graph.colors} -\alias{graph.colors} +\name{graph_colors} +\alias{graph_colors} \title{Return a list of n colors by the "best" color generator available} \usage{ -graph.colors(n, pal = NULL) +graph_colors(n, pal = NULL) } \arguments{ \item{n}{number of colors to get (caution, it can be fewer than expected for some palettes)} diff --git a/man/polygon.ic.Rd b/man/polygon_ic.Rd similarity index 82% rename from man/polygon.ic.Rd rename to man/polygon_ic.Rd index dc001cb..08f3c44 100644 --- a/man/polygon.ic.Rd +++ b/man/polygon_ic.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/graph.r -\name{polygon.ic} -\alias{polygon.ic} +\name{polygon_ic} +\alias{polygon_ic} \title{Draw confidence interval with polygon} \usage{ -polygon.ic(ii, col.x, col.up, col.low, col, ...) +polygon_ic(ii, col.x, col.up, col.low, col, ...) } \arguments{ \item{ii}{data.frame} diff --git a/man/recode.intake.Rd b/man/recode_intake.Rd similarity index 83% rename from man/recode.intake.Rd rename to man/recode_intake.Rd index 4e8ef3a..78160a9 100644 --- a/man/recode.intake.Rd +++ b/man/recode_intake.Rd @@ -1,11 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/recode.r -\name{recode.intake} -\alias{recode.intake} +\name{recode_intake} +\alias{recode_intake} \title{Recode Intake variables to more error proof labels by default translate labels used to recode variables} \usage{ -recode.intake(intake, translate = T, remove = T) +recode_intake(intake, translate = T, remove = T) } \arguments{ \item{intake}{data.frame() raw intake data} diff --git a/man/recode.weekly.Rd b/man/recode_weekly.Rd similarity index 83% rename from man/recode.weekly.Rd rename to man/recode_weekly.Rd index 4508d27..c61b364 100644 --- a/man/recode.weekly.Rd +++ b/man/recode_weekly.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/recode.r -\name{recode.weekly} -\alias{recode.weekly} +\name{recode_weekly} +\alias{recode_weekly} \title{Apply common recoding for weekly data} \usage{ -recode.weekly(weekly, health.status = T) +recode_weekly(weekly, health.status = T) } \arguments{ \item{weekly}{data.frame weekly data (return by survey_load_results)} diff --git a/man/recode.ynp.Rd b/man/recode_ynp.Rd similarity index 90% rename from man/recode.ynp.Rd rename to man/recode_ynp.Rd index 75921d0..4905d9f 100644 --- a/man/recode.ynp.Rd +++ b/man/recode_ynp.Rd @@ -1,12 +1,12 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/recode.r -\name{recode.ynp} -\alias{recode.ynp} +\name{recode_ynp} +\alias{recode_ynp} \title{recode Y/N/DNK where Y=0 to boolean (wow!) Used to recode some InfluenzaNet variables to more error-proof coding So TRUE is YES level, FALSE = NO level and NA missing value.} \usage{ -recode.ynp(x) +recode_ynp(x) } \arguments{ \item{x}{value to recode} diff --git a/man/segment.sd.Rd b/man/segment.sd.Rd deleted file mode 100644 index 9055e3e..0000000 --- a/man/segment.sd.Rd +++ /dev/null @@ -1,33 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/graph.r -\name{segment.sd} -\alias{segment.sd} -\title{Draw segments to represent a confidence Interval} -\usage{ -segment.sd(i, estim, up, low, k = 0.25, col = "grey", lty = 1, - lwd = 1, cex = 1, pch = 16) -} -\arguments{ -\item{i}{x values} - -\item{estim}{estimation point} - -\item{up}{upper bound} - -\item{low}{lower bound} - -\item{k}{size of the horizontal segment} - -\item{col}{color of the segments} - -\item{lty}{linetype (@seealso points)} - -\item{lwd}{line width} - -\item{cex}{cex of the estimation point} - -\item{pch}{for the estimation point} -} -\description{ -Draw segments to represent a confidence Interval -}