[Stacomir-commits] r447 - in pkg/stacomir: . R man man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 30 14:24:28 CEST 2017
Author: briand
Date: 2017-08-30 14:24:27 +0200 (Wed, 30 Aug 2017)
New Revision: 447
Added:
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
pkg/stacomir/man/figures/
pkg/stacomir/man/figures/logo.png
Modified:
pkg/stacomir/R/report_mig_mult.R
Log:
including readme file
Modified: pkg/stacomir/R/report_mig_mult.R
===================================================================
--- pkg/stacomir/R/report_mig_mult.R 2017-08-01 06:32:01 UTC (rev 446)
+++ pkg/stacomir/R/report_mig_mult.R 2017-08-30 12:24:27 UTC (rev 447)
@@ -196,7 +196,11 @@
#' \item{method}{In the case of instantaneous periods (video counting) the sum of daily values is done by the \link{fun_report_mig_mult} method and the value indicated in method is "sum".
#' If any migration monitoring period is longer than a day, then the migration is split using the \link{fun_report_mig_mult_overlaps} function and the value indicated in the
#' method is "overlaps" as the latter method uses the overlap package to split migration period.}
-#' \item{data}{the calculated data.}
+#' \item{data}{the calculated data. If weight are present, the columns display weight or numbers, the total number is
+#' "Effectif_total" and corresponds to the addition of numbers and numbers converted from weight,
+#' the total weight is "Poids_total"+"poids_depuis_effectifs" and corresponds to weighed glass eel plus glass eel number converted in weights.
+#' CALCULE corresponds to calulated number, MESURE to measured numbers, EXPERT to punctual expertise of migration (for instance measured in other path, or known migration
+#' of fishes passing the dam but not actually counted, PONCTUEL to fishes counted by visual identification but not by the counting apparatus (in case of technical problem for instance)}
#' \item{contient_poids}{A boolean which indicates, in the case of glass eel, that the function \link{fun_weight_conversion} has been run to convert the weights to numbers using the weight
#' to number coefficients in the database (see link{report_ge_weight}).}
#' \item{negative}{A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers,
@@ -975,7 +979,9 @@
#' test (the username and password for test are set in the calcmig.csv configuration file).
#' @return A data.frame with number summed over over the time.sequence.
#' The function returns the same output than \link{fun_report_mig_mult_overlaps}
-#' but is intended to work faster
+#' but is intended to work faster. In the data.frame, the total number is
+#' "Effectif_total" and corresponds to the addition of numbers and numbers converted from weight,
+#' the total weight is "Poids_total"+"poids_depuis_effectifs" and corresponds to weighed glass eel plus glass eel number converted in weights.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
fun_report_mig_mult <- function(time.sequence, datasub,negative=FALSE) {
Added: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd (rev 0)
+++ pkg/stacomir/README.Rmd 2017-08-30 12:24:27 UTC (rev 447)
@@ -0,0 +1,393 @@
+---
+output: github_document
+---
+
+[](https://cran.r-project.org/package=stacomiR)
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>",
+ fig.path = "man/figures/README-"
+)
+```
+
+# stacomiR <img src="man/figures/logo.png" align="right" />
+
+```{r echo=FALSE}
+library(stacomiR)
+
+```
+
+stacomiR
+========================================================
+
+
+
+
+Installation
+-------------------------
+
+The package is available from CRAN, a development version is available from
+R-Forge.
+
+```{r eval=FALSE}
+install.packages("stacomiR", repos="http://R-Forge.R-project.org")
+```
+
+Usage
+-------------------------
+
+Launch the graphical interface
+
+```{r eval=FALSE}
+stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = TRUE)
+```
+
+The program can be launched to use from the command line
+
+```{r eval=FALSE}
+stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
+```
+
+Palettes
+-------------------------
+
+The palette determines the colours of everything in a plot including the
+background, layers, gridlines, title text, axes lines, axes text and axes
+titles. The *swatch* is the the name given to the set of colours strictly used
+in styling the geoms/layer elements (e.g. the points in `geom_point()`, bars in
+`geom_bar()` etc.). At least six colours have been supplied in each palette's
+swatch.
+
+There are a wide variety of themes in this package (and more on the way). Some
+of them serious business... others are delibrately stylish and might not be that
+good for use in proper publications.
+
+### flat
+
+[Base 16](https://github.com/chriskempson/base16)
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('flat', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### flat dark
+
+[Base 16](https://github.com/chriskempson/base16)
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('flat dark', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### camoflauge
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('camoflauge', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### chalk
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('chalk', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### copper
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('copper', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### dust
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('dust', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### earth
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('earth', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### fresh
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('fresh', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### grape
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('grape', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### grass
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('grass', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### greyscale
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('greyscale', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### light
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('light', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### lilac
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('lilac', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### pale
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('pale', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### sea
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('sea', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### sky
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('sky', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+### solarized
+
+```{r fig.width=10, fig.height=6, echo=FALSE}
+ggthemr('solarized', spacing = 0.5, type = 'inner')
+preview_theme()
+```
+
+Custom Palettes
+-------------------------
+
+`define_palette()` lets you make your own themes that can be passed to
+`ggthemr()` just like any of the palettes above. Here's an example of a
+(probably ugly) palette using random colours:
+
+``` {r fig.width=5.5, fig.height=4.5}
+# Random colours that aren't white.
+set.seed(12345)
+random_colours <- sample(colors()[-c(1, 253, 361)], 10L)
+
+ugly <- define_palette(
+ swatch = random_colours,
+ gradient = c(lower = random_colours[1L], upper = random_colours[2L])
+)
+
+ggthemr(ugly)
+
+example_plot + ggtitle(':(')
+
+```
+
+You can define all elements of a palette using `define_palette()` including
+colours for the background, text, axes lines, swatch and gradients.
+
+
+Layouts
+-------------------------
+
+The layout of a theme controls the appearance and position of the axes,
+gridlines and text. Some folk prefer both major and minor gridlines, others
+prefer none or something in between.
+
+### Clean
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('grape', layout = 'clean', spacing = 0.5)
+preview_layout()
+```
+
+### Clear (default)
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('grape', layout = 'clear', spacing = 0.5)
+preview_layout()
+```
+
+### Minimal
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('grape', layout = 'minimal', spacing = 0.5)
+preview_layout()
+```
+
+### Plain
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('grape', layout = 'plain', spacing = 0.5)
+preview_layout()
+```
+
+### Scientific
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('grape', layout = 'scientific', spacing = 0.5)
+preview_layout()
+```
+
+Spacing
+-------------------------
+
+Plot margins and space between axes titles and lines etc. is controlled with the
+*spacing* parameter. Lower values will make plots more compact, higher values
+will give them more padding. Compare the plots below where the spacing has been
+set to 0, 1 and 2 respectively.
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('earth', spacing = 0, type = 'outer')
+preview_layout()
+```
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('earth', spacing = 1, type = 'outer')
+preview_layout()
+```
+
+```{r fig.width=5.5, fig.height=3.5, echo=FALSE}
+ggthemr('earth', spacing = 2, type = 'outer')
+preview_layout()
+```
+
+Type
+-------------------------
+
+The *type* parameter can be set to either *inner* or *outer*. When *inner*, the
+background colour of a plot will not extend past the plot area. *outer* will
+colour the entire plot and background.
+
+```{r fig.width=5.5, fig.height=3.5, echo=TRUE}
+ggthemr('earth', type = 'inner')
+example_plot
+```
+
+```{r fig.width=5.5, fig.height=3.5, echo=TRUE}
+ggthemr('earth', type = 'outer')
+example_plot
+```
+
+
+Tweaking Themes
+-------------------------
+
+Squinting at a chart? Low on printer ink? ggthemr includes some methods to tweak
+charts to make them lighter or darker. Here's a standard theme:
+
+```{r fig.width=7, fig.height=6, echo=TRUE}
+ggthemr('dust')
+example_plot
+```
+
+Maybe that plot comes out a bit pale looking when you print it. Here's how you
+can add a bit more contrast to the swatch:
+
+```{r fig.width=7, fig.height=6, echo=TRUE}
+darken_swatch(amount = 0.3)
+example_plot
+```
+
+The second parameter to `darken_swatch()` controls the degree to which the
+colours are made darker. Full list of methods with similar functionality:
+
+* `darken_swatch()` / `lighten_swatch()`: darker/lighter swatch colours.
+* `darken_gradient()` / `lighten_gradient()`: darker/lighter gradient colours.
+* `darken_palette()` / `lighten_palette()`: darker/lighter everything.
+
+I'll add methods to darken/lighten the axes lines and text soon too.
+
+
+Plot Adjustments
+-------------------------
+
+Most of the time you'll probably just want to set the theme and not worry about
+it. There may be times though where you'll want to make some small adjustment,
+or manually change what items appear as what colour in a plot.
+
+```{r fig.width=7, fig.height=6, echo=TRUE}
+ggthemr('dust')
+mpg_plot <- ggplot(mpg[mpg$drv != '4', ], aes(factor(cyl), cty, fill = drv)) +
+ geom_boxplot() + labs(x = 'Cylinders', y = 'City MPG', fill = 'Drive Type') +
+ theme(legend.position = 'bottom')
+mpg_plot
+```
+
+
+For some reason you decide you want to change those colours. Front-wheel drive
+vehicles should be orange. Rear-wheelers should be that red colour. You could
+change the order of the levels of your fill variable, but you shouldn't have to
+do that. You just want to switch those colours but you have no idea what they
+are. `swatch()` will give you the colours in the currently active ggthemr
+palette.
+
+```{r}
+swatch()
+```
+
+So you can manually swap the two colours around.
+
+```{r fig.width=7, fig.height=6, echo=TRUE}
+to_swap <- swatch()[2:3]
+mpg_plot + scale_fill_manual(values = rev(to_swap))
+```
+
+**Note:** the first colour in a swatch is a special one. It is reserved for
+outlining boxplots, text etc. So that's why the second and third colours were
+swapped.
+
+A note about theme setting
+--------------------------
+ggthemr does three different things while setting a theme.
+
+1. It updates the default ggplot2 theme with the specified ggthemr theme by
+ using the `ggplot2::theme_set()` function.
+2. It modifies the aesthetic defaults for all geoms using the
+ `ggplot2::update_geom_defaults()` function.
+3. It creates functions for all the different scales in the global environment.
+
+In case, if you do not want to set the theme this way, use the
+`set_theme = FALSE` option while using the `ggthemr` function. An example of
+setting theme, geom aesthetic defaults and scales manually:
+```{r}
+ggthemr_reset()
+dust_theme <- ggthemr('dust', set_theme = FALSE)
+example_plot
+example_plot + dust_theme$theme
+example_plot + dust_theme$theme + dust_theme$scales$scale_fill_discrete()
+do.call(what = ggplot2::update_geom_defaults, args = dust_theme$geom_defaults$new$bar)
+ggplot(diamonds, aes(price)) + geom_histogram(binwidth = 850) + dust_theme$theme
+```
+
+
+License
+-------
+Released under GPL-3.
\ No newline at end of file
Added: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md (rev 0)
+++ pkg/stacomir/README.md 2017-08-30 12:24:27 UTC (rev 447)
@@ -0,0 +1,413 @@
+---
+output: github_document
+---
+
+[](https://cran.r-project.org/package=stacomiR)
+
+
+
+# stacomiR <img src="man/figures/logo.png" align="right" />
+
+
+
+stacomiR
+========================================================
+
+
+
+
+Installation
+-------------------------
+
+The package is available from CRAN, a development version is available from
+R-Forge.
+
+
+```r
+install.packages("stacomiR", repos="http://R-Forge.R-project.org")
+```
+
+Usage
+-------------------------
+
+Launch the graphical interface
+
+
+```r
+stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = TRUE)
+```
+
+The program can be launched to use from the command line
+
+
+```r
+stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
+```
+
+Palettes
+-------------------------
+
+The palette determines the colours of everything in a plot including the
+background, layers, gridlines, title text, axes lines, axes text and axes
+titles. The *swatch* is the the name given to the set of colours strictly used
+in styling the geoms/layer elements (e.g. the points in `geom_point()`, bars in
+`geom_bar()` etc.). At least six colours have been supplied in each palette's
+swatch.
+
+There are a wide variety of themes in this package (and more on the way). Some
+of them serious business... others are delibrately stylish and might not be that
+good for use in proper publications.
+
+### flat
+
+[Base 16](https://github.com/chriskempson/base16)
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### flat dark
+
+[Base 16](https://github.com/chriskempson/base16)
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### camoflauge
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### chalk
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### copper
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### dust
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### earth
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### fresh
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### grape
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### grass
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### greyscale
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### light
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### lilac
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### pale
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### sea
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### sky
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+### solarized
+
+
+```
+#> Error in preview_theme(): could not find function "preview_theme"
+```
+
+Custom Palettes
+-------------------------
+
+`define_palette()` lets you make your own themes that can be passed to
+`ggthemr()` just like any of the palettes above. Here's an example of a
+(probably ugly) palette using random colours:
+
+
+```r
+# Random colours that aren't white.
+set.seed(12345)
+random_colours <- sample(colors()[-c(1, 253, 361)], 10L)
+
+ugly <- define_palette(
+ swatch = random_colours,
+ gradient = c(lower = random_colours[1L], upper = random_colours[2L])
+)
+
+ggthemr(ugly)
+
+example_plot + ggtitle(':(')
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+```
+
+You can define all elements of a palette using `define_palette()` including
+colours for the background, text, axes lines, swatch and gradients.
+
+
+Layouts
+-------------------------
+
+The layout of a theme controls the appearance and position of the axes,
+gridlines and text. Some folk prefer both major and minor gridlines, others
+prefer none or something in between.
+
+### Clean
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+### Clear (default)
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+### Minimal
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+### Plain
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+### Scientific
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+Spacing
+-------------------------
+
+Plot margins and space between axes titles and lines etc. is controlled with the
+*spacing* parameter. Lower values will make plots more compact, higher values
+will give them more padding. Compare the plots below where the spacing has been
+set to 0, 1 and 2 respectively.
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+
+```
+#> Error in preview_layout(): could not find function "preview_layout"
+```
+
+Type
+-------------------------
+
+The *type* parameter can be set to either *inner* or *outer*. When *inner*, the
+background colour of a plot will not extend past the plot area. *outer* will
+colour the entire plot and background.
+
+
+```r
+ggthemr('earth', type = 'inner')
+example_plot
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+```
+
+
+```r
+ggthemr('earth', type = 'outer')
+example_plot
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+```
+
+
+Tweaking Themes
+-------------------------
+
+Squinting at a chart? Low on printer ink? ggthemr includes some methods to tweak
+charts to make them lighter or darker. Here's a standard theme:
+
+
+```r
+ggthemr('dust')
+example_plot
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+```
+
+Maybe that plot comes out a bit pale looking when you print it. Here's how you
+can add a bit more contrast to the swatch:
+
+
+```r
+darken_swatch(amount = 0.3)
+example_plot
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+```
+
+The second parameter to `darken_swatch()` controls the degree to which the
+colours are made darker. Full list of methods with similar functionality:
+
+* `darken_swatch()` / `lighten_swatch()`: darker/lighter swatch colours.
+* `darken_gradient()` / `lighten_gradient()`: darker/lighter gradient colours.
+* `darken_palette()` / `lighten_palette()`: darker/lighter everything.
+
+I'll add methods to darken/lighten the axes lines and text soon too.
+
+
+Plot Adjustments
+-------------------------
+
+Most of the time you'll probably just want to set the theme and not worry about
+it. There may be times though where you'll want to make some small adjustment,
+or manually change what items appear as what colour in a plot.
+
+
+```r
+ggthemr('dust')
+mpg_plot <- ggplot(mpg[mpg$drv != '4', ], aes(factor(cyl), cty, fill = drv)) +
+ geom_boxplot() + labs(x = 'Cylinders', y = 'City MPG', fill = 'Drive Type') +
+ theme(legend.position = 'bottom')
+mpg_plot
+```
+
+
+
+
+For some reason you decide you want to change those colours. Front-wheel drive
+vehicles should be orange. Rear-wheelers should be that red colour. You could
+change the order of the levels of your fill variable, but you shouldn't have to
+do that. You just want to switch those colours but you have no idea what they
+are. `swatch()` will give you the colours in the currently active ggthemr
+palette.
+
+
+```r
+swatch()
+#> [1] "#555555" "#db735c" "#EFA86E" "#9A8A76" "#F3C57B" "#7A6752" "#2A91A2"
+#> [8] "#87F28A" "#6EDCEF"
+#> attr(,"class")
+#> [1] "ggthemr_swatch"
+```
+
+So you can manually swap the two colours around.
+
+
+```r
+to_swap <- swatch()[2:3]
+mpg_plot + scale_fill_manual(values = rev(to_swap))
+```
+
+
+
+**Note:** the first colour in a swatch is a special one. It is reserved for
+outlining boxplots, text etc. So that's why the second and third colours were
+swapped.
+
+A note about theme setting
+--------------------------
+ggthemr does three different things while setting a theme.
+
+1. It updates the default ggplot2 theme with the specified ggthemr theme by
+ using the `ggplot2::theme_set()` function.
+2. It modifies the aesthetic defaults for all geoms using the
+ `ggplot2::update_geom_defaults()` function.
+3. It creates functions for all the different scales in the global environment.
+
+In case, if you do not want to set the theme this way, use the
+`set_theme = FALSE` option while using the `ggthemr` function. An example of
+setting theme, geom aesthetic defaults and scales manually:
+
+```r
+ggthemr_reset()
+dust_theme <- ggthemr('dust', set_theme = FALSE)
+example_plot
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+example_plot + dust_theme$theme
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+example_plot + dust_theme$theme + dust_theme$scales$scale_fill_discrete()
+#> Error in eval(expr, envir, enclos): object 'example_plot' not found
+do.call(what = ggplot2::update_geom_defaults, args = dust_theme$geom_defaults$new$bar)
+ggplot(diamonds, aes(price)) + geom_histogram(binwidth = 850) + dust_theme$theme
+```
+
+
+
+
+License
+-------
+Released under GPL-3.
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