Compare ⋅ hugomflavio/actel

  p <- p + ggplot2::facet_grid(. ~ variable, scales = "free_x")
  p <- p + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, hjust = 1))
  p <- p + ggplot2::labs(x = "", y = "")
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)))
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)), limitsize = FALSE)
  appendTo("debug", "Terminating printDotplots.")
}


@@ -483,7 +483,7 @@

Loading

  p <- p + ggplot2::scale_y_continuous(limits = c(0, 1), expand = c(0, 0, 0.05, 0))
  p <- p + ggplot2::labs(x = "", y = "Survival")
  the.width <- max(2, sum(grepl("Disap.", colnames(section.overview))) * nrow(section.overview))
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4)
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4, limitsize = FALSE)
  appendTo("debug", "Terminating printSurvivalGraphic.")
}


@@ -704,7 +704,7 @@

Loading

      }
    }
    # Save
    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height)  # better to save in png to avoid point overlapping issues
    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height, limitsize = FALSE)  # better to save in png to avoid point overlapping issues

    if (counter %% 2 == 0) {
      individual.plots <<- paste0(individual.plots, "![](", tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension, "){ width=", the.width * 10, "% }\n")

@@ -1271,7 +1271,7 @@

Loading

      p <- p + ggplot2::scale_fill_manual(values = as.vector(cbPalette)[1:length(unique(plotdata$Group))], drop = FALSE)
    }
  
    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2)
    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2, limitsize = FALSE)
  })
}


@@ -1377,7 +1377,7 @@

Loading

  p <- p + ggplot2::labs(x = "", y = "n")
  p <- p + ggplot2::scale_y_continuous(expand = c(0, 0, 0.05, 0))
  the.width <- max(2, (ncol(input) - 1) * nrow(input) * 0.7)
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4)
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4, limitsize = FALSE)
}

#' Print a simple barplot with the number of tags last seen at each section

@@ -1409,7 +1409,7 @@

Loading

  p <- p + ggplot2::coord_flip()
  p <- p + ggplot2::guides(fill = ggplot2::guide_legend(reverse = TRUE))
  the.height <- max(2, ((length(levels(status.df$Very.last.array)) - 1) * 0.5))
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height)
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height, limitsize = FALSE)
}

#' Print sensor data for each individual tag

@@ -1488,7 +1488,7 @@

Loading

      }

      # Save
      ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height)  # better to save in png to avoid point overlapping issues
      ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height, limitsize = FALSE)  # better to save in png to avoid point overlapping issues

      n.plots <- n.plots + 1
      if (n.plots %% 2 == 0) {

@@ -1026,22 +1026,36 @@

Loading


  # check sensor names
  if (!expect_integer) { 
    if(!any(grepl("^Sensor.unit$", colnames(bio)))) {
    if (!any(grepl("^Sensor.unit$", colnames(bio)))) {
      appendTo(c("Screen", "Warning"), "Tags with multiple sensors are listed in the biometrics, but a 'Sensor.unit' column could not be found. Skipping sensor unit assignment.")
    } 
    else {
      bio$Sensor.unit <- as.character(bio$Sensor.unit) #failsafe in case all values are numeric, or NA.

      A <- sapply(strsplit(bio$Signal, "|", fixed = TRUE), length)
      pre_B <- strsplit(bio$Sensor.unit, "|", fixed = TRUE)
      B <- sapply(pre_B, length)
      B[sapply(pre_B, is.na)] <- 0

      if (any(A != B))
        stopAndReport("The number of provided sensor units and signals do not match for ", 
          ifelse(sum(A != B) <= 10,
                 paste0("row(s) ", paste0(which(A != B), collapse = ", ")), 
                 paste0(sum(A != B), " row(s)")),
      bio$Sensor.unit <- as.character(bio$Sensor.unit) # failsafe in case all values are numeric, or NA.
      bio$Sensor.unit[bio$Sensor.unit == ''] <- NA_character_

      if (any(link <- na.as.false(startsWith(bio$Sensor.unit, '|'))))
        appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
          ifelse(sum(link) <= 10,
                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
                 paste0(sum(link), " row(s)")),
          " of the biometrics starts with a '|' character. Could you have forgotten to include a sensor unit?"))

      if (any(link <- na.as.false(endsWith(bio$Sensor.unit, '|'))))
        appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
          ifelse(sum(link) <= 10,
                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
                 paste0(sum(link), " row(s)")),
          " of the biometrics ends with a '|' character. Could you have forgotten to include a sensor unit?"))

      signals_per_tag <- sapply(strsplit(bio$Signal, "|", fixed = TRUE), length) # number of signals per tag
      aux <- strsplit(bio$Sensor.unit, "|", fixed = TRUE)
      sensors_per_tag <- sapply(aux, length)

      if (any(link <- signals_per_tag != sensors_per_tag))
        stopAndReport("The number of provided sensor units does not match the number of signals for ", 
          ifelse(sum(link) <= 10,
                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
                 paste0(sum(link), " row(s)")),
          " of the biometrics.")
    }
  }

@@ -1623,9 +1637,13 @@

Loading

    } else { # otherwise, prepare tag name and include sensor units if present
      trimmed_list_names <<- c(trimmed_list_names, paste0(the_codespace, "-", min(bio_aux$Signal_expanded[[i]])))
      output <- my.list[list_matches]

      # Find Sensor.unit column in the biometrics
      if (any(grepl("^Sensor.unit$", colnames(bio)))) {
        # Replace sensor units...
        for (j in 1:length(output)) {
          sensor_index <- match(extractSignals(names(output)[j]), bio_aux$Signal_expanded[[i]])
          # but only if the the sensor unit provided is not NA
          if (!is.na(bio_aux$Sensor.unit_expanded[[i]][sensor_index])) {
            output[[j]]$Sensor.Unit <- rep(bio_aux$Sensor.unit_expanded[[i]][sensor_index], nrow(output[[j]]))
          }

Everything is accounted for!

No changes detected that need to be reviewed.

What changes does Codecov check for?

Lines, not adjusted in diff, that have changed coverage data.

Files that introduced coverage data that had none before.

Files that have missing coverage data that once were tracked.

93.12% 100.00% -0.13%

disable ggplot's size safety break

hugomflavio

5935e19

CI Passed

Hiding 1 contexual commits

+12

+2

+10

93.24% 78.13% -0.08%

prevent residency crashes due to an overabundance of exact-time detections

hugomflavio

7dae136

CI Passed

Files		•	•	•	Coverage
R	+12	+2	ø	+10	^-0.13% 93.12%
Project Totals (15 files)	7,335	6,830	0	505	93.12%

431	431		p <- p + ggplot2::facet_grid(. ~ variable, scales = "free_x")
432	432		p <- p + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, hjust = 1))
433	433		p <- p + ggplot2::labs(x = "", y = "")
434		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)))
	434	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)), limitsize = FALSE)
435	435		appendTo("debug", "Terminating printDotplots.")
436	436		}
437	437

704	704		}
705	705		}
706	706		# Save
707		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height) # better to save in png to avoid point overlapping issues
	707	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height, limitsize = FALSE) # better to save in png to avoid point overlapping issues
708	708
709	709		if (counter %% 2 == 0) {
710	710		individual.plots <<- paste0(individual.plots, "![](", tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension, "){ width=", the.width * 10, "% }\n")

1271	1271		p <- p + ggplot2::scale_fill_manual(values = as.vector(cbPalette)[1:length(unique(plotdata$Group))], drop = FALSE)
1272	1272		}
1273	1273
1274		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2)
	1274	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2, limitsize = FALSE)
1275	1275		})
1276	1276		}
1277	1277

1377	1377		p <- p + ggplot2::labs(x = "", y = "n")
1378	1378		p <- p + ggplot2::scale_y_continuous(expand = c(0, 0, 0.05, 0))
1379	1379		the.width <- max(2, (ncol(input) - 1) * nrow(input) * 0.7)
1380		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4)
	1380	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4, limitsize = FALSE)
1381	1381		}
1382	1382
1383	1383		#' Print a simple barplot with the number of tags last seen at each section

1409	1409		p <- p + ggplot2::coord_flip()
1410	1410		p <- p + ggplot2::guides(fill = ggplot2::guide_legend(reverse = TRUE))
1411	1411		the.height <- max(2, ((length(levels(status.df$Very.last.array)) - 1) * 0.5))
1412		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height)
	1412	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height, limitsize = FALSE)
1413	1413		}
1414	1414
1415	1415		#' Print sensor data for each individual tag

Compare `7dae136 ... +1 ... 5935e19`

No flags found

Everything is accounted for!

What changes does Codecov check for?

Show failed CI and contexual commits `c`

3 Commits

483	483		p <- p + ggplot2::scale_y_continuous(limits = c(0, 1), expand = c(0, 0, 0.05, 0))
484	484		p <- p + ggplot2::labs(x = "", y = "Survival")
485	485		the.width <- max(2, sum(grepl("Disap.", colnames(section.overview))) * nrow(section.overview))
486		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4)
	486	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4, limitsize = FALSE)
487	487		appendTo("debug", "Terminating printSurvivalGraphic.")
488	488		}
489	489

1488	1488		}
1489	1489
1490	1490		# Save
1491		-	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height) # better to save in png to avoid point overlapping issues
	1491	+	ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height, limitsize = FALSE) # better to save in png to avoid point overlapping issues
1492	1492
1493	1493		n.plots <- n.plots + 1
1494	1494		if (n.plots %% 2 == 0) {

1026	1026
1027	1027		# check sensor names
1028	1028		if (!expect_integer) {
1029		-	if(!any(grepl("^Sensor.unit$", colnames(bio)))) {
	1029	+	if (!any(grepl("^Sensor.unit$", colnames(bio)))) {
1030	1030		appendTo(c("Screen", "Warning"), "Tags with multiple sensors are listed in the biometrics, but a 'Sensor.unit' column could not be found. Skipping sensor unit assignment.")
1031	1031		}
1032	1032		else {
1033		-	bio$Sensor.unit <- as.character(bio$Sensor.unit) #failsafe in case all values are numeric, or NA.
1034		-
1035		-	A <- sapply(strsplit(bio$Signal, "\|", fixed = TRUE), length)
1036		-	pre_B <- strsplit(bio$Sensor.unit, "\|", fixed = TRUE)
1037		-	B <- sapply(pre_B, length)
1038		-	B[sapply(pre_B, is.na)] <- 0
1039		-
1040		-	if (any(A != B))
1041		-	stopAndReport("The number of provided sensor units and signals do not match for ",
1042		-	ifelse(sum(A != B) <= 10,
1043		-	paste0("row(s) ", paste0(which(A != B), collapse = ", ")),
1044		-	paste0(sum(A != B), " row(s)")),
	1033	+	bio$Sensor.unit <- as.character(bio$Sensor.unit) # failsafe in case all values are numeric, or NA.
	1034	+	bio$Sensor.unit[bio$Sensor.unit == ''] <- NA_character_
	1035	+
	1036	+	if (any(link <- na.as.false(startsWith(bio$Sensor.unit, '\|'))))
	1037	+	appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
	1038	+	ifelse(sum(link) <= 10,
	1039	+	paste0("row(s) ", paste0(which(link), collapse = ", ")),
	1040	+	paste0(sum(link), " row(s)")),
	1041	+	" of the biometrics starts with a '\|' character. Could you have forgotten to include a sensor unit?"))
	1042	+
	1043	+	if (any(link <- na.as.false(endsWith(bio$Sensor.unit, '\|'))))
	1044	+	appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
	1045	+	ifelse(sum(link) <= 10,
	1046	+	paste0("row(s) ", paste0(which(link), collapse = ", ")),
	1047	+	paste0(sum(link), " row(s)")),
	1048	+	" of the biometrics ends with a '\|' character. Could you have forgotten to include a sensor unit?"))
	1049	+
	1050	+	signals_per_tag <- sapply(strsplit(bio$Signal, "\|", fixed = TRUE), length) # number of signals per tag
	1051	+	aux <- strsplit(bio$Sensor.unit, "\|", fixed = TRUE)
	1052	+	sensors_per_tag <- sapply(aux, length)
	1053	+
	1054	+	if (any(link <- signals_per_tag != sensors_per_tag))
	1055	+	stopAndReport("The number of provided sensor units does not match the number of signals for ",
	1056	+	ifelse(sum(link) <= 10,
	1057	+	paste0("row(s) ", paste0(which(link), collapse = ", ")),
	1058	+	paste0(sum(link), " row(s)")),
1045	1059		" of the biometrics.")
1046	1060		}
1047	1061		}

1623	1637		} else { # otherwise, prepare tag name and include sensor units if present
1624	1638		trimmed_list_names <<- c(trimmed_list_names, paste0(the_codespace, "-", min(bio_aux$Signal_expanded[[i]])))
1625	1639		output <- my.list[list_matches]
	1640	+
	1641	+	# Find Sensor.unit column in the biometrics
1626	1642		if (any(grepl("^Sensor.unit$", colnames(bio)))) {
	1643	+	# Replace sensor units...
1627	1644		for (j in 1:length(output)) {
1628	1645		sensor_index <- match(extractSignals(names(output)[j]), bio_aux$Signal_expanded[[i]])
	1646	+	# but only if the the sensor unit provided is not NA
1629	1647		if (!is.na(bio_aux$Sensor.unit_expanded[[i]][sensor_index])) {
1630	1648		output[[j]]$Sensor.Unit <- rep(bio_aux$Sensor.unit_expanded[[i]][sensor_index], nrow(output[[j]]))
1631	1649		}

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Compare 7dae136 ... +1 ... 5935e19

No flags found

Everything is accounted for!

What changes does Codecov check for?

Show failed CI and contexual commits c 3 Commits

Compare `7dae136 ... +1 ... 5935e19`

Show failed CI and contexual commits `c`

3 Commits